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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-cobra">Debian Med / python-cobra</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cobra/commit/ef4663936cb3797028e60b60160d41ca04fc8a5f">ef466393</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-17T18:16:04Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">python3-depinfo is available now
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cobra/commit/13239c5c4b3d242daf71306032ffb533a0175cbe">13239c5c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-17T18:18:22Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.13.4</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cobra/commit/c5f3728f068b51a4c95ad575cbf49dd9f11df5e7">c5f3728f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-17T18:18:29Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.13.4'
Update to upstream version '0.13.4'
with Debian dir 4489dd011abc622ebcec18d930e78fb34f86badc</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cobra/commit/7e3c90aa804ccf30c961d5a19266bc3cb09e93ef">7e3c90aa</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-17T18:18:29Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cobra/commit/3aad7e9a3ce8ebc81c3cfe117e4745682b2a96d7">3aad7e9a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-17T18:22:19Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cme fix dpkg-control
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cobra/commit/f18abfe154a8615f726c8be4487117cc09874674">f18abfe1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-17T18:22:35Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adapt patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cobra/commit/2aa17ff4c6b870d1d3af3b497fd59f7c632c4908">2aa17ff4</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-17T18:45:28Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Silence lintian about wrong Python version of data file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cobra/commit/0e8f2bd4031444d314fd2cc63b62e322e2474c4d">0e8f2bd4</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-17T18:45:59Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove unneeded patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cobra/commit/24bf110998eaa22b8d0b873e3d47faf6e457397a">24bf1109</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-17T19:20:55Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop autopkgtest for Python2 version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cobra/commit/11d80fce5d66886597adffefca19de87bde01fd2">11d80fce</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-17T19:32:00Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>30 changed files:</h4>
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<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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<a href="#2562dc47c12586d518db2b6ce12e991436fe5c6a">
cobra/__init__.py
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<a href="#75574437901dbfe16fda8f95a55f147885fc8d5c">
cobra/io/mat.py
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<li class="file-stats">
<a href="#2326c21019b717e8f2121177bf5afaf4eacb0328">
cobra/io/yaml.py
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<a href="#8c8be9f5bd5b01368eaf5c1d028ee66ec71057ca">
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cobra/test/test_flux_analysis/conftest.py
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cobra/test/test_flux_analysis/test_deletion.py
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cobra/test/test_flux_analysis/test_gapfilling.py
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cobra/test/test_flux_analysis/test_geometric.py
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debian/changelog
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debian/control
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debian/patches/series
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debian/patches/testsuite-check-jsonschema.patch
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debian/tests/Makefile
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debian/tests/control.autodep8
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release-notes/0.13.4.md
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setup.cfg
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setup.py
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tox.ini
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<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/python-cobra/compare/fff89040cdb873308a398a97bc8a778b455ced12...11d80fce5d66886597adffefca19de87bde01fd2#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -34,6 +34,9 @@ matrix:</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: teal;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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<td class="diff-line-num new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC35" class="line" lang="yaml"> <span class="na" style="color: teal;">python</span><span class="pi">:</span> <span class="s" style="color: #d14;">3.6</span></span>
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<td class="diff-line-num old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC36" class="line" lang="yaml"> <span class="na" style="color: teal;">env</span><span class="pi">:</span> <span class="s" style="color: #d14;">TOXENV=py36</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: teal;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="yaml"> <span class="na" style="color: teal;">python</span><span class="pi">:</span> <span class="s" style="color: #d14;">3.7-dev</span></span>
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<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="yaml"> <span class="na" style="color: teal;">env</span><span class="pi">:</span> <span class="s" style="color: #d14;">TOXENV=py37</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: teal;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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<td class="diff-line-num new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="yaml"> <span class="na" style="color: teal;">python</span><span class="pi">:</span> <span class="s" style="color: #d14;">3.5</span></span>
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<td class="diff-line-num old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="yaml"> <span class="na" style="color: teal;">env</span><span class="pi">:</span> <span class="s" style="color: #d14;">TOXENV=sbml</span></span>
</pre>
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<br>
</li>
<li id="2562dc47c12586d518db2b6ce12e991436fe5c6a">
<a href="https://salsa.debian.org/med-team/python-cobra/compare/fff89040cdb873308a398a97bc8a778b455ced12...11d80fce5d66886597adffefca19de87bde01fd2#2562dc47c12586d518db2b6ce12e991436fe5c6a"><strong>cobra/__init__.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,7 +13,7 @@ from cobra.core import (</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">DictList</span><span class="p">,</span> <span class="n" style="color: #333;">Gene</span><span class="p">,</span> <span class="n" style="color: #333;">Metabolite</span><span class="p">,</span> <span class="n" style="color: #333;">Model</span><span class="p">,</span> <span class="n" style="color: #333;">Object</span><span class="p">,</span> <span class="n" style="color: #333;">Reaction</span><span class="p">,</span> <span class="n" style="color: #333;">Species</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.util</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">show_versions</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.13.<span class="idiff left right">3</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.13.<span class="idiff left right">4</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># set the warning format to be prettier and fit on one line</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="n" style="color: #333;">_cobra_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_dirname</span><span class="p">(</span><span class="n" style="color: #333;">_abspath</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">))</span></span>
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<a href="https://salsa.debian.org/med-team/python-cobra/compare/fff89040cdb873308a398a97bc8a778b455ced12...11d80fce5d66886597adffefca19de87bde01fd2#75574437901dbfe16fda8f95a55f147885fc8d5c"><strong>cobra/io/mat.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,7 +24,7 @@ except ImportError:</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># precompiled regular expressions</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"><span class="n" style="color: #333;">_bracket_re</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">"r</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">[[a-z]</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">]$"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"><span class="n" style="color: #333;">_bracket_re</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">r"</span>\[[a-z]\]$"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"><span class="n" style="color: #333;">_underscore_re</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;">r"_[a-z]$"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/python-cobra/compare/fff89040cdb873308a398a97bc8a778b455ced12...11d80fce5d66886597adffefca19de87bde01fd2#2326c21019b717e8f2121177bf5afaf4eacb0328"><strong>cobra/io/yaml.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,11 +5,26 @@ from __future__ import absolute_import</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">io</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">six</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">string_types</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">ruamel</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">yaml</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">ruamel.yaml</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">YAML</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">ruamel.yaml.compat</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">StringIO</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.io.dict</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">model_to_dict</span><span class="p">,</span> <span class="n" style="color: #333;">model_from_dict</span></span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"><span class="n" style="color: #333;">YAML_SPEC</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1"</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="n" style="color: #333;">YAML_SPEC</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1.2"</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">MyYAML</span><span class="p">(</span><span class="n" style="color: #333;">YAML</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">dump</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">stream</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">inefficient</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">stream</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">inefficient</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StringIO</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">YAML</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dump</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">stream</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">inefficient</span><span class="p">:</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">stream</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getvalue</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"><span class="n" style="color: #333;">yaml</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MyYAML</span><span class="p">(</span><span class="n" style="color: #333;">typ</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"rt"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">to_yaml</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">sort</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -36,9 +51,10 @@ def to_yaml(model, sort=False, **kwargs):</td>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"><span class="s" style="color: #d14;"> save_yaml_model : Write directly to a file.</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"><span class="s" style="color: #d14;"> ruamel.yaml.dump : Base function.</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">obj</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model_to_dict</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">sort</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sort</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">obj</span><span class="p">[</span><span class="s" style="color: #d14;">"version"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">YAML_SPEC</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">yaml</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dump</span><span class="p">(</span><span class="n" style="color: #333;">obj</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">Dumper</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">yaml</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">RoundTripDumper</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">yaml</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dump</span><span class="p">(</span><span class="n" style="color: #333;">obj</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">from_yaml</span><span class="p">(</span><span class="n" style="color: #333;">document</span><span class="p">):</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -59,7 +75,8 @@ def from_yaml(document):</td>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"><span class="s" style="color: #d14;"> --------</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"><span class="s" style="color: #d14;"> load_yaml_model : Load directly from a file.</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">model_from_dict</span><span class="p">(</span><span class="n" style="color: #333;">yaml</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">document</span><span class="p">,</span> <span class="n" style="color: #333;">yaml</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">RoundTripLoader</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">content</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StringIO</span><span class="p">(</span><span class="n" style="color: #333;">document</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">model_from_dict</span><span class="p">(</span><span class="n" style="color: #333;">yaml</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">content</span><span class="p">))</span></span>
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">save_yaml_model</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">sort</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -88,9 +105,9 @@ def save_yaml_model(model, filename, sort=False, **kwargs):</td>
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88
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">obj</span><span class="p">[</span><span class="s" style="color: #d14;">"version"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">YAML_SPEC</span></span>
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">string_types</span><span class="p">):</span></span>
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90
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">io</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">file_handle</span><span class="p">:</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">yaml</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dump</span><span class="p">(</span><span class="n" style="color: #333;">obj</span><span class="p">,</span> <span class="n" style="color: #333;">file_handle</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">Dumper</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">yaml</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">RoundTripDumper</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">yaml</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dump</span><span class="p">(</span><span class="n" style="color: #333;">obj</span><span class="p">,</span> <span class="n" style="color: #333;">file_handle</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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92
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">yaml</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dump</span><span class="p">(</span><span class="n" style="color: #333;">obj</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">Dumper</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">yaml</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">RoundTripDumper</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">yaml</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dump</span><span class="p">(</span><span class="n" style="color: #333;">obj</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"></span>
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">load_yaml_model</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -114,7 +131,6 @@ def load_yaml_model(filename):</td>
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">string_types</span><span class="p">):</span></span>
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116
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">io</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">file_handle</span><span class="p">:</span></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">model_from_dict</span><span class="p">(</span><span class="n" style="color: #333;">yaml</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">file_handle</span><span class="p">,</span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">yaml</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">RoundTripLoader</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">model_from_dict</span><span class="p">(</span><span class="n" style="color: #333;">yaml</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">file_handle</span><span class="p">))</span></span>
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">model_from_dict</span><span class="p">(</span><span class="n" style="color: #333;">yaml</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">yaml</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">RoundTripLoader</span></span><span class="p">))</span></span></pre>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">model_from_dict</span><span class="p">(</span><span class="n" style="color: #333;">yaml</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">))</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-cobra/compare/fff89040cdb873308a398a97bc8a778b455ced12...11d80fce5d66886597adffefca19de87bde01fd2#8c8be9f5bd5b01368eaf5c1d028ee66ec71057ca"><strong>cobra/test/test_flux_analysis.py</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># -*- coding: utf-8 -*-</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">absolute_import</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">warnings</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">math</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pandas</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Series</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">contextlib</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">contextmanager</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">optlang.interface</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">OPTIMAL</span><span class="p">,</span> <span class="n" style="color: #333;">INFEASIBLE</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">six</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">StringIO</span><span class="p">,</span> <span class="n" style="color: #333;">iteritems</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">cobra.util.solver</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">sutil</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.core</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Metabolite</span><span class="p">,</span> <span class="n" style="color: #333;">Model</span><span class="p">,</span> <span class="n" style="color: #333;">Reaction</span><span class="p">,</span> <span class="n" style="color: #333;">Solution</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.flux_analysis</span> <span class="kn" style="font-weight: 600;">import</span> <span class="o" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.flux_analysis.parsimonious</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">add_pfba</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.flux_analysis</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">geometric_fba</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.flux_analysis.sampling</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ACHRSampler</span><span class="p">,</span> <span class="n" style="color: #333;">OptGPSampler</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.flux_analysis.reaction</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">assess</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.exceptions</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Infeasible</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.flux_analysis.moma</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">add_moma</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.flux_analysis.room</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">add_room</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># The scipy interface is currently unstable and may yield errors or infeasible</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># solutions.</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"><span class="n" style="color: #333;">all_solvers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">s</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"glpk"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cplex"</span><span class="p">,</span> <span class="s" style="color: #d14;">"gurobi"</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solvers</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"><span class="n" style="color: #333;">qp_solvers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">s</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"cplex"</span><span class="p">,</span> <span class="s" style="color: #d14;">"gurobi"</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solvers</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">construct_ll_test_model</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Model</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">(</span><span class="n" style="color: #333;">Metabolite</span><span class="p">(</span><span class="s" style="color: #d14;">"A"</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">(</span><span class="n" style="color: #333;">Metabolite</span><span class="p">(</span><span class="s" style="color: #d14;">"B"</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">(</span><span class="n" style="color: #333;">Metabolite</span><span class="p">(</span><span class="s" style="color: #d14;">"C"</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">EX_A</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"EX_A"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">EX_A</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">A</span><span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">})</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">DM_C</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"DM_C"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">DM_C</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">C</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">})</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">v1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"v1"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">v1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">A</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">B</span><span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">})</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">v2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"v2"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">v2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">B</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">C</span><span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">})</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">v3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"v3"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">v3</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">C</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">A</span><span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">})</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_reactions</span><span class="p">([</span><span class="n" style="color: #333;">EX_A</span><span class="p">,</span> <span class="n" style="color: #333;">DM_C</span><span class="p">,</span> <span class="n" style="color: #333;">v1</span><span class="p">,</span> <span class="n" style="color: #333;">v2</span><span class="p">,</span> <span class="n" style="color: #333;">v3</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">DM_C</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective_coefficient</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">test_model</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"><span class="nd">@pytest.fixture</span><span class="p">(</span><span class="n" style="color: #333;">scope</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"function"</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">all_solvers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">ll_test_model</span><span class="p">(</span><span class="n" style="color: #333;">request</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">construct_ll_test_model</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">request</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">param</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">test_model</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">construct_room_model</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Model</span><span class="p">(</span><span class="s" style="color: #d14;">"papin_2003"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">v1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"v1"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">v2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"v2"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">v3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"v3"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">v4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"v4"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">v5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"v5"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">v6</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"v6"</span><span class="p">,</span> <span class="n" style="color: #333;">upper_bound</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">b1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"b1"</span><span class="p">,</span> <span class="n" style="color: #333;">upper_bound</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">10.0</span><span class="p">,</span> <span class="n" style="color: #333;">lower_bound</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">b2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"b2"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">b3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"b3"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_reactions</span><span class="p">([</span><span class="n" style="color: #333;">v1</span><span class="p">,</span> <span class="n" style="color: #333;">v2</span><span class="p">,</span> <span class="n" style="color: #333;">v3</span><span class="p">,</span> <span class="n" style="color: #333;">v4</span><span class="p">,</span> <span class="n" style="color: #333;">v5</span><span class="p">,</span> <span class="n" style="color: #333;">v6</span><span class="p">,</span> <span class="n" style="color: #333;">b1</span><span class="p">,</span> <span class="n" style="color: #333;">b2</span><span class="p">,</span> <span class="n" style="color: #333;">b3</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">v1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reaction</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"A -> B"</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">v2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reaction</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2 B -> C + byp"</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">v3</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reaction</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2 B + cof -> D"</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">v4</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reaction</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"D -> E + cof"</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">v5</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reaction</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"C + cof -> D"</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">v6</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reaction</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"C -> E"</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">b1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reaction</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-> A"</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">b2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reaction</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"E ->"</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">b3</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reaction</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"byp ->"</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'b2'</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">test_model</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">construct_room_solution</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">fluxes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Series</span><span class="p">({</span><span class="s" style="color: #d14;">'b1'</span><span class="p">:</span> <span class="mf" style="color: #099;">10.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'b2'</span><span class="p">:</span> <span class="mf" style="color: #099;">5.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'b3'</span><span class="p">:</span> <span class="mf" style="color: #099;">5.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v1'</span><span class="p">:</span> <span class="mf" style="color: #099;">10.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v2'</span><span class="p">:</span> <span class="mf" style="color: #099;">5.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"> <span class="s" style="color: #d14;">'v3'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v4'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v5'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v6'</span><span class="p">:</span> <span class="mf" style="color: #099;">5.0</span><span class="p">})</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">reduced_costs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Series</span><span class="p">({</span><span class="s" style="color: #d14;">'b1'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'b2'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'b3'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v1'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"> <span class="s" style="color: #d14;">'v2'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v3'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v4'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v5'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"> <span class="s" style="color: #d14;">'v6'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">})</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">shadow_prices</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Series</span><span class="p">({</span><span class="s" style="color: #d14;">'b1'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'b2'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'b3'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v1'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"> <span class="s" style="color: #d14;">'v2'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v3'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v4'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v5'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"> <span class="s" style="color: #d14;">'v6'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">})</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Solution</span><span class="p">(</span><span class="n" style="color: #333;">objective_value</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">5.000</span><span class="p">,</span> <span class="n" style="color: #333;">status</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'optimal'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">fluxes</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fluxes</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">reduced_costs</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reduced_costs</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">shadow_prices</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shadow_prices</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sol</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">construct_geometric_fba_model</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Model</span><span class="p">(</span><span class="s" style="color: #d14;">'geometric_fba_paper_model'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">(</span><span class="n" style="color: #333;">Metabolite</span><span class="p">(</span><span class="s" style="color: #d14;">'A'</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">(</span><span class="n" style="color: #333;">Metabolite</span><span class="p">(</span><span class="s" style="color: #d14;">'B'</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">v1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">'v1'</span><span class="p">,</span> <span class="n" style="color: #333;">upper_bound</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1.0</span><span class="p">)</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">v1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">A</span><span class="p">:</span> <span class="mf" style="color: #099;">1.0</span><span class="p">})</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">v2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">'v2'</span><span class="p">,</span> <span class="n" style="color: #333;">lower_bound</span><span class="o" style="font-weight: 600;">=-</span><span class="mf" style="color: #099;">1000.0</span><span class="p">)</span></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">v2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">A</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">B</span><span class="p">:</span> <span class="mf" style="color: #099;">1.0</span><span class="p">})</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">v3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">'v3'</span><span class="p">,</span> <span class="n" style="color: #333;">lower_bound</span><span class="o" style="font-weight: 600;">=-</span><span class="mf" style="color: #099;">1000.0</span><span class="p">)</span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">v3</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">A</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">B</span><span class="p">:</span> <span class="mf" style="color: #099;">1.0</span><span class="p">})</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;">v4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">'v4'</span><span class="p">,</span> <span class="n" style="color: #333;">lower_bound</span><span class="o" style="font-weight: 600;">=-</span><span class="mf" style="color: #099;">1000.0</span><span class="p">)</span></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"> <span class="n" style="color: #333;">v4</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">A</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">B</span><span class="p">:</span> <span class="mf" style="color: #099;">1.0</span><span class="p">})</span></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">v5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">'v5'</span><span class="p">)</span></span>
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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">v5</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">A</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">B</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span><span class="p">})</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_reactions</span><span class="p">([</span><span class="n" style="color: #333;">v1</span><span class="p">,</span> <span class="n" style="color: #333;">v2</span><span class="p">,</span> <span class="n" style="color: #333;">v3</span><span class="p">,</span> <span class="n" style="color: #333;">v4</span><span class="p">,</span> <span class="n" style="color: #333;">v5</span><span class="p">])</span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'v5'</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">test_model</span></span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"></span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python"><span class="nd">@contextmanager</span></span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">captured_output</span><span class="p">():</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python"> <span class="s" style="color: #d14;">"""A context manager to test the IO summary methods."""</span></span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">new_out</span><span class="p">,</span> <span class="n" style="color: #333;">new_err</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StringIO</span><span class="p">(),</span> <span class="n" style="color: #333;">StringIO</span><span class="p">()</span></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">old_out</span><span class="p">,</span> <span class="n" style="color: #333;">old_err</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span></span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_out</span><span class="p">,</span> <span class="n" style="color: #333;">new_err</span></span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"> <span class="k" style="font-weight: 600;">finally</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">old_out</span><span class="p">,</span> <span class="n" style="color: #333;">old_err</span></span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestCobraFluxAnalysis</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test the simulation functions in cobra.flux_analysis."""</span></span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"solver"</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_pfba_benchmark</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">large_model</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">,</span> <span class="n" style="color: #333;">solver</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">large_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solver</span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="n" style="color: #333;">pfba</span><span class="p">,</span> <span class="n" style="color: #333;">large_model</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"solver"</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_pfba</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">solver</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solver</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">add_pfba</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">add_pfba</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">)</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">expression</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">expression</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">n_constraints</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">constraints</span><span class="p">)</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">solution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pfba</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"optimal"</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">x_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"Biomass_Ecoli_core"</span><span class="p">],</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="python"> <span class="mf" style="color: #099;">0.8739</span><span class="p">,</span> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1e-4</span><span class="p">,</span> <span class="n" style="color: #333;">rtol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">)</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">abs_x</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">x</span><span class="p">]</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">abs_x</span><span class="p">),</span> <span class="mf" style="color: #099;">518.4221</span><span class="p">,</span> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1e-4</span><span class="p">,</span> <span class="n" style="color: #333;">rtol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">)</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># test changes to model reverted</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expression</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">expression</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">constraints</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">n_constraints</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="python"></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># needed?</span></span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Test desired_objective_value</span></span>
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># desired_objective = 0.8</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># pfba(model, solver=solver,</span></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># desired_objective_value=desired_objective)</span></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># abs_x = [abs(i) for i in model.solution.x]</span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># assert model.solution.status == "optimal"</span></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># assert abs(model.solution.f - desired_objective) < 0.001</span></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># assert abs(sum(abs_x) - 476.1594) < 0.001</span></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="python"></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># TODO: parametrize fraction (DRY it up)</span></span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Test fraction_of_optimum</span></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="python"> <span class="n" style="color: #333;">solution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pfba</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">fraction_of_optimum</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.95</span><span class="p">)</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"optimal"</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">x_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"Biomass_Ecoli_core"</span><span class="p">],</span></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="python"> <span class="mf" style="color: #099;">0.95</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">0.8739</span><span class="p">,</span> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1e-4</span><span class="p">,</span> <span class="n" style="color: #333;">rtol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">)</span></span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">abs_x</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">x</span><span class="p">]</span></span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">abs_x</span><span class="p">),</span> <span class="mf" style="color: #099;">493.4400</span><span class="p">,</span> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1e-4</span><span class="p">,</span> <span class="n" style="color: #333;">rtol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">)</span></span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="python"></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Infeasible solution</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ATPM</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower_bound</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">500</span></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">catch_warnings</span><span class="p">():</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="python"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">simplefilter</span><span class="p">(</span><span class="s" style="color: #d14;">"error"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">UserWarning</span><span class="p">)</span></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">((</span><span class="nb" style="color: #0086b3;">UserWarning</span><span class="p">,</span> <span class="n" style="color: #333;">Infeasible</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">)):</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">pfba</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">)</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python"></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"solver"</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_geometric_fba_benchmark</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">,</span> <span class="n" style="color: #333;">solver</span><span class="p">):</span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solver</span></span>
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="n" style="color: #333;">geometric_fba</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">)</span></span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python"></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"solver"</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_geometric_fba</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">solver</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">model</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">construct_geometric_fba_model</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solver</span></span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">geometric_fba_sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">geometric_fba</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">)</span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Series</span><span class="p">({</span><span class="s" style="color: #d14;">'v1'</span><span class="p">:</span> <span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v2'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.33</span><span class="p">,</span> <span class="s" style="color: #d14;">'v3'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.33</span><span class="p">,</span> <span class="s" style="color: #d14;">'v4'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.33</span><span class="p">,</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="python"> <span class="s" style="color: #d14;">'v5'</span><span class="p">:</span> <span class="mf" style="color: #099;">1.0</span><span class="p">},</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'v1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'v2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'v3'</span><span class="p">,</span> <span class="s" style="color: #d14;">'v4'</span><span class="p">,</span> <span class="s" style="color: #d14;">'v5'</span><span class="p">])</span></span>
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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">allclose</span><span class="p">(</span><span class="n" style="color: #333;">geometric_fba_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">,</span> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1E-02</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"solver"</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_gene_deletion_fba_benchmark</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">solver</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solver</span></span>
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="n" style="color: #333;">single_gene_deletion</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"solver"</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_gene_deletion_fba</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">solver</span><span class="p">):</span></span>
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215
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># expected knockouts for textbook model</span></span>
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216
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solver</span></span>
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217
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="python"> <span class="n" style="color: #333;">growth_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"b0008"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.87</span><span class="p">,</span> <span class="s" style="color: #d14;">"b0114"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.80</span><span class="p">,</span> <span class="s" style="color: #d14;">"b0116"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.78</span><span class="p">,</span></span>
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218
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python"> <span class="s" style="color: #d14;">"b2276"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.21</span><span class="p">,</span> <span class="s" style="color: #d14;">"b1779"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.00</span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">single_gene_deletion</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">model</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python"> <span class="n" style="color: #333;">gene_list</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">growth_dict</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"fba"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="python"> <span class="p">)[</span><span class="s" style="color: #d14;">"growth"</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">gene</span><span class="p">,</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iteritems</span><span class="p">(</span><span class="n" style="color: #333;">growth_dict</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">[</span><span class="nb" style="color: #0086b3;">frozenset</span><span class="p">([</span><span class="n" style="color: #333;">gene</span><span class="p">])],</span> <span class="n" style="color: #333;">value</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="python"> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1E-02</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"solver"</span><span class="p">,</span> <span class="n" style="color: #333;">qp_solvers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_gene_deletion_moma_benchmark</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="python"> <span class="n" style="color: #333;">solver</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solver</span></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="python"> <span class="n" style="color: #333;">genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'b0008'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b0114'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b2276'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b1779'</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="n" style="color: #333;">single_gene_deletion</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">gene_list</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">genes</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="python"> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"moma"</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"solver"</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_gene_deletion_linear_moma_benchmark</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">,</span> <span class="n" style="color: #333;">solver</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solver</span></span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="python"> <span class="n" style="color: #333;">genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'b0008'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b0114'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b2276'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b1779'</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="n" style="color: #333;">single_gene_deletion</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">gene_list</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">genes</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="python"> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"linear moma"</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"solver"</span><span class="p">,</span> <span class="n" style="color: #333;">qp_solvers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_moma_sanity</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">solver</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test optimization criterion and optimality."""</span></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solver</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="python"> <span class="n" style="color: #333;">sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PFK</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">knock_out</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="python"> <span class="n" style="color: #333;">knock_sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="python"> <span class="n" style="color: #333;">ssq</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">knock_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">pow</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="python"> <span class="n" style="color: #333;">add_moma</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">linear</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PFK</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">knock_out</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="python"> <span class="n" style="color: #333;">moma_sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="python"> <span class="n" style="color: #333;">moma_ssq</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">moma_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">pow</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Use normal FBA as reference solution.</span></span>
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="python"> <span class="n" style="color: #333;">add_moma</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sol</span><span class="p">,</span> <span class="n" style="color: #333;">linear</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PFK</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">knock_out</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="python"> <span class="n" style="color: #333;">moma_ref_sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="python"> <span class="n" style="color: #333;">moma_ref_ssq</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">moma_ref_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">pow</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">moma_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective_value</span><span class="p">,</span> <span class="n" style="color: #333;">moma_ssq</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">moma_ssq</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">ssq</span></span>
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">moma_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective_value</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="python"> <span class="n" style="color: #333;">moma_ref_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective_value</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">moma_ssq</span><span class="p">,</span> <span class="n" style="color: #333;">moma_ref_ssq</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"solver"</span><span class="p">,</span> <span class="n" style="color: #333;">qp_solvers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_gene_deletion_moma</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">solver</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solver</span></span>
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="python"></span>
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279
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># expected knockouts for textbook model</span></span>
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="python"> <span class="n" style="color: #333;">growth_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"b0008"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.87</span><span class="p">,</span> <span class="s" style="color: #d14;">"b0114"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.71</span><span class="p">,</span> <span class="s" style="color: #d14;">"b0116"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.56</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="python"> <span class="s" style="color: #d14;">"b2276"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.11</span><span class="p">,</span> <span class="s" style="color: #d14;">"b1779"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.00</span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">single_gene_deletion</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">model</span><span class="p">,</span></span>
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285
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="python"> <span class="n" style="color: #333;">gene_list</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">growth_dict</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="python"> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"moma"</span><span class="p">,</span></span>
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287
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="python"> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="python"> <span class="p">)[</span><span class="s" style="color: #d14;">"growth"</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">gene</span><span class="p">,</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iteritems</span><span class="p">(</span><span class="n" style="color: #333;">growth_dict</span><span class="p">):</span></span>
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290
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">[</span><span class="nb" style="color: #0086b3;">frozenset</span><span class="p">([</span><span class="n" style="color: #333;">gene</span><span class="p">])],</span> <span class="n" style="color: #333;">value</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="python"> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1E-02</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"solver"</span><span class="p">,</span> <span class="n" style="color: #333;">qp_solvers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_gene_deletion_moma_reference</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">solver</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solver</span></span>
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># expected knockouts for textbook model</span></span>
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="python"> <span class="n" style="color: #333;">growth_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"b0008"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.87</span><span class="p">,</span> <span class="s" style="color: #d14;">"b0114"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.71</span><span class="p">,</span> <span class="s" style="color: #d14;">"b0116"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.56</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="python"> <span class="s" style="color: #d14;">"b2276"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.11</span><span class="p">,</span> <span class="s" style="color: #d14;">"b1779"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.00</span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="python"> <span class="n" style="color: #333;">sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">single_gene_deletion</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">model</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="python"> <span class="n" style="color: #333;">gene_list</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">growth_dict</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="python"> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"moma"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="python"> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sol</span><span class="p">,</span></span>
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307
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="python"> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="python"> <span class="p">)[</span><span class="s" style="color: #d14;">"growth"</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">gene</span><span class="p">,</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iteritems</span><span class="p">(</span><span class="n" style="color: #333;">growth_dict</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">[</span><span class="nb" style="color: #0086b3;">frozenset</span><span class="p">([</span><span class="n" style="color: #333;">gene</span><span class="p">])],</span> <span class="n" style="color: #333;">value</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="python"> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1E-02</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"solver"</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_linear_moma_sanity</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">solver</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test optimization criterion and optimality."""</span></span>
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solver</span></span>
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="python"> <span class="n" style="color: #333;">sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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320
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PFK</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">knock_out</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="python"> <span class="n" style="color: #333;">knock_sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="python"> <span class="n" style="color: #333;">sabs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">knock_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="python"> <span class="n" style="color: #333;">add_moma</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">linear</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PFK</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">knock_out</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="python"> <span class="n" style="color: #333;">moma_sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="python"> <span class="n" style="color: #333;">moma_sabs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">moma_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Use normal FBA as reference solution.</span></span>
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="python"> <span class="n" style="color: #333;">add_moma</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sol</span><span class="p">,</span> <span class="n" style="color: #333;">linear</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PFK</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">knock_out</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="python"> <span class="n" style="color: #333;">moma_ref_sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="python"> <span class="n" style="color: #333;">moma_ref_sabs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">moma_ref_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">allclose</span><span class="p">(</span><span class="n" style="color: #333;">moma_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective_value</span><span class="p">,</span> <span class="n" style="color: #333;">moma_sabs</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">moma_sabs</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">sabs</span></span>
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">moma_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective_value</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="python"> <span class="n" style="color: #333;">moma_ref_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective_value</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">moma_sabs</span><span class="p">,</span> <span class="n" style="color: #333;">moma_ref_sabs</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="python"> <span class="n" style="color: #333;">add_moma</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">linear</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="python"> <span class="n" style="color: #333;">add_moma</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"solver"</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_gene_deletion_linear_moma</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">solver</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># expected knockouts for textbook model</span></span>
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="python"> <span class="n" style="color: #333;">growth_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"b0008"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.87</span><span class="p">,</span> <span class="s" style="color: #d14;">"b0114"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.76</span><span class="p">,</span> <span class="s" style="color: #d14;">"b0116"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.65</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="python"> <span class="s" style="color: #d14;">"b2276"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.08</span><span class="p">,</span> <span class="s" style="color: #d14;">"b1779"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.00</span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solver</span></span>
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="python"> <span class="n" style="color: #333;">sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">single_gene_deletion</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">model</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="python"> <span class="n" style="color: #333;">gene_list</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">growth_dict</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="python"> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"linear moma"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="python"> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sol</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="python"> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="python"> <span class="p">)[</span><span class="s" style="color: #d14;">"growth"</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">gene</span><span class="p">,</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iteritems</span><span class="p">(</span><span class="n" style="color: #333;">growth_dict</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">[</span><span class="nb" style="color: #0086b3;">frozenset</span><span class="p">([</span><span class="n" style="color: #333;">gene</span><span class="p">])],</span> <span class="n" style="color: #333;">value</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="python"> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1E-02</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"solver"</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_gene_deletion_benchmark</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="python"> <span class="n" style="color: #333;">solver</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solver</span></span>
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="n" style="color: #333;">single_reaction_deletion</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"solver"</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_gene_deletion_room_benchmark</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="python"> <span class="n" style="color: #333;">solver</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"glpk"</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="python"> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">skip</span><span class="p">(</span><span class="s" style="color: #d14;">"GLPK is too slow to run ROOM."</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solver</span></span>
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<pre style="margin: 0;">-<span id="LC379" class="line" lang="python"> <span class="n" style="color: #333;">genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'b0008'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b0114'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b2276'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b1779'</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="n" style="color: #333;">single_gene_deletion</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">gene_list</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">genes</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="python"> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"room"</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"solver"</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_gene_deletion_linear_room_benchmark</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">,</span> <span class="n" style="color: #333;">solver</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solver</span></span>
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="python"> <span class="n" style="color: #333;">genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'b0008'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b0114'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b2276'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b1779'</span><span class="p">]</span></span>
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388
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="n" style="color: #333;">single_gene_deletion</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">gene_list</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">genes</span><span class="p">,</span></span>
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389
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="python"> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"linear room"</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"solver"</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_room_sanity</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">solver</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solver</span></span>
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="python"> <span class="n" style="color: #333;">sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PYK</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">knock_out</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="python"> <span class="n" style="color: #333;">knock_sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Internally uses pFBA as reference solution.</span></span>
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="python"> <span class="n" style="color: #333;">add_room</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PYK</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">knock_out</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="python"> <span class="n" style="color: #333;">room_sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC404" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC405" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Use FBA as reference solution.</span></span>
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="python"> <span class="n" style="color: #333;">add_room</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sol</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PYK</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">knock_out</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="python"> <span class="n" style="color: #333;">room_sol_ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC411" class="line" lang="python"> <span class="n" style="color: #333;">flux_change</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">knock_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="python"> <span class="n" style="color: #333;">flux_change_room</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">room_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="python"> <span class="n" style="color: #333;">flux_change_room_ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">room_sol_ref</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Expect the ROOM solution to have smaller flux changes in</span></span>
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># reactions compared to a normal FBA.</span></span>
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">flux_change_room</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">flux_change</span> <span class="ow" style="font-weight: 600;">or</span> \</span>
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<pre style="margin: 0;">-<span id="LC417" class="line" lang="python"> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">flux_change_room</span><span class="p">,</span> <span class="n" style="color: #333;">flux_change</span><span class="p">,</span> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1E-06</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC418" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Expect the FBA-based reference to have less change in</span></span>
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<pre style="margin: 0;">-<span id="LC419" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># flux distribution.</span></span>
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">flux_change_room_ref</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">flux_change_room</span> <span class="ow" style="font-weight: 600;">or</span> \</span>
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="python"> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">flux_change_room_ref</span><span class="p">,</span> <span class="n" style="color: #333;">flux_change_room</span><span class="p">,</span> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1E-06</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"solver"</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_linear_room_sanity</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">solver</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC425" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solver</span></span>
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="python"> <span class="n" style="color: #333;">sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PYK</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">knock_out</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="python"> <span class="n" style="color: #333;">knock_sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC432" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Internally uses pFBA as reference solution.</span></span>
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<pre style="margin: 0;">-<span id="LC433" class="line" lang="python"> <span class="n" style="color: #333;">add_room</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">linear</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC434" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PYK</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">knock_out</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC435" class="line" lang="python"> <span class="n" style="color: #333;">room_sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC436" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC437" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC438" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Use FBA as reference solution.</span></span>
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="python"> <span class="n" style="color: #333;">add_room</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sol</span><span class="p">,</span> <span class="n" style="color: #333;">linear</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC440" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PYK</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">knock_out</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC441" class="line" lang="python"> <span class="n" style="color: #333;">room_sol_ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC442" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC443" class="line" lang="python"> <span class="n" style="color: #333;">flux_change</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">knock_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC444" class="line" lang="python"> <span class="n" style="color: #333;">flux_change_room</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">room_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC445" class="line" lang="python"> <span class="n" style="color: #333;">flux_change_room_ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">room_sol_ref</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC446" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Expect the ROOM solution to have smaller flux changes in</span></span>
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<pre style="margin: 0;">-<span id="LC447" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># reactions compared to a normal FBA.</span></span>
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<pre style="margin: 0;">-<span id="LC448" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">flux_change_room</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">flux_change</span> <span class="ow" style="font-weight: 600;">or</span> \</span>
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<pre style="margin: 0;">-<span id="LC449" class="line" lang="python"> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">flux_change_room</span><span class="p">,</span> <span class="n" style="color: #333;">flux_change</span><span class="p">,</span> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1E-06</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC450" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Expect the FBA-based reference to have less change in</span></span>
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<pre style="margin: 0;">-<span id="LC451" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># flux distribution.</span></span>
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<pre style="margin: 0;">-<span id="LC452" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">flux_change_room_ref</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">flux_change_room</span> <span class="ow" style="font-weight: 600;">or</span> \</span>
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<pre style="margin: 0;">-<span id="LC453" class="line" lang="python"> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">flux_change_room_ref</span><span class="p">,</span> <span class="n" style="color: #333;">flux_change_room</span><span class="p">,</span> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1E-06</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC454" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC455" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"solver"</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC456" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_reaction_deletion_room</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">solver</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC457" class="line" lang="python"> <span class="n" style="color: #333;">model</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">construct_room_model</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC458" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solver</span></span>
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<pre style="margin: 0;">-<span id="LC459" class="line" lang="python"> <span class="n" style="color: #333;">sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">construct_room_solution</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC460" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Series</span><span class="p">({</span><span class="s" style="color: #d14;">'v1'</span><span class="p">:</span> <span class="mf" style="color: #099;">10.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v2'</span><span class="p">:</span> <span class="mf" style="color: #099;">5.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v3'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v4'</span><span class="p">:</span> <span class="mf" style="color: #099;">5.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC461" class="line" lang="python"> <span class="s" style="color: #d14;">'v5'</span><span class="p">:</span> <span class="mf" style="color: #099;">5.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v6'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'b1'</span><span class="p">:</span> <span class="mf" style="color: #099;">10.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'b2'</span><span class="p">:</span> <span class="mf" style="color: #099;">5.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC462" class="line" lang="python"> <span class="s" style="color: #d14;">'b3'</span><span class="p">:</span> <span class="mf" style="color: #099;">5.0</span><span class="p">},</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'v1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'v2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'v3'</span><span class="p">,</span> <span class="s" style="color: #d14;">'v4'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC463" class="line" lang="python"> <span class="s" style="color: #d14;">'v5'</span><span class="p">,</span> <span class="s" style="color: #d14;">'v6'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b2'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC464" class="line" lang="python"> <span class="s" style="color: #d14;">'b3'</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC465" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC466" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">v6</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">knock_out</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC467" class="line" lang="python"> <span class="n" style="color: #333;">add_room</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sol</span><span class="p">,</span> <span class="n" style="color: #333;">delta</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="n" style="color: #333;">epsilon</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="python"> <span class="n" style="color: #333;">room_sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC469" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC470" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">allclose</span><span class="p">(</span><span class="n" style="color: #333;">room_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC471" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC472" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"solver"</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC473" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_reaction_deletion_room_linear</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">solver</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC474" class="line" lang="python"> <span class="n" style="color: #333;">model</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">construct_room_model</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC475" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solver</span></span>
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<pre style="margin: 0;">-<span id="LC476" class="line" lang="python"> <span class="n" style="color: #333;">sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">construct_room_solution</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC477" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Series</span><span class="p">({</span><span class="s" style="color: #d14;">'v1'</span><span class="p">:</span> <span class="mf" style="color: #099;">10.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v2'</span><span class="p">:</span> <span class="mf" style="color: #099;">5.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v3'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v4'</span><span class="p">:</span> <span class="mf" style="color: #099;">5.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC478" class="line" lang="python"> <span class="s" style="color: #d14;">'v5'</span><span class="p">:</span> <span class="mf" style="color: #099;">5.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v6'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'b1'</span><span class="p">:</span> <span class="mf" style="color: #099;">10.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'b2'</span><span class="p">:</span> <span class="mf" style="color: #099;">5.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC479" class="line" lang="python"> <span class="s" style="color: #d14;">'b3'</span><span class="p">:</span> <span class="mf" style="color: #099;">5.0</span><span class="p">},</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'v1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'v2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'v3'</span><span class="p">,</span> <span class="s" style="color: #d14;">'v4'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC480" class="line" lang="python"> <span class="s" style="color: #d14;">'v5'</span><span class="p">,</span> <span class="s" style="color: #d14;">'v6'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b2'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC481" class="line" lang="python"> <span class="s" style="color: #d14;">'b3'</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC482" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC483" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">v6</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">knock_out</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC484" class="line" lang="python"> <span class="n" style="color: #333;">add_room</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sol</span><span class="p">,</span> <span class="n" style="color: #333;">delta</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="n" style="color: #333;">epsilon</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC485" class="line" lang="python"> <span class="n" style="color: #333;">linear</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC486" class="line" lang="python"> <span class="n" style="color: #333;">linear_room_sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC487" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC488" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">allclose</span><span class="p">(</span><span class="n" style="color: #333;">linear_room_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC489" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC490" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"solver"</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC491" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_reaction_deletion</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">solver</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC492" class="line" lang="python"> <span class="n" style="color: #333;">expected_results</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'FBA'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.70404</span><span class="p">,</span> <span class="s" style="color: #d14;">'FBP'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.87392</span><span class="p">,</span> <span class="s" style="color: #d14;">'CS'</span><span class="p">:</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="python"> <span class="s" style="color: #d14;">'FUM'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.81430</span><span class="p">,</span> <span class="s" style="color: #d14;">'GAPD'</span><span class="p">:</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">'GLUDy'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.85139</span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC494" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC495" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solver</span></span>
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<pre style="margin: 0;">-<span id="LC496" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">single_reaction_deletion</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC497" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">model</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC498" class="line" lang="python"> <span class="n" style="color: #333;">reaction_list</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">expected_results</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC499" class="line" lang="python"> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC500" class="line" lang="python"> <span class="p">)[</span><span class="s" style="color: #d14;">'growth'</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC501" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">reaction</span><span class="p">,</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iteritems</span><span class="p">(</span><span class="n" style="color: #333;">expected_results</span><span class="p">):</span></span>
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502
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<pre style="margin: 0;">-<span id="LC502" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">[</span><span class="nb" style="color: #0086b3;">frozenset</span><span class="p">([</span><span class="n" style="color: #333;">reaction</span><span class="p">])],</span> <span class="n" style="color: #333;">value</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC503" class="line" lang="python"> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1E-05</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC504" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC505" class="line" lang="python"> <span class="nd">@classmethod</span></span>
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<pre style="margin: 0;">-<span id="LC506" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">compare_matrices</span><span class="p">(</span><span class="n" style="color: #333;">cls</span><span class="p">,</span> <span class="n" style="color: #333;">matrix1</span><span class="p">,</span> <span class="n" style="color: #333;">matrix2</span><span class="p">,</span> <span class="n" style="color: #333;">places</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC507" class="line" lang="python"> <span class="n" style="color: #333;">nrows</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">matrix1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC508" class="line" lang="python"> <span class="n" style="color: #333;">ncols</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">matrix1</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC509" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">nrows</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">matrix2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC510" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">ncols</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">matrix2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC511" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">nrows</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC512" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">j</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">ncols</span><span class="p">):</span></span>
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513
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<pre style="margin: 0;">-<span id="LC513" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">matrix1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">matrix2</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">**</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">places</span></span>
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<pre style="margin: 0;">-<span id="LC514" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC515" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_double_gene_deletion_benchmark</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">large_model</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">):</span></span>
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516
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<pre style="margin: 0;">-<span id="LC516" class="line" lang="python"> <span class="n" style="color: #333;">genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"b0726"</span><span class="p">,</span> <span class="s" style="color: #d14;">"b4025"</span><span class="p">,</span> <span class="s" style="color: #d14;">"b0724"</span><span class="p">,</span> <span class="s" style="color: #d14;">"b0720"</span><span class="p">,</span> <span class="s" style="color: #d14;">"b2935"</span><span class="p">,</span> <span class="s" style="color: #d14;">"b2935"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC517" class="line" lang="python"> <span class="s" style="color: #d14;">"b1276"</span><span class="p">,</span></span>
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518
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<pre style="margin: 0;">-<span id="LC518" class="line" lang="python"> <span class="s" style="color: #d14;">"b1241"</span><span class="p">]</span></span>
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519
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<pre style="margin: 0;">-<span id="LC519" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="n" style="color: #333;">double_gene_deletion</span><span class="p">,</span> <span class="n" style="color: #333;">large_model</span><span class="p">,</span> <span class="n" style="color: #333;">gene_list1</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">genes</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC520" class="line" lang="python"> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC521" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_double_gene_deletion</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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523
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<pre style="margin: 0;">-<span id="LC523" class="line" lang="python"> <span class="n" style="color: #333;">genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"b0726"</span><span class="p">,</span> <span class="s" style="color: #d14;">"b4025"</span><span class="p">,</span> <span class="s" style="color: #d14;">"b0724"</span><span class="p">,</span> <span class="s" style="color: #d14;">"b0720"</span><span class="p">,</span> <span class="s" style="color: #d14;">"b2935"</span><span class="p">,</span> <span class="s" style="color: #d14;">"b2935"</span><span class="p">,</span></span>
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524
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="python"> <span class="s" style="color: #d14;">"b1276"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC525" class="line" lang="python"> <span class="s" style="color: #d14;">"b1241"</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC526" class="line" lang="python"> <span class="n" style="color: #333;">growth_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'b0720'</span><span class="p">:</span> <span class="p">{</span><span class="s" style="color: #d14;">'b0720'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC527" class="line" lang="python"> <span class="s" style="color: #d14;">'b0724'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC528" class="line" lang="python"> <span class="s" style="color: #d14;">'b0726'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC529" class="line" lang="python"> <span class="s" style="color: #d14;">'b1241'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC530" class="line" lang="python"> <span class="s" style="color: #d14;">'b1276'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC531" class="line" lang="python"> <span class="s" style="color: #d14;">'b2935'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC532" class="line" lang="python"> <span class="s" style="color: #d14;">'b4025'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC533" class="line" lang="python"> <span class="s" style="color: #d14;">'b0724'</span><span class="p">:</span> <span class="p">{</span><span class="s" style="color: #d14;">'b0720'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC534" class="line" lang="python"> <span class="s" style="color: #d14;">'b0724'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.814</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC535" class="line" lang="python"> <span class="s" style="color: #d14;">'b0726'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.814</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC536" class="line" lang="python"> <span class="s" style="color: #d14;">'b1241'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.814</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC537" class="line" lang="python"> <span class="s" style="color: #d14;">'b1276'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.814</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC538" class="line" lang="python"> <span class="s" style="color: #d14;">'b2935'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.814</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC539" class="line" lang="python"> <span class="s" style="color: #d14;">'b4025'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.739</span><span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC540" class="line" lang="python"> <span class="s" style="color: #d14;">'b0726'</span><span class="p">:</span> <span class="p">{</span><span class="s" style="color: #d14;">'b0720'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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541
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<pre style="margin: 0;">-<span id="LC541" class="line" lang="python"> <span class="s" style="color: #d14;">'b0724'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.814</span><span class="p">,</span></span>
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542
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<pre style="margin: 0;">-<span id="LC542" class="line" lang="python"> <span class="s" style="color: #d14;">'b0726'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.858</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC543" class="line" lang="python"> <span class="s" style="color: #d14;">'b1241'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.858</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC544" class="line" lang="python"> <span class="s" style="color: #d14;">'b1276'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.858</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC545" class="line" lang="python"> <span class="s" style="color: #d14;">'b2935'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.858</span><span class="p">,</span></span>
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546
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<pre style="margin: 0;">-<span id="LC546" class="line" lang="python"> <span class="s" style="color: #d14;">'b4025'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.857</span><span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC547" class="line" lang="python"> <span class="s" style="color: #d14;">'b1241'</span><span class="p">:</span> <span class="p">{</span><span class="s" style="color: #d14;">'b0720'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC548" class="line" lang="python"> <span class="s" style="color: #d14;">'b0724'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.814</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC549" class="line" lang="python"> <span class="s" style="color: #d14;">'b0726'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.858</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC550" class="line" lang="python"> <span class="s" style="color: #d14;">'b1241'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.874</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC551" class="line" lang="python"> <span class="s" style="color: #d14;">'b1276'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.874</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC552" class="line" lang="python"> <span class="s" style="color: #d14;">'b2935'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.874</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC553" class="line" lang="python"> <span class="s" style="color: #d14;">'b4025'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.863</span><span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC554" class="line" lang="python"> <span class="s" style="color: #d14;">'b1276'</span><span class="p">:</span> <span class="p">{</span><span class="s" style="color: #d14;">'b0720'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC555" class="line" lang="python"> <span class="s" style="color: #d14;">'b0724'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.814</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC556" class="line" lang="python"> <span class="s" style="color: #d14;">'b0726'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.858</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC557" class="line" lang="python"> <span class="s" style="color: #d14;">'b1241'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.874</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC558" class="line" lang="python"> <span class="s" style="color: #d14;">'b1276'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.874</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC559" class="line" lang="python"> <span class="s" style="color: #d14;">'b2935'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.874</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC560" class="line" lang="python"> <span class="s" style="color: #d14;">'b4025'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.863</span><span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC561" class="line" lang="python"> <span class="s" style="color: #d14;">'b2935'</span><span class="p">:</span> <span class="p">{</span><span class="s" style="color: #d14;">'b0720'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC562" class="line" lang="python"> <span class="s" style="color: #d14;">'b0724'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.814</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC563" class="line" lang="python"> <span class="s" style="color: #d14;">'b0726'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.858</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC564" class="line" lang="python"> <span class="s" style="color: #d14;">'b1241'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.874</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC565" class="line" lang="python"> <span class="s" style="color: #d14;">'b1276'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.874</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC566" class="line" lang="python"> <span class="s" style="color: #d14;">'b2935'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.874</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC567" class="line" lang="python"> <span class="s" style="color: #d14;">'b4025'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.863</span><span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC568" class="line" lang="python"> <span class="s" style="color: #d14;">'b4025'</span><span class="p">:</span> <span class="p">{</span><span class="s" style="color: #d14;">'b0720'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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569
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<pre style="margin: 0;">-<span id="LC569" class="line" lang="python"> <span class="s" style="color: #d14;">'b0724'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.739</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
570
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<pre style="margin: 0;">-<span id="LC570" class="line" lang="python"> <span class="s" style="color: #d14;">'b0726'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.857</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
571
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<pre style="margin: 0;">-<span id="LC571" class="line" lang="python"> <span class="s" style="color: #d14;">'b1241'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.863</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
572
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<pre style="margin: 0;">-<span id="LC572" class="line" lang="python"> <span class="s" style="color: #d14;">'b1276'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.863</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
573
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<pre style="margin: 0;">-<span id="LC573" class="line" lang="python"> <span class="s" style="color: #d14;">'b2935'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.863</span><span class="p">,</span></span>
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574
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<pre style="margin: 0;">-<span id="LC574" class="line" lang="python"> <span class="s" style="color: #d14;">'b4025'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.863</span><span class="p">}}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
575
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<pre style="margin: 0;">-<span id="LC575" class="line" lang="python"> <span class="n" style="color: #333;">solution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">double_gene_deletion</span><span class="p">(</span></span>
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576
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<pre style="margin: 0;">-<span id="LC576" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">gene_list1</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">genes</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)[</span><span class="s" style="color: #d14;">'growth'</span><span class="p">]</span></span>
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577
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<pre style="margin: 0;">-<span id="LC577" class="line" lang="python"> <span class="n" style="color: #333;">solution_one_process</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">double_gene_deletion</span><span class="p">(</span></span>
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578
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<pre style="margin: 0;">-<span id="LC578" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">gene_list1</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">genes</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)[</span><span class="s" style="color: #d14;">'growth'</span><span class="p">]</span></span>
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<td class="diff-line-num old old_line" data-linenumber="579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
579
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<pre style="margin: 0;">-<span id="LC579" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">rxn_a</span><span class="p">,</span> <span class="n" style="color: #333;">sub</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iteritems</span><span class="p">(</span><span class="n" style="color: #333;">growth_dict</span><span class="p">):</span></span>
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580
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<pre style="margin: 0;">-<span id="LC580" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">rxn_b</span><span class="p">,</span> <span class="n" style="color: #333;">growth</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iteritems</span><span class="p">(</span><span class="n" style="color: #333;">sub</span><span class="p">):</span></span>
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<td class="diff-line-num old old_line" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
581
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<pre style="margin: 0;">-<span id="LC581" class="line" lang="python"> <span class="n" style="color: #333;">sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solution</span><span class="p">[</span><span class="nb" style="color: #0086b3;">frozenset</span><span class="p">([</span><span class="n" style="color: #333;">rxn_a</span><span class="p">,</span> <span class="n" style="color: #333;">rxn_b</span><span class="p">])]</span></span>
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582
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<pre style="margin: 0;">-<span id="LC582" class="line" lang="python"> <span class="n" style="color: #333;">sol_one</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solution_one_process</span><span class="p">[</span><span class="nb" style="color: #0086b3;">frozenset</span><span class="p">([</span><span class="n" style="color: #333;">rxn_a</span><span class="p">,</span> <span class="n" style="color: #333;">rxn_b</span><span class="p">])]</span></span>
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583
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<pre style="margin: 0;">-<span id="LC583" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">sol</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">growth</span></span>
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<td class="diff-line-num old old_line" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
584
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<pre style="margin: 0;">-<span id="LC584" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">sol_one</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">growth</span></span>
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585
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<pre style="margin: 0;">-<span id="LC585" class="line" lang="python"></span>
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586
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<pre style="margin: 0;">-<span id="LC586" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_double_reaction_deletion</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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587
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<pre style="margin: 0;">-<span id="LC587" class="line" lang="python"> <span class="n" style="color: #333;">reactions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'FBA'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ATPS4r'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ENO'</span><span class="p">,</span> <span class="s" style="color: #d14;">'FRUpts2'</span><span class="p">]</span></span>
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588
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<pre style="margin: 0;">-<span id="LC588" class="line" lang="python"> <span class="n" style="color: #333;">growth_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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589
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<pre style="margin: 0;">-<span id="LC589" class="line" lang="python"> <span class="s" style="color: #d14;">"FBA"</span><span class="p">:</span> <span class="p">{</span></span>
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590
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<pre style="margin: 0;">-<span id="LC590" class="line" lang="python"> <span class="s" style="color: #d14;">"ATPS4r"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.135</span><span class="p">,</span></span>
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591
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<pre style="margin: 0;">-<span id="LC591" class="line" lang="python"> <span class="s" style="color: #d14;">"ENO"</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="s" style="color: #d14;">'nan'</span><span class="p">),</span></span>
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592
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<pre style="margin: 0;">-<span id="LC592" class="line" lang="python"> <span class="s" style="color: #d14;">"FRUpts2"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.704</span></span>
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593
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<pre style="margin: 0;">-<span id="LC593" class="line" lang="python"> <span class="p">},</span></span>
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594
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<pre style="margin: 0;">-<span id="LC594" class="line" lang="python"> <span class="s" style="color: #d14;">"ATPS4r"</span><span class="p">:</span> <span class="p">{</span></span>
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595
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<pre style="margin: 0;">-<span id="LC595" class="line" lang="python"> <span class="s" style="color: #d14;">"ENO"</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="s" style="color: #d14;">'nan'</span><span class="p">),</span></span>
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596
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<pre style="margin: 0;">-<span id="LC596" class="line" lang="python"> <span class="s" style="color: #d14;">"FRUpts2"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.374</span></span>
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597
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<pre style="margin: 0;">-<span id="LC597" class="line" lang="python"> <span class="p">},</span></span>
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598
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<pre style="margin: 0;">-<span id="LC598" class="line" lang="python"> <span class="s" style="color: #d14;">"ENO"</span><span class="p">:</span> <span class="p">{</span></span>
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599
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<pre style="margin: 0;">-<span id="LC599" class="line" lang="python"> <span class="s" style="color: #d14;">"FRUpts2"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span></span>
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600
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<pre style="margin: 0;">-<span id="LC600" class="line" lang="python"> <span class="p">},</span></span>
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601
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<pre style="margin: 0;">-<span id="LC601" class="line" lang="python"> <span class="p">}</span></span>
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602
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<pre style="margin: 0;">-<span id="LC602" class="line" lang="python"></span>
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603
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<pre style="margin: 0;">-<span id="LC603" class="line" lang="python"> <span class="n" style="color: #333;">solution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">double_reaction_deletion</span><span class="p">(</span></span>
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<td class="diff-line-num old old_line" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
604
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<pre style="margin: 0;">-<span id="LC604" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">reaction_list1</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reactions</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)[</span><span class="s" style="color: #d14;">'growth'</span><span class="p">]</span></span>
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605
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<pre style="margin: 0;">-<span id="LC605" class="line" lang="python"> <span class="n" style="color: #333;">solution_one_process</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">double_reaction_deletion</span><span class="p">(</span></span>
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606
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<pre style="margin: 0;">-<span id="LC606" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">reaction_list1</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reactions</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)[</span><span class="s" style="color: #d14;">'growth'</span><span class="p">]</span></span>
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<td class="diff-line-num old old_line" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
607
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<pre style="margin: 0;">-<span id="LC607" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">rxn_a</span><span class="p">,</span> <span class="n" style="color: #333;">sub</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iteritems</span><span class="p">(</span><span class="n" style="color: #333;">growth_dict</span><span class="p">):</span></span>
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<td class="diff-line-num old old_line" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
608
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<pre style="margin: 0;">-<span id="LC608" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">rxn_b</span><span class="p">,</span> <span class="n" style="color: #333;">growth</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iteritems</span><span class="p">(</span><span class="n" style="color: #333;">sub</span><span class="p">):</span></span>
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<td class="diff-line-num old old_line" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
609
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<pre style="margin: 0;">-<span id="LC609" class="line" lang="python"> <span class="n" style="color: #333;">sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solution</span><span class="p">[</span><span class="nb" style="color: #0086b3;">frozenset</span><span class="p">([</span><span class="n" style="color: #333;">rxn_a</span><span class="p">,</span> <span class="n" style="color: #333;">rxn_b</span><span class="p">])]</span></span>
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610
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<pre style="margin: 0;">-<span id="LC610" class="line" lang="python"> <span class="n" style="color: #333;">sol_one</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solution_one_process</span><span class="p">[</span><span class="nb" style="color: #0086b3;">frozenset</span><span class="p">([</span><span class="n" style="color: #333;">rxn_a</span><span class="p">,</span> <span class="n" style="color: #333;">rxn_b</span><span class="p">])]</span></span>
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<pre style="margin: 0;">-<span id="LC611" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">math</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isnan</span><span class="p">(</span><span class="n" style="color: #333;">growth</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC612" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">math</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isnan</span><span class="p">(</span><span class="n" style="color: #333;">sol</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC613" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">math</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isnan</span><span class="p">(</span><span class="n" style="color: #333;">sol_one</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC614" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC615" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">sol</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">growth</span></span>
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616
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<pre style="margin: 0;">-<span id="LC616" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">sol_one</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">growth</span></span>
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<pre style="margin: 0;">-<span id="LC617" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC618" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_double_reaction_deletion_benchmark</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">large_model</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC619" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC620" class="line" lang="python"> <span class="n" style="color: #333;">reactions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">large_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">::</span><span class="mi" style="color: #099;">100</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC621" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="n" style="color: #333;">double_reaction_deletion</span><span class="p">,</span> <span class="n" style="color: #333;">large_model</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC622" class="line" lang="python"> <span class="n" style="color: #333;">reaction_list1</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reactions</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC623" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC624" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"solver"</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC625" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_flux_variability_benchmark</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">large_model</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC626" class="line" lang="python"> <span class="n" style="color: #333;">solver</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC627" class="line" lang="python"> <span class="n" style="color: #333;">large_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solver</span></span>
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<pre style="margin: 0;">-<span id="LC628" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="n" style="color: #333;">flux_variability_analysis</span><span class="p">,</span> <span class="n" style="color: #333;">large_model</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC629" class="line" lang="python"> <span class="n" style="color: #333;">reaction_list</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">large_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">::</span><span class="mi" style="color: #099;">3</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC630" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC631" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"solver"</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC632" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_flux_variability_loopless_benchmark</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC633" class="line" lang="python"> <span class="n" style="color: #333;">solver</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC634" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solver</span></span>
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<pre style="margin: 0;">-<span id="LC635" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="n" style="color: #333;">flux_variability_analysis</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">loopless</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC636" class="line" lang="python"> <span class="n" style="color: #333;">reaction_list</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">::</span><span class="mi" style="color: #099;">3</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC637" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC638" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"solver"</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC639" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_pfba_flux_variability</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">pfba_fva_results</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC640" class="line" lang="python"> <span class="n" style="color: #333;">fva_results</span><span class="p">,</span> <span class="n" style="color: #333;">solver</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC641" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solver</span></span>
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<pre style="margin: 0;">-<span id="LC642" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warns</span><span class="p">(</span><span class="nb" style="color: #0086b3;">UserWarning</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC643" class="line" lang="python"> <span class="n" style="color: #333;">flux_variability_analysis</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC644" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">pfba_factor</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.1</span><span class="p">,</span> <span class="n" style="color: #333;">reaction_list</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">::</span><span class="mi" style="color: #099;">3</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC645" class="line" lang="python"> <span class="n" style="color: #333;">fva_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flux_variability_analysis</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC646" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">pfba_factor</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1.1</span><span class="p">,</span> <span class="n" style="color: #333;">reaction_list</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC647" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">result</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iteritems</span><span class="p">(</span><span class="n" style="color: #333;">fva_out</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">T</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC648" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iteritems</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC649" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">pfba_fva_results</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">][</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">v</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">0.00001</span></span>
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<pre style="margin: 0;">-<span id="LC650" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">pfba_fva_results</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">][</span><span class="n" style="color: #333;">name</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><=</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC651" class="line" lang="python"> <span class="n" style="color: #333;">fva_results</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">][</span><span class="n" style="color: #333;">name</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC652" class="line" lang="python"> <span class="n" style="color: #333;">loop_reactions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_by_id</span><span class="p">(</span><span class="n" style="color: #333;">rid</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC653" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">rid</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">"FRD7"</span><span class="p">,</span> <span class="s" style="color: #d14;">"SUCDi"</span><span class="p">)]</span></span>
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<pre style="margin: 0;">-<span id="LC654" class="line" lang="python"> <span class="n" style="color: #333;">fva_loopless</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flux_variability_analysis</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC655" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">pfba_factor</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1.1</span><span class="p">,</span> <span class="n" style="color: #333;">reaction_list</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">loop_reactions</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC656" class="line" lang="python"> <span class="n" style="color: #333;">loopless</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC657" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">allclose</span><span class="p">(</span><span class="n" style="color: #333;">fva_loopless</span><span class="p">[</span><span class="s" style="color: #d14;">"maximum"</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC658" class="line" lang="python"> <span class="n" style="color: #333;">fva_loopless</span><span class="p">[</span><span class="s" style="color: #d14;">"minimum"</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC659" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC660" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"solver"</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC661" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_flux_variability</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">fva_results</span><span class="p">,</span> <span class="n" style="color: #333;">solver</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC662" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solver</span></span>
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<pre style="margin: 0;">-<span id="LC663" class="line" lang="python"> <span class="n" style="color: #333;">fva_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flux_variability_analysis</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC664" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">reaction_list</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC665" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">result</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iteritems</span><span class="p">(</span><span class="n" style="color: #333;">fva_out</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">T</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC666" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iteritems</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC667" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">fva_results</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">][</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">v</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">0.00001</span></span>
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<pre style="margin: 0;">-<span id="LC668" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC669" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"solver"</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC670" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_flux_variability_loopless</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">solver</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC671" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solver</span></span>
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<pre style="margin: 0;">-<span id="LC672" class="line" lang="python"> <span class="n" style="color: #333;">loop_reactions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_by_id</span><span class="p">(</span><span class="n" style="color: #333;">rid</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC673" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">rid</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">"FRD7"</span><span class="p">,</span> <span class="s" style="color: #d14;">"SUCDi"</span><span class="p">)]</span></span>
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<pre style="margin: 0;">-<span id="LC674" class="line" lang="python"> <span class="n" style="color: #333;">fva_normal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flux_variability_analysis</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC675" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">reaction_list</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">loop_reactions</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC676" class="line" lang="python"> <span class="n" style="color: #333;">fva_loopless</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flux_variability_analysis</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC677" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">reaction_list</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">loop_reactions</span><span class="p">,</span> <span class="n" style="color: #333;">loopless</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC678" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC679" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">allclose</span><span class="p">(</span><span class="n" style="color: #333;">fva_normal</span><span class="p">[</span><span class="s" style="color: #d14;">"maximum"</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC680" class="line" lang="python"> <span class="n" style="color: #333;">fva_normal</span><span class="p">[</span><span class="s" style="color: #d14;">"minimum"</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC681" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">allclose</span><span class="p">(</span><span class="n" style="color: #333;">fva_loopless</span><span class="p">[</span><span class="s" style="color: #d14;">"maximum"</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC682" class="line" lang="python"> <span class="n" style="color: #333;">fva_loopless</span><span class="p">[</span><span class="s" style="color: #d14;">"minimum"</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC683" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC684" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fva_data_frame</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC685" class="line" lang="python"> <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flux_variability_analysis</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC686" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">all</span><span class="p">([</span><span class="n" style="color: #333;">df</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">'minimum'</span><span class="p">,</span> <span class="s" style="color: #d14;">'maximum'</span><span class="p">]])</span></span>
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<pre style="margin: 0;">-<span id="LC687" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC688" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fva_infeasible</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC689" class="line" lang="python"> <span class="n" style="color: #333;">infeasible_model</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC690" class="line" lang="python"> <span class="n" style="color: #333;">infeasible_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_by_id</span><span class="p">(</span><span class="s" style="color: #d14;">"EX_glc__D_e"</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower_bound</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">-<span id="LC691" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># ensure that an infeasible model does not run FVA</span></span>
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<pre style="margin: 0;">-<span id="LC692" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">Infeasible</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC693" class="line" lang="python"> <span class="n" style="color: #333;">flux_variability_analysis</span><span class="p">(</span><span class="n" style="color: #333;">infeasible_model</span><span class="p">)</span></span>
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694
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<pre style="margin: 0;">-<span id="LC694" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC695" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fva_minimization</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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696
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<pre style="margin: 0;">-<span id="LC696" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">EX_glc__D_e</span></span>
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697
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<pre style="margin: 0;">-<span id="LC697" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective_direction</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'min'</span></span>
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698
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<pre style="margin: 0;">-<span id="LC698" class="line" lang="python"> <span class="n" style="color: #333;">solution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flux_variability_analysis</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">fraction_of_optimum</span><span class="o" style="font-weight: 600;">=.</span><span class="mi" style="color: #099;">95</span><span class="p">)</span></span>
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699
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<pre style="margin: 0;">-<span id="LC699" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">at</span><span class="p">[</span><span class="s" style="color: #d14;">'EX_glc__D_e'</span><span class="p">,</span> <span class="s" style="color: #d14;">'minimum'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">10.0</span></span>
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700
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<pre style="margin: 0;">-<span id="LC700" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">at</span><span class="p">[</span><span class="s" style="color: #d14;">'EX_glc__D_e'</span><span class="p">,</span> <span class="s" style="color: #d14;">'maximum'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">9.5</span></span>
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701
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<pre style="margin: 0;">-<span id="LC701" class="line" lang="python"></span>
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702
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<pre style="margin: 0;">-<span id="LC702" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_find_blocked_reactions_solver_none</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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703
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<pre style="margin: 0;">-<span id="LC703" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">find_blocked_reactions</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="p">[</span><span class="mi" style="color: #099;">40</span><span class="p">:</span><span class="mi" style="color: #099;">46</span><span class="p">])</span></span>
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704
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<pre style="margin: 0;">-<span id="LC704" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">'FRUpts2'</span><span class="p">]</span></span>
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705
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<pre style="margin: 0;">-<span id="LC705" class="line" lang="python"></span>
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706
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<pre style="margin: 0;">-<span id="LC706" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_essential_genes</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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707
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<pre style="margin: 0;">-<span id="LC707" class="line" lang="python"> <span class="n" style="color: #333;">essential_genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'b2779'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b1779'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b0720'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b2416'</span><span class="p">,</span></span>
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708
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<pre style="margin: 0;">-<span id="LC708" class="line" lang="python"> <span class="s" style="color: #d14;">'b2926'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b1136'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b2415'</span><span class="p">}</span></span>
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709
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<pre style="margin: 0;">-<span id="LC709" class="line" lang="python"> <span class="n" style="color: #333;">observed_essential_genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">g</span> <span class="ow" style="font-weight: 600;">in</span></span>
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<pre style="margin: 0;">-<span id="LC710" class="line" lang="python"> <span class="n" style="color: #333;">find_essential_genes</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">)}</span></span>
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<pre style="margin: 0;">-<span id="LC711" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">observed_essential_genes</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">essential_genes</span></span>
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<pre style="margin: 0;">-<span id="LC712" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC713" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_essential_reactions</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC714" class="line" lang="python"> <span class="n" style="color: #333;">essential_reactions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'GLNS'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Biomass_Ecoli_core'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PIt2r'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC715" class="line" lang="python"> <span class="s" style="color: #d14;">'GAPD'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC716" class="line" lang="python"> <span class="s" style="color: #d14;">'ACONTb'</span><span class="p">,</span> <span class="s" style="color: #d14;">'EX_nh4_e'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ENO'</span><span class="p">,</span> <span class="s" style="color: #d14;">'EX_h_e'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC717" class="line" lang="python"> <span class="s" style="color: #d14;">'EX_glc__D_e'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ICDHyr'</span><span class="p">,</span> <span class="s" style="color: #d14;">'CS'</span><span class="p">,</span> <span class="s" style="color: #d14;">'NH4t'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC718" class="line" lang="python"> <span class="s" style="color: #d14;">'GLCpts'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC719" class="line" lang="python"> <span class="s" style="color: #d14;">'PGM'</span><span class="p">,</span> <span class="s" style="color: #d14;">'EX_pi_e'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PGK'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RPI'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ACONTa'</span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC720" class="line" lang="python"> <span class="n" style="color: #333;">observed_essential_reactions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span></span>
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<pre style="margin: 0;">-<span id="LC721" class="line" lang="python"> <span class="n" style="color: #333;">find_essential_reactions</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">)}</span></span>
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<pre style="margin: 0;">-<span id="LC722" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">observed_essential_reactions</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">essential_reactions</span></span>
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<pre style="margin: 0;">-<span id="LC723" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC724" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"solver"</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC725" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_find_blocked_reactions</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">solver</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC726" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solver</span></span>
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<pre style="margin: 0;">-<span id="LC727" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">find_blocked_reactions</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="p">[</span><span class="mi" style="color: #099;">40</span><span class="p">:</span><span class="mi" style="color: #099;">46</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC728" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">'FRUpts2'</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC729" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC730" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">find_blocked_reactions</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="p">[</span><span class="mi" style="color: #099;">42</span><span class="p">:</span><span class="mi" style="color: #099;">48</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC731" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span><span class="s" style="color: #d14;">'FUMt2_2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'FRUpts2'</span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC732" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC733" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">find_blocked_reactions</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="p">[</span><span class="mi" style="color: #099;">30</span><span class="p">:</span><span class="mi" style="color: #099;">50</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC734" class="line" lang="python"> <span class="n" style="color: #333;">open_exchanges</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC735" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC736" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC737" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_loopless_benchmark_before</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC738" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">construct_ll_test_model</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC739" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC740" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC741" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">test_model</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC742" class="line" lang="python"> <span class="n" style="color: #333;">add_loopless</span><span class="p">(</span><span class="n" style="color: #333;">test_model</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC743" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC744" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC745" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="n" style="color: #333;">_</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC746" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC747" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_loopless_benchmark_after</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC748" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">construct_ll_test_model</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC749" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="n" style="color: #333;">loopless_solution</span><span class="p">,</span> <span class="n" style="color: #333;">test_model</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC750" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC751" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_loopless_solution</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">ll_test_model</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC752" class="line" lang="python"> <span class="n" style="color: #333;">solution_feasible</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loopless_solution</span><span class="p">(</span><span class="n" style="color: #333;">ll_test_model</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC753" class="line" lang="python"> <span class="n" style="color: #333;">ll_test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">v3</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower_bound</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC754" class="line" lang="python"> <span class="n" style="color: #333;">ll_test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC755" class="line" lang="python"> <span class="n" style="color: #333;">solution_infeasible</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loopless_solution</span><span class="p">(</span><span class="n" style="color: #333;">ll_test_model</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC756" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">solution_feasible</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">[</span><span class="s" style="color: #d14;">"v3"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mf" style="color: #099;">0.0</span></span>
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<pre style="margin: 0;">-<span id="LC757" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">solution_infeasible</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">[</span><span class="s" style="color: #d14;">"v3"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mf" style="color: #099;">1.0</span></span>
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758
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<pre style="margin: 0;">-<span id="LC758" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC759" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_loopless_solution_fluxes</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC760" class="line" lang="python"> <span class="n" style="color: #333;">fluxes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span></span>
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<pre style="margin: 0;">-<span id="LC761" class="line" lang="python"> <span class="n" style="color: #333;">ll_solution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loopless_solution</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">fluxes</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fluxes</span><span class="p">)</span></span>
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762
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<pre style="margin: 0;">-<span id="LC762" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">ll_solution</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC763" class="line" lang="python"></span>
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764
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<pre style="margin: 0;">-<span id="LC764" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_add_loopless</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">ll_test_model</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC765" class="line" lang="python"> <span class="n" style="color: #333;">add_loopless</span><span class="p">(</span><span class="n" style="color: #333;">ll_test_model</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC766" class="line" lang="python"> <span class="n" style="color: #333;">feasible_status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ll_test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">status</span></span>
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767
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<pre style="margin: 0;">-<span id="LC767" class="line" lang="python"> <span class="n" style="color: #333;">ll_test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">v3</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower_bound</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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768
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<pre style="margin: 0;">-<span id="LC768" class="line" lang="python"> <span class="n" style="color: #333;">ll_test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">slim_optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC769" class="line" lang="python"> <span class="n" style="color: #333;">infeasible_status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ll_test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">status</span></span>
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770
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<pre style="margin: 0;">-<span id="LC770" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">feasible_status</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">OPTIMAL</span></span>
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771
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<pre style="margin: 0;">-<span id="LC771" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">infeasible_status</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">INFEASIBLE</span></span>
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<pre style="margin: 0;">-<span id="LC772" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC773" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_gapfilling</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">salmonella</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC774" class="line" lang="python"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Model</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC775" class="line" lang="python"> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">([</span><span class="n" style="color: #333;">Metabolite</span><span class="p">(</span><span class="n" style="color: #333;">m_id</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">m_id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"b"</span><span class="p">,</span> <span class="s" style="color: #d14;">"c"</span><span class="p">]])</span></span>
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<pre style="margin: 0;">-<span id="LC776" class="line" lang="python"> <span class="n" style="color: #333;">exa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"EX_a"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC777" class="line" lang="python"> <span class="n" style="color: #333;">exa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">})</span></span>
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<pre style="margin: 0;">-<span id="LC778" class="line" lang="python"> <span class="n" style="color: #333;">b2c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"b2c"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC779" class="line" lang="python"> <span class="n" style="color: #333;">b2c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">b</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">c</span><span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">})</span></span>
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<pre style="margin: 0;">-<span id="LC780" class="line" lang="python"> <span class="n" style="color: #333;">dmc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"DM_c"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC781" class="line" lang="python"> <span class="n" style="color: #333;">dmc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">c</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">})</span></span>
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<pre style="margin: 0;">-<span id="LC782" class="line" lang="python"> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_reactions</span><span class="p">([</span><span class="n" style="color: #333;">exa</span><span class="p">,</span> <span class="n" style="color: #333;">b2c</span><span class="p">,</span> <span class="n" style="color: #333;">dmc</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC783" class="line" lang="python"> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'DM_c'</span></span>
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<pre style="margin: 0;">-<span id="LC784" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC785" class="line" lang="python"> <span class="n" style="color: #333;">universal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Model</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC786" class="line" lang="python"> <span class="n" style="color: #333;">a2b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"a2b"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC787" class="line" lang="python"> <span class="n" style="color: #333;">a2d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"a2d"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC788" class="line" lang="python"> <span class="n" style="color: #333;">universal</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_reactions</span><span class="p">([</span><span class="n" style="color: #333;">a2b</span><span class="p">,</span> <span class="n" style="color: #333;">a2d</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC789" class="line" lang="python"> <span class="n" style="color: #333;">a2b</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">build_reaction_from_string</span><span class="p">(</span><span class="s" style="color: #d14;">"a --> b"</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC790" class="line" lang="python"> <span class="n" style="color: #333;">a2d</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">build_reaction_from_string</span><span class="p">(</span><span class="s" style="color: #d14;">"a --> d"</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC791" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC792" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># # GrowMatch</span></span>
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<pre style="margin: 0;">-<span id="LC793" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># result = gapfilling.growMatch(m, universal)[0]</span></span>
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<pre style="margin: 0;">-<span id="LC794" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapfilling</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">gapfill</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">universal</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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795
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<pre style="margin: 0;">-<span id="LC795" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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796
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<pre style="margin: 0;">-<span id="LC796" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"a2b"</span></span>
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<pre style="margin: 0;">-<span id="LC797" class="line" lang="python"></span>
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798
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<pre style="margin: 0;">-<span id="LC798" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># # SMILEY</span></span>
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799
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<pre style="margin: 0;">-<span id="LC799" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># result = gapfilling.SMILEY(m, "b", universal)[0]</span></span>
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800
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<pre style="margin: 0;">-<span id="LC800" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">m</span><span class="p">:</span></span>
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801
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<pre style="margin: 0;">-<span id="LC801" class="line" lang="python"> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_boundary</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'demand'</span><span class="p">)</span></span>
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802
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<pre style="margin: 0;">-<span id="LC802" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapfilling</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">gapfill</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">universal</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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803
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<pre style="margin: 0;">-<span id="LC803" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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804
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<pre style="margin: 0;">-<span id="LC804" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"a2b"</span></span>
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805
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<pre style="margin: 0;">-<span id="LC805" class="line" lang="python"></span>
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806
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<pre style="margin: 0;">-<span id="LC806" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># # 2 rounds of GrowMatch with exchange reactions</span></span>
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807
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<pre style="margin: 0;">-<span id="LC807" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># result = gapfilling.growMatch(m, None, ex_rxns=True, iterations=2)</span></span>
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808
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<pre style="margin: 0;">-<span id="LC808" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapfilling</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">gapfill</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">exchange_reactions</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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809
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<pre style="margin: 0;">-<span id="LC809" class="line" lang="python"> <span class="n" style="color: #333;">iterations</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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810
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<pre style="margin: 0;">-<span id="LC810" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span></span>
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811
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<pre style="margin: 0;">-<span id="LC811" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC812" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC813" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">{</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">result</span><span class="p">}</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span><span class="s" style="color: #d14;">"EX_b"</span><span class="p">,</span> <span class="s" style="color: #d14;">"EX_c"</span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC814" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC815" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># somewhat bigger model</span></span>
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<pre style="margin: 0;">-<span id="LC816" class="line" lang="python"> <span class="n" style="color: #333;">universal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Model</span><span class="p">(</span><span class="s" style="color: #d14;">"universal_reactions"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC817" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">salmonella</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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818
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<pre style="margin: 0;">-<span id="LC818" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">f6p_c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="p">]:</span></span>
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<pre style="margin: 0;">-<span id="LC819" class="line" lang="python"> <span class="n" style="color: #333;">reaction</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_by_id</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC820" class="line" lang="python"> <span class="n" style="color: #333;">universal</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_reactions</span><span class="p">([</span><span class="n" style="color: #333;">reaction</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">()])</span></span>
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<pre style="margin: 0;">-<span id="LC821" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove_reactions</span><span class="p">([</span><span class="n" style="color: #333;">reaction</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC822" class="line" lang="python"> <span class="n" style="color: #333;">gf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapfilling</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">GapFiller</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">universal</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC823" class="line" lang="python"> <span class="n" style="color: #333;">penalties</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'TKT2'</span><span class="p">:</span> <span class="mf" style="color: #099;">1e3</span><span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC824" class="line" lang="python"> <span class="n" style="color: #333;">demand_reactions</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC825" class="line" lang="python"> <span class="n" style="color: #333;">solution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fill</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC826" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">'TKT2'</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">{</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">solution</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]}</span></span>
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<pre style="margin: 0;">-<span id="LC827" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">gf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">(</span><span class="n" style="color: #333;">solution</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC828" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC829" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">check_line</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="n" style="color: #333;">expected_entries</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC830" class="line" lang="python"> <span class="n" style="color: #333;">pattern</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;">r"\s"</span><span class="p">)):</span></span>
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<pre style="margin: 0;">-<span id="LC831" class="line" lang="python"> <span class="s" style="color: #d14;">"""Ensure each expected entry is in the output."""</span></span>
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<pre style="margin: 0;">-<span id="LC832" class="line" lang="python"> <span class="n" style="color: #333;">output_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span></span>
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833
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<pre style="margin: 0;">-<span id="LC833" class="line" lang="python"> <span class="n" style="color: #333;">pattern</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sub</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitlines</span><span class="p">())</span></span>
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834
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<pre style="margin: 0;">-<span id="LC834" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">elem</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">expected_entries</span><span class="p">:</span></span>
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835
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<pre style="margin: 0;">-<span id="LC835" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">pattern</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sub</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">elem</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">output_set</span></span>
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836
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<pre style="margin: 0;">-<span id="LC836" class="line" lang="python"></span>
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837
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<pre style="margin: 0;">-<span id="LC837" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">check_in_line</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="n" style="color: #333;">expected_entries</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC838" class="line" lang="python"> <span class="n" style="color: #333;">pattern</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;">r"\s"</span><span class="p">)):</span></span>
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<pre style="margin: 0;">-<span id="LC839" class="line" lang="python"> <span class="s" style="color: #d14;">"""Ensure each expected entry is contained in the output."""</span></span>
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<pre style="margin: 0;">-<span id="LC840" class="line" lang="python"> <span class="n" style="color: #333;">output_strip</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">pattern</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sub</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span></span>
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<pre style="margin: 0;">-<span id="LC841" class="line" lang="python"> <span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitlines</span><span class="p">()]</span></span>
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<pre style="margin: 0;">-<span id="LC842" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">elem</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">expected_entries</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC843" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">(</span></span>
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844
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<pre style="margin: 0;">-<span id="LC844" class="line" lang="python"> <span class="n" style="color: #333;">pattern</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sub</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">elem</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">output_strip</span><span class="p">),</span> \</span>
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<pre style="margin: 0;">-<span id="LC845" class="line" lang="python"> <span class="s" style="color: #d14;">"Not found: {} in:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">{}"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format</span><span class="p">(</span><span class="n" style="color: #333;">pattern</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sub</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">elem</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC846" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">output_strip</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC847" class="line" lang="python"></span>
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848
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<pre style="margin: 0;">-<span id="LC848" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"names"</span><span class="p">,</span> <span class="p">[</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">])</span></span>
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849
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<pre style="margin: 0;">-<span id="LC849" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_model_summary_previous_solution</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">opt_solver</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">):</span></span>
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850
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<pre style="margin: 0;">-<span id="LC850" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt_solver</span></span>
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<pre style="margin: 0;">-<span id="LC851" class="line" lang="python"> <span class="n" style="color: #333;">solution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC852" class="line" lang="python"> <span class="n" style="color: #333;">rxn_test</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exchanges</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC853" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">names</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC854" class="line" lang="python"> <span class="n" style="color: #333;">met_test</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">rxn_test</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">())[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>
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855
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<pre style="margin: 0;">-<span id="LC855" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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856
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<pre style="margin: 0;">-<span id="LC856" class="line" lang="python"> <span class="n" style="color: #333;">met_test</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">rxn_test</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">())[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span></span>
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857
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<pre style="margin: 0;">-<span id="LC857" class="line" lang="python"></span>
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858
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<pre style="margin: 0;">-<span id="LC858" class="line" lang="python"> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">[</span><span class="n" style="color: #333;">rxn_test</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">321</span></span>
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859
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<pre style="margin: 0;">-<span id="LC859" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC860" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">captured_output</span><span class="p">()</span> <span class="k" style="font-weight: 600;">as</span> <span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">err</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC861" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">summary</span><span class="p">(</span><span class="n" style="color: #333;">solution</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">names</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC862" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_in_line</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getvalue</span><span class="p">(),</span> <span class="p">[</span><span class="n" style="color: #333;">met_test</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'321'</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC863" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC864" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"names"</span><span class="p">,</span> <span class="p">[</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">])</span></span>
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865
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<pre style="margin: 0;">-<span id="LC865" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_model_summary</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">opt_solver</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC866" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt_solver</span></span>
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<pre style="margin: 0;">-<span id="LC867" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># test non-fva version (these should be fixed for textbook model</span></span>
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868
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<pre style="margin: 0;">-<span id="LC868" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">names</span><span class="p">:</span></span>
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869
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<pre style="margin: 0;">-<span id="LC869" class="line" lang="python"> <span class="n" style="color: #333;">expected_entries</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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870
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<pre style="margin: 0;">-<span id="LC870" class="line" lang="python"> <span class="s" style="color: #d14;">'O2 21.8'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC871" class="line" lang="python"> <span class="s" style="color: #d14;">'D-Glucose 10'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC873" class="line" lang="python"> <span class="s" style="color: #d14;">'Phosphate 3.21'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC874" class="line" lang="python"> <span class="s" style="color: #d14;">'H2O 29.2'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC875" class="line" lang="python"> <span class="s" style="color: #d14;">'CO2 22.8'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC876" class="line" lang="python"> <span class="s" style="color: #d14;">'H+ 17.5'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC877" class="line" lang="python"> <span class="s" style="color: #d14;">'Biomass_Ecol... 0.874'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC878" class="line" lang="python"> <span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC879" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC880" class="line" lang="python"> <span class="n" style="color: #333;">expected_entries</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC881" class="line" lang="python"> <span class="s" style="color: #d14;">'o2_e 21.8'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC882" class="line" lang="python"> <span class="s" style="color: #d14;">'glc__D_e 10'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC883" class="line" lang="python"> <span class="s" style="color: #d14;">'nh4_e 4.77'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC884" class="line" lang="python"> <span class="s" style="color: #d14;">'pi_e 3.21'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC885" class="line" lang="python"> <span class="s" style="color: #d14;">'h2o_e 29.2'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC886" class="line" lang="python"> <span class="s" style="color: #d14;">'co2_e 22.8'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC887" class="line" lang="python"> <span class="s" style="color: #d14;">'h_e 17.5'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC888" class="line" lang="python"> <span class="s" style="color: #d14;">'Biomass_Ecol... 0.874'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC889" class="line" lang="python"> <span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC890" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Need to use a different method here because</span></span>
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<pre style="margin: 0;">-<span id="LC891" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># there are multiple entries per line.</span></span>
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<pre style="margin: 0;">-<span id="LC892" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC893" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">captured_output</span><span class="p">()</span> <span class="k" style="font-weight: 600;">as</span> <span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">err</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC894" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">summary</span><span class="p">(</span><span class="n" style="color: #333;">names</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">names</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC895" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_in_line</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getvalue</span><span class="p">(),</span> <span class="n" style="color: #333;">expected_entries</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC896" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC897" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># with model:</span></span>
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<pre style="margin: 0;">-<span id="LC898" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># model.objective = model.exchanges[0]</span></span>
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<pre style="margin: 0;">-<span id="LC899" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># model.summary()</span></span>
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<pre style="margin: 0;">-<span id="LC900" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC901" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"fraction"</span><span class="p">,</span> <span class="p">[</span><span class="mf" style="color: #099;">0.95</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC902" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_model_summary_with_fva</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">opt_solver</span><span class="p">,</span> <span class="n" style="color: #333;">fraction</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC903" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opt_solver</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"optlang-gurobi"</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC904" class="line" lang="python"> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">xfail</span><span class="p">(</span><span class="s" style="color: #d14;">"FVA currently buggy"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC905" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># test non-fva version (these should be fixed for textbook model</span></span>
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<pre style="margin: 0;">-<span id="LC906" class="line" lang="python"> <span class="n" style="color: #333;">expected_entries</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC907" class="line" lang="python"> <span class="s" style="color: #d14;">'idFluxRangeidFluxRangeBiomass_Ecol...0.874'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC908" class="line" lang="python"> <span class="s" style="color: #d14;">'o2_e 21.8 [19.9, 23.7]'</span></span>
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<pre style="margin: 0;">-<span id="LC909" class="line" lang="python"> <span class="s" style="color: #d14;">'h2o_e 29.2 [25, 30.7]'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC910" class="line" lang="python"> <span class="s" style="color: #d14;">'glc__D_e 10 [9.52, 10]'</span></span>
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<pre style="margin: 0;">-<span id="LC911" class="line" lang="python"> <span class="s" style="color: #d14;">'co2_e 22.8 [18.9, 24.7]'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC912" class="line" lang="python"> <span class="s" style="color: #d14;">'nh4_e 4.77 [4.53, 5.16]'</span></span>
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<pre style="margin: 0;">-<span id="LC913" class="line" lang="python"> <span class="s" style="color: #d14;">'h_e 17.5 [16.7, 22.4]'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC914" class="line" lang="python"> <span class="s" style="color: #d14;">'pi_e 3.21 [3.05, 3.21]'</span></span>
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<pre style="margin: 0;">-<span id="LC915" class="line" lang="python"> <span class="s" style="color: #d14;">'for_e 0 [0, 5.72]'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC916" class="line" lang="python"> <span class="s" style="color: #d14;">'ac_e 0 [0, 1.91]'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC917" class="line" lang="python"> <span class="s" style="color: #d14;">'pyr_e 0 [0, 1.27]'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC918" class="line" lang="python"> <span class="s" style="color: #d14;">'lac__D_e 0 [0, 1.07]'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC919" class="line" lang="python"> <span class="s" style="color: #d14;">'succ_e 0 [0, 0.837]'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC920" class="line" lang="python"> <span class="s" style="color: #d14;">'glu__L_e 0 [0, 0.636]'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC921" class="line" lang="python"> <span class="s" style="color: #d14;">'akg_e 0 [0, 0.715]'</span><span class="p">,</span></span>
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922
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<pre style="margin: 0;">-<span id="LC922" class="line" lang="python"> <span class="s" style="color: #d14;">'etoh_e 0 [0, 1.11]'</span><span class="p">,</span></span>
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923
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<pre style="margin: 0;">-<span id="LC923" class="line" lang="python"> <span class="s" style="color: #d14;">'acald_e 0 [0, 1.27]'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC924" class="line" lang="python"> <span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC925" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Need to use a different method here because</span></span>
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926
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<pre style="margin: 0;">-<span id="LC926" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># there are multiple entries per line.</span></span>
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<pre style="margin: 0;">-<span id="LC927" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt_solver</span></span>
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<pre style="margin: 0;">-<span id="LC928" class="line" lang="python"> <span class="n" style="color: #333;">solution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<td class="diff-line-num old old_line" data-linenumber="929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC929" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">captured_output</span><span class="p">()</span> <span class="k" style="font-weight: 600;">as</span> <span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">err</span><span class="p">):</span></span>
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930
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<pre style="margin: 0;">-<span id="LC930" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">summary</span><span class="p">(</span><span class="n" style="color: #333;">solution</span><span class="p">,</span> <span class="n" style="color: #333;">fva</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fraction</span><span class="p">)</span></span>
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931
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<pre style="margin: 0;">-<span id="LC931" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_in_line</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getvalue</span><span class="p">(),</span> <span class="n" style="color: #333;">expected_entries</span><span class="p">)</span></span>
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932
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<pre style="margin: 0;">-<span id="LC932" class="line" lang="python"></span>
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933
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<pre style="margin: 0;">-<span id="LC933" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"met"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"q8_c"</span><span class="p">])</span></span>
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934
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<pre style="margin: 0;">-<span id="LC934" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_metabolite_summary_previous_solution</span><span class="p">(</span></span>
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935
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<pre style="margin: 0;">-<span id="LC935" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">opt_solver</span><span class="p">,</span> <span class="n" style="color: #333;">met</span><span class="p">):</span></span>
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936
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<pre style="margin: 0;">-<span id="LC936" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt_solver</span></span>
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937
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<pre style="margin: 0;">-<span id="LC937" class="line" lang="python"> <span class="n" style="color: #333;">solution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pfba</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
938
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<pre style="margin: 0;">-<span id="LC938" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_by_id</span><span class="p">(</span><span class="n" style="color: #333;">met</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">summary</span><span class="p">(</span><span class="n" style="color: #333;">solution</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC939" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC940" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"met, names"</span><span class="p">,</span> <span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC941" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"q8_c"</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC942" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"q8_c"</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC943" class="line" lang="python"> <span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC944" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_metabolite_summary</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">opt_solver</span><span class="p">,</span> <span class="n" style="color: #333;">met</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC945" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt_solver</span></span>
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<pre style="margin: 0;">-<span id="LC946" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC947" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">captured_output</span><span class="p">()</span> <span class="k" style="font-weight: 600;">as</span> <span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">err</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC948" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_by_id</span><span class="p">(</span><span class="n" style="color: #333;">met</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">summary</span><span class="p">(</span><span class="n" style="color: #333;">names</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">names</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC949" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC950" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">names</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC951" class="line" lang="python"> <span class="n" style="color: #333;">expected_entries</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC952" class="line" lang="python"> <span class="s" style="color: #d14;">'PRODUCING REACTIONS -- Ubiquinone-8 (q8_c)'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC953" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">% </span><span class="s" style="color: #d14;">FLUX RXN ID REACTION'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC954" class="line" lang="python"> <span class="s" style="color: #d14;">'100</span><span class="si" style="color: #d14;">% 43.6</span><span class="s" style="color: #d14;"> cytochr... 2.0 H+ + 0.5 O2 + Ubiquinol-8 --> '</span></span>
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<pre style="margin: 0;">-<span id="LC955" class="line" lang="python"> <span class="s" style="color: #d14;">'H2O + 2.0 H+ ...'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC956" class="line" lang="python"> <span class="s" style="color: #d14;">'CONSUMING REACTIONS -- Ubiquinone-8 (q8_c)'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC957" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">% </span><span class="s" style="color: #d14;">FLUX RXN ID REACTION'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC958" class="line" lang="python"> <span class="s" style="color: #d14;">'88</span><span class="si" style="color: #d14;">% 38.5</span><span class="s" style="color: #d14;"> NADH de... 4.0 H+ + Nicotinamide adenine '</span></span>
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<pre style="margin: 0;">-<span id="LC959" class="line" lang="python"> <span class="s" style="color: #d14;">'dinucleotide - re...'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC960" class="line" lang="python"> <span class="s" style="color: #d14;">'12</span><span class="si" style="color: #d14;">% 5.06</span><span class="s" style="color: #d14;"> succina... Ubiquinone-8 + Succinate --> '</span></span>
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961
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<pre style="margin: 0;">-<span id="LC961" class="line" lang="python"> <span class="s" style="color: #d14;">'Fumarate + Ubiquin...'</span></span>
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962
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<pre style="margin: 0;">-<span id="LC962" class="line" lang="python"> <span class="p">]</span></span>
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963
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<pre style="margin: 0;">-<span id="LC963" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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964
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<pre style="margin: 0;">-<span id="LC964" class="line" lang="python"> <span class="n" style="color: #333;">expected_entries</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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965
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<pre style="margin: 0;">-<span id="LC965" class="line" lang="python"> <span class="s" style="color: #d14;">'PRODUCING REACTIONS -- Ubiquinone-8 (q8_c)'</span><span class="p">,</span></span>
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966
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<pre style="margin: 0;">-<span id="LC966" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">% </span><span class="s" style="color: #d14;">FLUX RXN ID REACTION'</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
967
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<pre style="margin: 0;">-<span id="LC967" class="line" lang="python"> <span class="s" style="color: #d14;">'100</span><span class="si" style="color: #d14;">% 43.6</span><span class="s" style="color: #d14;"> CYTBD '</span></span>
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968
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<pre style="margin: 0;">-<span id="LC968" class="line" lang="python"> <span class="s" style="color: #d14;">'2.0 h_c + 0.5 o2_c + q8h2_c --> h2o_c + 2.0 h_e...'</span><span class="p">,</span></span>
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969
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<pre style="margin: 0;">-<span id="LC969" class="line" lang="python"> <span class="s" style="color: #d14;">'CONSUMING REACTIONS -- Ubiquinone-8 (q8_c)'</span><span class="p">,</span></span>
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970
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<pre style="margin: 0;">-<span id="LC970" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">% </span><span class="s" style="color: #d14;">FLUX RXN ID REACTION'</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
971
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<pre style="margin: 0;">-<span id="LC971" class="line" lang="python"> <span class="s" style="color: #d14;">'88</span><span class="si" style="color: #d14;">% 38.5</span><span class="s" style="color: #d14;"> NADH16 '</span></span>
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972
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<pre style="margin: 0;">-<span id="LC972" class="line" lang="python"> <span class="s" style="color: #d14;">'4.0 h_c + nadh_c + q8_c --> 3.0 h_e + nad_c + q...'</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
973
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<pre style="margin: 0;">-<span id="LC973" class="line" lang="python"> <span class="s" style="color: #d14;">'12</span><span class="si" style="color: #d14;">% 5.06</span><span class="s" style="color: #d14;"> SUCDi q8_c + succ_c --> fum_c + q8h2_c'</span><span class="p">,</span></span>
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974
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<pre style="margin: 0;">-<span id="LC974" class="line" lang="python"> <span class="p">]</span></span>
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975
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<pre style="margin: 0;">-<span id="LC975" class="line" lang="python"></span>
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976
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<pre style="margin: 0;">-<span id="LC976" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_in_line</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getvalue</span><span class="p">(),</span> <span class="n" style="color: #333;">expected_entries</span><span class="p">)</span></span>
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977
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<pre style="margin: 0;">-<span id="LC977" class="line" lang="python"></span>
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978
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<pre style="margin: 0;">-<span id="LC978" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"fraction, met"</span><span class="p">,</span> <span class="p">[(</span><span class="mf" style="color: #099;">0.99</span><span class="p">,</span> <span class="s" style="color: #d14;">"fdp_c"</span><span class="p">)])</span></span>
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979
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<pre style="margin: 0;">-<span id="LC979" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_metabolite_summary_with_fva</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">opt_solver</span><span class="p">,</span> <span class="n" style="color: #333;">fraction</span><span class="p">,</span></span>
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980
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<pre style="margin: 0;">-<span id="LC980" class="line" lang="python"> <span class="n" style="color: #333;">met</span><span class="p">):</span></span>
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981
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<pre style="margin: 0;">-<span id="LC981" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># pytest.xfail("FVA currently buggy")</span></span>
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982
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<pre style="margin: 0;">-<span id="LC982" class="line" lang="python"></span>
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983
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<pre style="margin: 0;">-<span id="LC983" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt_solver</span></span>
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<pre style="margin: 0;">-<span id="LC984" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC985" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">captured_output</span><span class="p">()</span> <span class="k" style="font-weight: 600;">as</span> <span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">err</span><span class="p">):</span></span>
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986
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<pre style="margin: 0;">-<span id="LC986" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_by_id</span><span class="p">(</span><span class="n" style="color: #333;">met</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">summary</span><span class="p">(</span><span class="n" style="color: #333;">fva</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fraction</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC987" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC988" class="line" lang="python"> <span class="n" style="color: #333;">expected_entries</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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989
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<pre style="margin: 0;">-<span id="LC989" class="line" lang="python"> <span class="s" style="color: #d14;">'PRODUCING REACTIONS -- D-Fructose 1,6-bisphosphate (fdp_c)'</span><span class="p">,</span></span>
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990
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<pre style="margin: 0;">-<span id="LC990" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">% </span><span class="s" style="color: #d14;">FLUX RANGE RXN ID REACTION'</span><span class="p">,</span></span>
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991
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<pre style="margin: 0;">-<span id="LC991" class="line" lang="python"> <span class="s" style="color: #d14;">'100</span><span class="si" style="color: #d14;">% 7.48</span><span class="s" style="color: #d14;"> [6.17, 9.26] PFK '</span></span>
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992
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<pre style="margin: 0;">-<span id="LC992" class="line" lang="python"> <span class="s" style="color: #d14;">'atp_c + f6p_c --> adp_c + fdp_c + h_c'</span><span class="p">,</span></span>
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993
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<pre style="margin: 0;">-<span id="LC993" class="line" lang="python"> <span class="s" style="color: #d14;">'CONSUMING REACTIONS -- D-Fructose 1,6-bisphosphate (fdp_c)'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC994" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">% </span><span class="s" style="color: #d14;">FLUX RANGE RXN ID REACTION'</span><span class="p">,</span></span>
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995
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<pre style="margin: 0;">-<span id="LC995" class="line" lang="python"> <span class="s" style="color: #d14;">'100</span><span class="si" style="color: #d14;">% 7.48</span><span class="s" style="color: #d14;"> [6.17, 8.92] FBA fdp_c <=> dhap_c + g3p_c'</span><span class="p">,</span></span>
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996
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<pre style="margin: 0;">-<span id="LC996" class="line" lang="python"> <span class="s" style="color: #d14;">'0</span><span class="si" style="color: #d14;">% 0 </span><span class="s" style="color: #d14;">[0, 1.72] FBP '</span></span>
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<pre style="margin: 0;">-<span id="LC997" class="line" lang="python"> <span class="s" style="color: #d14;">'fdp_c + h2o_c --> f6p_c + pi_c'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC998" class="line" lang="python"> <span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC999" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC1000" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_line</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getvalue</span><span class="p">(),</span> <span class="n" style="color: #333;">expected_entries</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1001" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC1002" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC1003" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestCobraFluxSampling</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC1004" class="line" lang="python"> <span class="s" style="color: #d14;">"""Tests and benchmark flux sampling."""</span></span>
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<pre style="margin: 0;">-<span id="LC1005" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC1006" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_achr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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1007
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<pre style="margin: 0;">-<span id="LC1007" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"achr"</span><span class="p">)</span></span>
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1008
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<pre style="margin: 0;">-<span id="LC1008" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shape</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="p">))</span></span>
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1009
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<pre style="margin: 0;">-<span id="LC1009" class="line" lang="python"></span>
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1010
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<pre style="margin: 0;">-<span id="LC1010" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_optgp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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1011
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<pre style="margin: 0;">-<span id="LC1011" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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1012
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<pre style="margin: 0;">-<span id="LC1012" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shape</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="p">))</span></span>
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1013
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<pre style="margin: 0;">-<span id="LC1013" class="line" lang="python"></span>
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1014
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<pre style="margin: 0;">-<span id="LC1014" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_multi_optgp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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1015
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<pre style="margin: 0;">-<span id="LC1015" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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1016
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<pre style="margin: 0;">-<span id="LC1016" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shape</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="p">))</span></span>
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1017
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<pre style="margin: 0;">-<span id="LC1017" class="line" lang="python"></span>
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1018
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<pre style="margin: 0;">-<span id="LC1018" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_wrong_method</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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1019
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<pre style="margin: 0;">-<span id="LC1019" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">):</span></span>
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1020
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<pre style="margin: 0;">-<span id="LC1020" class="line" lang="python"> <span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"schwupdiwupp"</span><span class="p">)</span></span>
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1021
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<pre style="margin: 0;">-<span id="LC1021" class="line" lang="python"></span>
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1022
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<pre style="margin: 0;">-<span id="LC1022" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_validate_wrong_sample</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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1023
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<pre style="margin: 0;">-<span id="LC1023" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">achr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">)</span></span>
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1024
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<pre style="margin: 0;">-<span id="LC1024" class="line" lang="python"> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="s" style="color: #d14;">"hello"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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1025
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<pre style="margin: 0;">-<span id="LC1025" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">):</span></span>
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1026
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<pre style="margin: 0;">-<span id="LC1026" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">achr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span></span>
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1027
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<pre style="margin: 0;">-<span id="LC1027" class="line" lang="python"></span>
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1028
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<pre style="margin: 0;">-<span id="LC1028" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fixed_seed</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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1029
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<pre style="margin: 0;">-<span id="LC1029" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">seed</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">42</span><span class="p">)</span></span>
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1030
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<pre style="margin: 0;">-<span id="LC1030" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">allclose</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TPI</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="mf" style="color: #099;">9.12037487</span><span class="p">)</span></span>
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1031
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<pre style="margin: 0;">-<span id="LC1031" class="line" lang="python"></span>
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1032
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<pre style="margin: 0;">-<span id="LC1032" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_equality_constraint</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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1033
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<pre style="margin: 0;">-<span id="LC1033" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ACALD</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.5</span><span class="p">)</span></span>
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1034
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<pre style="margin: 0;">-<span id="LC1034" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">)</span></span>
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1035
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<pre style="margin: 0;">-<span id="LC1035" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">allclose</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ACALD</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.5</span><span class="p">,</span> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1e-6</span><span class="p">,</span> <span class="n" style="color: #333;">rtol</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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1036
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<pre style="margin: 0;">-<span id="LC1036" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"achr"</span><span class="p">)</span></span>
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1037
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<pre style="margin: 0;">-<span id="LC1037" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">allclose</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ACALD</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.5</span><span class="p">,</span> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1e-6</span><span class="p">,</span> <span class="n" style="color: #333;">rtol</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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1038
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<pre style="margin: 0;">-<span id="LC1038" class="line" lang="python"></span>
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1039
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<pre style="margin: 0;">-<span id="LC1039" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_inequality_constraint</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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1040
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<pre style="margin: 0;">-<span id="LC1040" class="line" lang="python"> <span class="n" style="color: #333;">co</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">problem</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Constraint</span><span class="p">(</span></span>
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1041
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<pre style="margin: 0;">-<span id="LC1041" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ACALD</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">flux_expression</span><span class="p">,</span> <span class="n" style="color: #333;">lb</span><span class="o" style="font-weight: 600;">=-</span><span class="mf" style="color: #099;">0.5</span><span class="p">)</span></span>
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1042
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<pre style="margin: 0;">-<span id="LC1042" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_cons_vars</span><span class="p">(</span><span class="n" style="color: #333;">co</span><span class="p">)</span></span>
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1043
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<pre style="margin: 0;">-<span id="LC1043" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">)</span></span>
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1044
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<pre style="margin: 0;">-<span id="LC1044" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ACALD</span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">0.5</span> <span class="o" style="font-weight: 600;">-</span> <span class="mf" style="color: #099;">1e-6</span><span class="p">)</span></span>
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1045
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<pre style="margin: 0;">-<span id="LC1045" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"achr"</span><span class="p">)</span></span>
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1046
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<pre style="margin: 0;">-<span id="LC1046" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ACALD</span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">0.5</span> <span class="o" style="font-weight: 600;">-</span> <span class="mf" style="color: #099;">1e-6</span><span class="p">)</span></span>
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1047
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<pre style="margin: 0;">-<span id="LC1047" class="line" lang="python"></span>
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<td class="diff-line-num old old_line" data-linenumber="1048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1048
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<pre style="margin: 0;">-<span id="LC1048" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setup_class</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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1049
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<pre style="margin: 0;">-<span id="LC1049" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">create_test_model</span></span>
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1050
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<pre style="margin: 0;">-<span id="LC1050" class="line" lang="python"> <span class="n" style="color: #333;">model</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">create_test_model</span><span class="p">(</span><span class="s" style="color: #d14;">"textbook"</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1051
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<pre style="margin: 0;">-<span id="LC1051" class="line" lang="python"> <span class="n" style="color: #333;">achr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ACHRSampler</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">thinning</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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1052
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<pre style="margin: 0;">-<span id="LC1052" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">((</span><span class="n" style="color: #333;">achr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">n_warmup</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span></span>
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1053
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<pre style="margin: 0;">-<span id="LC1053" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">achr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">n_warmup</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">variables</span><span class="p">)))</span></span>
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1054
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<pre style="margin: 0;">-<span id="LC1054" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">achr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">(</span><span class="n" style="color: #333;">achr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warmup</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"v"</span><span class="p">)</span></span>
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1055
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<pre style="margin: 0;">-<span id="LC1055" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">achr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">achr</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1056
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<pre style="margin: 0;">-<span id="LC1056" class="line" lang="python"></span>
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<td class="diff-line-num old old_line" data-linenumber="1057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1057
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1057" class="line" lang="python"> <span class="n" style="color: #333;">optgp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OptGPSampler</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">thinning</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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1058
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<pre style="margin: 0;">-<span id="LC1058" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">((</span><span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">n_warmup</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1059
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1059" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">n_warmup</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">variables</span><span class="p">)))</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1060
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<pre style="margin: 0;">-<span id="LC1060" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">(</span><span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warmup</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"v"</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1061
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<pre style="margin: 0;">-<span id="LC1061" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optgp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optgp</span></span>
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1062
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<pre style="margin: 0;">-<span id="LC1062" class="line" lang="python"></span>
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1063
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<pre style="margin: 0;">-<span id="LC1063" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_achr_init_benchmark</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">):</span></span>
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1064
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<pre style="margin: 0;">-<span id="LC1064" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span><span class="p">:</span> <span class="n" style="color: #333;">ACHRSampler</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">))</span></span>
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1065
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<pre style="margin: 0;">-<span id="LC1065" class="line" lang="python"></span>
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1066
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<pre style="margin: 0;">-<span id="LC1066" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_optgp_init_benchmark</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">):</span></span>
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1067
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<pre style="margin: 0;">-<span id="LC1067" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span><span class="p">:</span> <span class="n" style="color: #333;">OptGPSampler</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">))</span></span>
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1068
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<pre style="margin: 0;">-<span id="LC1068" class="line" lang="python"></span>
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<td class="diff-line-num old old_line" data-linenumber="1069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1069
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<pre style="margin: 0;">-<span id="LC1069" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_sampling</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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1070
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<pre style="margin: 0;">-<span id="LC1070" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">achr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">)</span></span>
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1071
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<pre style="margin: 0;">-<span id="LC1071" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">achr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"v"</span><span class="p">)</span></span>
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1072
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<pre style="margin: 0;">-<span id="LC1072" class="line" lang="python"></span>
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1073
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<pre style="margin: 0;">-<span id="LC1073" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">)</span></span>
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1074
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<pre style="margin: 0;">-<span id="LC1074" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"v"</span><span class="p">)</span></span>
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1075
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<pre style="margin: 0;">-<span id="LC1075" class="line" lang="python"></span>
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1076
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<pre style="margin: 0;">-<span id="LC1076" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_achr_sample_benchmark</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">):</span></span>
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1077
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<pre style="margin: 0;">-<span id="LC1077" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">achr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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1078
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<pre style="margin: 0;">-<span id="LC1078" class="line" lang="python"></span>
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1079
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<pre style="margin: 0;">-<span id="LC1079" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_optgp_sample_benchmark</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">):</span></span>
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1080
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<pre style="margin: 0;">-<span id="LC1080" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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1081
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<pre style="margin: 0;">-<span id="LC1081" class="line" lang="python"></span>
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1082
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<pre style="margin: 0;">-<span id="LC1082" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_batch_sampling</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC1083" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">b</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">achr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">batch</span><span class="p">(</span><span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">):</span></span>
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1084
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<pre style="margin: 0;">-<span id="LC1084" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">achr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"v"</span><span class="p">)</span></span>
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1085
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<pre style="margin: 0;">-<span id="LC1085" class="line" lang="python"></span>
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1086
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<pre style="margin: 0;">-<span id="LC1086" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">b</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">batch</span><span class="p">(</span><span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">):</span></span>
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1087
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<pre style="margin: 0;">-<span id="LC1087" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"v"</span><span class="p">)</span></span>
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1088
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<pre style="margin: 0;">-<span id="LC1088" class="line" lang="python"></span>
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<td class="diff-line-num old old_line" data-linenumber="1089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1089
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<pre style="margin: 0;">-<span id="LC1089" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_variables_samples</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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1090
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<pre style="margin: 0;">-<span id="LC1090" class="line" lang="python"> <span class="n" style="color: #333;">vnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">achr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">variables</span><span class="p">])</span></span>
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1091
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<pre style="margin: 0;">-<span id="LC1091" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">achr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">fluxes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1092" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shape</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">achr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warmup</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shape</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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1093
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<pre style="margin: 0;">-<span id="LC1093" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">columns</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">vnames</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">all</span><span class="p">()</span></span>
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1094
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<pre style="margin: 0;">-<span id="LC1094" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">achr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"v"</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">all</span><span class="p">()</span></span>
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1095
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<pre style="margin: 0;">-<span id="LC1095" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">fluxes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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1096
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<pre style="margin: 0;">-<span id="LC1096" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shape</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warmup</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shape</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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1097
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<pre style="margin: 0;">-<span id="LC1097" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">columns</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">vnames</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">all</span><span class="p">()</span></span>
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1098
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<pre style="margin: 0;">-<span id="LC1098" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"v"</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">all</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC1099" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC1100" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_inhomogeneous_sanity</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC1101" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test whether inhomogeneous sampling gives approximately the same</span></span>
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<pre style="margin: 0;">-<span id="LC1102" class="line" lang="python"><span class="s" style="color: #d14;"> standard deviation as a homogeneous version."""</span></span>
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<pre style="margin: 0;">-<span id="LC1103" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ACALD</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.5</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1104" class="line" lang="python"> <span class="n" style="color: #333;">s_inhom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;">64</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1105" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ACALD</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.5</span> <span class="o" style="font-weight: 600;">-</span> <span class="mf" style="color: #099;">1e-3</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.5</span> <span class="o" style="font-weight: 600;">+</span> <span class="mf" style="color: #099;">1e-3</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1106" class="line" lang="python"> <span class="n" style="color: #333;">s_hom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;">64</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1107" class="line" lang="python"> <span class="n" style="color: #333;">relative_diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">s_inhom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">std</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mf" style="color: #099;">1e-12</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">s_hom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">std</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mf" style="color: #099;">1e-12</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1108" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="mf" style="color: #099;">0.5</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">relative_diff</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mean</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span></span>
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<pre style="margin: 0;">-<span id="LC1109" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC1110" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ACALD</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.5</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1111" class="line" lang="python"> <span class="n" style="color: #333;">s_inhom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;">64</span><span class="p">,</span> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"achr"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1112" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ACALD</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.5</span> <span class="o" style="font-weight: 600;">-</span> <span class="mf" style="color: #099;">1e-3</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.5</span> <span class="o" style="font-weight: 600;">+</span> <span class="mf" style="color: #099;">1e-3</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1113" class="line" lang="python"> <span class="n" style="color: #333;">s_hom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;">64</span><span class="p">,</span> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"achr"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1114" class="line" lang="python"> <span class="n" style="color: #333;">relative_diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">s_inhom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">std</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mf" style="color: #099;">1e-12</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">s_hom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">std</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mf" style="color: #099;">1e-12</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1115" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="mf" style="color: #099;">0.5</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">relative_diff</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mean</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span></span>
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<pre style="margin: 0;">-<span id="LC1116" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC1117" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_reproject</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC1118" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">fluxes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span></span>
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<pre style="margin: 0;">-<span id="LC1119" class="line" lang="python"> <span class="n" style="color: #333;">proj</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">apply_along_axis</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_reproject</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1120" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">(</span><span class="n" style="color: #333;">proj</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"v"</span><span class="p">)</span></span>
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1121
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<pre style="margin: 0;">-<span id="LC1121" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">random</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rand</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warmup</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shape</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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1122
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<pre style="margin: 0;">-<span id="LC1122" class="line" lang="python"> <span class="n" style="color: #333;">proj</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">apply_along_axis</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_reproject</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1123" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">(</span><span class="n" style="color: #333;">proj</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"v"</span><span class="p">)</span></span>
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1124
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<pre style="margin: 0;">-<span id="LC1124" class="line" lang="python"></span>
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1125
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<pre style="margin: 0;">-<span id="LC1125" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_complicated_model</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC1126" class="line" lang="python"> <span class="s" style="color: #d14;">"""Difficult model since the online mean calculation is numerically</span></span>
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1127
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<pre style="margin: 0;">-<span id="LC1127" class="line" lang="python"><span class="s" style="color: #d14;"> unstable so many samples weakly violate the equality constraints."""</span></span>
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1128
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<pre style="margin: 0;">-<span id="LC1128" class="line" lang="python"> <span class="n" style="color: #333;">model</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Model</span><span class="p">(</span><span class="s" style="color: #d14;">'flux_split'</span><span class="p">)</span></span>
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1129
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<pre style="margin: 0;">-<span id="LC1129" class="line" lang="python"> <span class="n" style="color: #333;">reaction1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">'V1'</span><span class="p">)</span></span>
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1130
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<pre style="margin: 0;">-<span id="LC1130" class="line" lang="python"> <span class="n" style="color: #333;">reaction2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">'V2'</span><span class="p">)</span></span>
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1131
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<pre style="margin: 0;">-<span id="LC1131" class="line" lang="python"> <span class="n" style="color: #333;">reaction3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">'V3'</span><span class="p">)</span></span>
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1132
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<pre style="margin: 0;">-<span id="LC1132" class="line" lang="python"> <span class="n" style="color: #333;">reaction1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower_bound</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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1133
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<pre style="margin: 0;">-<span id="LC1133" class="line" lang="python"> <span class="n" style="color: #333;">reaction2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower_bound</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">-<span id="LC1134" class="line" lang="python"> <span class="n" style="color: #333;">reaction3</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower_bound</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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1135
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<pre style="margin: 0;">-<span id="LC1135" class="line" lang="python"> <span class="n" style="color: #333;">reaction1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">upper_bound</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">6</span></span>
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1136
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<pre style="margin: 0;">-<span id="LC1136" class="line" lang="python"> <span class="n" style="color: #333;">reaction2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">upper_bound</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">8</span></span>
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1137
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<pre style="margin: 0;">-<span id="LC1137" class="line" lang="python"> <span class="n" style="color: #333;">reaction3</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">upper_bound</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10</span></span>
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1138
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<pre style="margin: 0;">-<span id="LC1138" class="line" lang="python"> <span class="n" style="color: #333;">A</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Metabolite</span><span class="p">(</span><span class="s" style="color: #d14;">'A'</span><span class="p">)</span></span>
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1139
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<pre style="margin: 0;">-<span id="LC1139" class="line" lang="python"> <span class="n" style="color: #333;">reaction1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">A</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">})</span></span>
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1140
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<pre style="margin: 0;">-<span id="LC1140" class="line" lang="python"> <span class="n" style="color: #333;">reaction2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">A</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">})</span></span>
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1141
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<pre style="margin: 0;">-<span id="LC1141" class="line" lang="python"> <span class="n" style="color: #333;">reaction3</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">A</span><span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">})</span></span>
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1142
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<pre style="margin: 0;">-<span id="LC1142" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_reactions</span><span class="p">([</span><span class="n" style="color: #333;">reaction1</span><span class="p">])</span></span>
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1143
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<pre style="margin: 0;">-<span id="LC1143" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_reactions</span><span class="p">([</span><span class="n" style="color: #333;">reaction2</span><span class="p">])</span></span>
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1144
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<pre style="margin: 0;">-<span id="LC1144" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_reactions</span><span class="p">([</span><span class="n" style="color: #333;">reaction3</span><span class="p">])</span></span>
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1145
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<pre style="margin: 0;">-<span id="LC1145" class="line" lang="python"></span>
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1146
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<pre style="margin: 0;">-<span id="LC1146" class="line" lang="python"> <span class="n" style="color: #333;">optgp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OptGPSampler</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">seed</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">42</span><span class="p">)</span></span>
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1147
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<pre style="margin: 0;">-<span id="LC1147" class="line" lang="python"> <span class="n" style="color: #333;">achr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ACHRSampler</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">seed</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">42</span><span class="p">)</span></span>
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1148
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<pre style="margin: 0;">-<span id="LC1148" class="line" lang="python"> <span class="n" style="color: #333;">optgp_samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="mi" style="color: #099;">100</span><span class="p">)</span></span>
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1149
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<pre style="margin: 0;">-<span id="LC1149" class="line" lang="python"> <span class="n" style="color: #333;">achr_samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">achr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="mi" style="color: #099;">100</span><span class="p">)</span></span>
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1150
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<pre style="margin: 0;">-<span id="LC1150" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">(</span><span class="n" style="color: #333;">optgp_samples</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">corr</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">1.0</span><span class="p">)</span></span>
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1151
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<pre style="margin: 0;">-<span id="LC1151" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">(</span><span class="n" style="color: #333;">achr_samples</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">corr</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">1.0</span><span class="p">)</span></span>
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1152
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<pre style="margin: 0;">-<span id="LC1152" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># > 95% are valid</span></span>
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1153
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<pre style="margin: 0;">-<span id="LC1153" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">(</span><span class="n" style="color: #333;">optgp_samples</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"v"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">95</span><span class="p">)</span></span>
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1154
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<pre style="margin: 0;">-<span id="LC1154" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">achr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">(</span><span class="n" style="color: #333;">achr_samples</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"v"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">95</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1155" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC1156" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_point_space</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC1157" class="line" lang="python"> <span class="s" style="color: #d14;">"""Model where constraints reduce the sampling space to one point."""</span></span>
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1158
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<pre style="margin: 0;">-<span id="LC1158" class="line" lang="python"> <span class="n" style="color: #333;">pfba_sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pfba</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">)</span></span>
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1159
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<pre style="margin: 0;">-<span id="LC1159" class="line" lang="python"> <span class="n" style="color: #333;">pfba_const</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">problem</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Constraint</span><span class="p">(</span></span>
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1160
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<pre style="margin: 0;">-<span id="LC1160" class="line" lang="python"> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">variables</span><span class="p">),</span> <span class="n" style="color: #333;">ub</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">pfba_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective_value</span><span class="p">)</span></span>
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1161
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<pre style="margin: 0;">-<span id="LC1161" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_cons_vars</span><span class="p">(</span><span class="n" style="color: #333;">pfba_const</span><span class="p">)</span></span>
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1162
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<pre style="margin: 0;">-<span id="LC1162" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Biomass_Ecoli_core</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower_bound</span> <span class="o" style="font-weight: 600;">=</span> \</span>
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<pre style="margin: 0;">-<span id="LC1163" class="line" lang="python"> <span class="n" style="color: #333;">pfba_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Biomass_Ecoli_core</span></span>
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<pre style="margin: 0;">-<span id="LC1164" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC1165" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1166" class="line" lang="python"></span>
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1167
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<pre style="margin: 0;">-<span id="LC1167" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC1168" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestProductionEnvelope</span><span class="p">:</span></span>
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1169
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<pre style="margin: 0;">-<span id="LC1169" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test the production envelope."""</span></span>
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1170
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<pre style="margin: 0;">-<span id="LC1170" class="line" lang="python"></span>
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1171
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<pre style="margin: 0;">-<span id="LC1171" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_envelope_one</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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1172
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<pre style="margin: 0;">-<span id="LC1172" class="line" lang="python"> <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">production_envelope</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"EX_o2_e"</span><span class="p">])</span></span>
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1173
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<pre style="margin: 0;">-<span id="LC1173" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"flux_maximum"</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(),</span> <span class="mf" style="color: #099;">9.342</span><span class="p">,</span> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1e-3</span><span class="p">)</span></span>
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1174
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<pre style="margin: 0;">-<span id="LC1174" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC1175" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_envelope_multi_reaction_objective</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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1176
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<pre style="margin: 0;">-<span id="LC1176" class="line" lang="python"> <span class="n" style="color: #333;">obj</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">EX_ac_e</span><span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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1177
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<pre style="margin: 0;">-<span id="LC1177" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">EX_co2_e</span><span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">}</span></span>
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1178
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<pre style="margin: 0;">-<span id="LC1178" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">):</span></span>
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1179
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<pre style="margin: 0;">-<span id="LC1179" class="line" lang="python"> <span class="n" style="color: #333;">production_envelope</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="s" style="color: #d14;">"EX_o2_e"</span><span class="p">,</span> <span class="n" style="color: #333;">obj</span><span class="p">)</span></span>
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1180
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<pre style="margin: 0;">-<span id="LC1180" class="line" lang="python"></span>
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1181
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<pre style="margin: 0;">-<span id="LC1181" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"variables, num"</span><span class="p">,</span> <span class="p">[</span></span>
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1182
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<pre style="margin: 0;">-<span id="LC1182" class="line" lang="python"> <span class="p">([</span><span class="s" style="color: #d14;">"EX_glc__D_e"</span><span class="p">],</span> <span class="mi" style="color: #099;">30</span><span class="p">),</span></span>
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1183
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<pre style="margin: 0;">-<span id="LC1183" class="line" lang="python"> <span class="p">([</span><span class="s" style="color: #d14;">"EX_glc__D_e"</span><span class="p">,</span> <span class="s" style="color: #d14;">"EX_o2_e"</span><span class="p">],</span> <span class="mi" style="color: #099;">20</span><span class="p">),</span></span>
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1184
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<pre style="margin: 0;">-<span id="LC1184" class="line" lang="python"> <span class="p">([</span><span class="s" style="color: #d14;">"EX_glc__D_e"</span><span class="p">,</span> <span class="s" style="color: #d14;">"EX_o2_e"</span><span class="p">,</span> <span class="s" style="color: #d14;">"EX_ac_e"</span><span class="p">],</span> <span class="mi" style="color: #099;">10</span><span class="p">)</span></span>
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1185
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<pre style="margin: 0;">-<span id="LC1185" class="line" lang="python"> <span class="p">])</span></span>
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1186
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<pre style="margin: 0;">-<span id="LC1186" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_multi_variable_envelope</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">variables</span><span class="p">,</span> <span class="n" style="color: #333;">num</span><span class="p">):</span></span>
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1187
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<pre style="margin: 0;">-<span id="LC1187" class="line" lang="python"> <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">production_envelope</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">variables</span><span class="p">,</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">num</span><span class="p">)</span></span>
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1188
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<pre style="margin: 0;">-<span id="LC1188" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">num</span> <span class="o" style="font-weight: 600;">**</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">variables</span><span class="p">)</span></span>
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1189
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<pre style="margin: 0;">-<span id="LC1189" class="line" lang="python"></span>
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1190
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<pre style="margin: 0;">-<span id="LC1190" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_envelope_two</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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1191
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<pre style="margin: 0;">-<span id="LC1191" class="line" lang="python"> <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">production_envelope</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"EX_glc__D_e"</span><span class="p">,</span> <span class="s" style="color: #d14;">"EX_o2_e"</span><span class="p">],</span></span>
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1192
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<pre style="margin: 0;">-<span id="LC1192" class="line" lang="python"> <span class="n" style="color: #333;">objective</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"EX_ac_e"</span><span class="p">)</span></span>
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1193
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<pre style="margin: 0;">-<span id="LC1193" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"flux_maximum"</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(),</span> <span class="mf" style="color: #099;">1737.466</span><span class="p">,</span> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1e-3</span><span class="p">)</span></span>
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1194
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<pre style="margin: 0;">-<span id="LC1194" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"carbon_yield_maximum"</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(),</span> <span class="mf" style="color: #099;">83.579</span><span class="p">,</span></span>
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1195
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<pre style="margin: 0;">-<span id="LC1195" class="line" lang="python"> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1e-3</span><span class="p">)</span></span>
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1196
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<pre style="margin: 0;">-<span id="LC1196" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"mass_yield_maximum"</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(),</span> <span class="mf" style="color: #099;">82.176</span><span class="p">,</span></span>
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1197
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<pre style="margin: 0;">-<span id="LC1197" class="line" lang="python"> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1e-3</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1198" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC1199" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC1200" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestReactionUtils</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC1201" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test the assess_ functions in reactions.py."""</span></span>
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1202
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<pre style="margin: 0;">-<span id="LC1202" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC1203" class="line" lang="python"> <span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"solver"</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1204" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_assess</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">solver</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC1205" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC1206" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">assess</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">GLCpts</span><span class="p">,</span></span>
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1207
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<pre style="margin: 0;">-<span id="LC1207" class="line" lang="python"> <span class="n" style="color: #333;">solver</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">solver</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">True</span></span>
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1208
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<pre style="margin: 0;">-<span id="LC1208" class="line" lang="python"> <span class="n" style="color: #333;">pyr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pyr_c</span></span>
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1209
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<pre style="margin: 0;">-<span id="LC1209" class="line" lang="python"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Metabolite</span><span class="p">(</span><span class="s" style="color: #d14;">'a'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1210" class="line" lang="python"> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Metabolite</span><span class="p">(</span><span class="s" style="color: #d14;">'b'</span><span class="p">)</span></span>
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1211
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<pre style="margin: 0;">-<span id="LC1211" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">([</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">])</span></span>
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1212
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<pre style="margin: 0;">-<span id="LC1212" class="line" lang="python"> <span class="n" style="color: #333;">pyr_a2b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">'pyr_a2b'</span><span class="p">)</span></span>
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1213
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<pre style="margin: 0;">-<span id="LC1213" class="line" lang="python"> <span class="n" style="color: #333;">pyr_a2b</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">pyr</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">a</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">})</span></span>
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<pre style="margin: 0;">-<span id="LC1214" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_reactions</span><span class="p">([</span><span class="n" style="color: #333;">pyr_a2b</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC1215" class="line" lang="python"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">assess</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">pyr_a2b</span><span class="p">,</span> <span class="mf" style="color: #099;">0.01</span><span class="p">,</span> <span class="n" style="color: #333;">solver</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">solver</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1216" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1217" class="line" lang="python"> <span class="s" style="color: #d14;">'precursors'</span><span class="p">:</span> <span class="p">{</span><span class="n" style="color: #333;">a</span><span class="p">:</span> <span class="p">{</span><span class="s" style="color: #d14;">'required'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.01</span><span class="p">,</span> <span class="s" style="color: #d14;">'produced'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">}},</span></span>
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<pre style="margin: 0;">-<span id="LC1218" class="line" lang="python"> <span class="s" style="color: #d14;">'products'</span><span class="p">:</span> <span class="p">{</span><span class="n" style="color: #333;">b</span><span class="p">:</span> <span class="p">{</span><span class="s" style="color: #d14;">'required'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.01</span><span class="p">,</span> <span class="s" style="color: #d14;">'capacity'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">}}}</span></span>
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<pre style="margin: 0;">-<span id="LC1219" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected</span></span></pre>
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<li id="522c7a888526694d96d267729e9ba39e2bf6a93a">
<a href="https://salsa.debian.org/med-team/python-cobra/compare/fff89040cdb873308a398a97bc8a778b455ced12...11d80fce5d66886597adffefca19de87bde01fd2#522c7a888526694d96d267729e9ba39e2bf6a93a"><strong>cobra/test/test_flux_analysis/conftest.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># -*- coding: utf-8 -*-</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">"""Define module level fixtures."""</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">absolute_import</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pandas</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Series</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">cobra.util.solver</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">sutil</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.core</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Metabolite</span><span class="p">,</span> <span class="n" style="color: #333;">Model</span><span class="p">,</span> <span class="n" style="color: #333;">Reaction</span><span class="p">,</span> <span class="n" style="color: #333;">Solution</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># The scipy interface is currently unstable and may yield errors or infeasible</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># solutions.</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="nd">@pytest.fixture</span><span class="p">(</span><span class="n" style="color: #333;">scope</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"session"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">s</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"glpk"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cplex"</span><span class="p">,</span> <span class="s" style="color: #d14;">"gurobi"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solvers</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">all_solvers</span><span class="p">(</span><span class="n" style="color: #333;">request</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="s" style="color: #d14;">"""Return the avaialble solvers."""</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">request</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">param</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="nd">@pytest.fixture</span><span class="p">(</span><span class="n" style="color: #333;">scope</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"session"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">s</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"cplex"</span><span class="p">,</span> <span class="s" style="color: #d14;">"gurobi"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solvers</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">qp_solvers</span><span class="p">(</span><span class="n" style="color: #333;">request</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="s" style="color: #d14;">"""Return the available QP solvers."""</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">request</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">param</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"><span class="nd">@pytest.fixture</span><span class="p">(</span><span class="n" style="color: #333;">scope</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"module"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">room_model</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"><span class="s" style="color: #d14;"> Generate ROOM model as described in [1]_</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"><span class="s" style="color: #d14;"> References</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"><span class="s" style="color: #d14;"> ----------</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"><span class="s" style="color: #d14;"> .. [1] Tomer Shlomi, Omer Berkman and Eytan Ruppin, "Regulatory on/off</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"><span class="s" style="color: #d14;"> minimization of metabolic flux changes after genetic perturbations",</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"><span class="s" style="color: #d14;"> PNAS 2005 102 (21) 7695-7700; doi:10.1073/pnas.0406346102</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Model</span><span class="p">(</span><span class="s" style="color: #d14;">"papin_2003"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">v_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"v1"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">v_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"v2"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">v_3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"v3"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">v_4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"v4"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">v_5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"v5"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">v_6</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"v6"</span><span class="p">,</span> <span class="n" style="color: #333;">upper_bound</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">b_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"b1"</span><span class="p">,</span> <span class="n" style="color: #333;">upper_bound</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">10.0</span><span class="p">,</span> <span class="n" style="color: #333;">lower_bound</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">b_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"b2"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">b_3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"b3"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_reactions</span><span class="p">([</span><span class="n" style="color: #333;">v_1</span><span class="p">,</span> <span class="n" style="color: #333;">v_2</span><span class="p">,</span> <span class="n" style="color: #333;">v_3</span><span class="p">,</span> <span class="n" style="color: #333;">v_4</span><span class="p">,</span> <span class="n" style="color: #333;">v_5</span><span class="p">,</span> <span class="n" style="color: #333;">v_6</span><span class="p">,</span> <span class="n" style="color: #333;">b_1</span><span class="p">,</span> <span class="n" style="color: #333;">b_2</span><span class="p">,</span> <span class="n" style="color: #333;">b_3</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">v_1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reaction</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"A -> B"</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">v_2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reaction</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2 B -> C + byp"</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">v_3</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reaction</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2 B + cof -> D"</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">v_4</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reaction</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"D -> E + cof"</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">v_5</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reaction</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"C + cof -> D"</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">v_6</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reaction</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"C -> E"</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">b_1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reaction</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-> A"</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">b_2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reaction</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"E ->"</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">b_3</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reaction</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"byp ->"</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'b2'</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">test_model</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"><span class="nd">@pytest.fixture</span><span class="p">(</span><span class="n" style="color: #333;">scope</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"module"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">room_solution</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"><span class="s" style="color: #d14;"> Generate ROOM solution as described in [1]_</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"><span class="s" style="color: #d14;"> References</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"><span class="s" style="color: #d14;"> ----------</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"><span class="s" style="color: #d14;"> .. [1] Tomer Shlomi, Omer Berkman and Eytan Ruppin, "Regulatory on/off</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"><span class="s" style="color: #d14;"> minimization of metabolic flux changes after genetic perturbations",</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"><span class="s" style="color: #d14;"> PNAS 2005 102 (21) 7695-7700; doi:10.1073/pnas.0406346102</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">fluxes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Series</span><span class="p">({</span><span class="s" style="color: #d14;">'b1'</span><span class="p">:</span> <span class="mf" style="color: #099;">10.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'b2'</span><span class="p">:</span> <span class="mf" style="color: #099;">5.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'b3'</span><span class="p">:</span> <span class="mf" style="color: #099;">5.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v1'</span><span class="p">:</span> <span class="mf" style="color: #099;">10.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v2'</span><span class="p">:</span> <span class="mf" style="color: #099;">5.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="s" style="color: #d14;">'v3'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v4'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v5'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v6'</span><span class="p">:</span> <span class="mf" style="color: #099;">5.0</span><span class="p">})</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">reduced_costs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Series</span><span class="p">({</span><span class="s" style="color: #d14;">'b1'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'b2'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'b3'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v1'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="s" style="color: #d14;">'v2'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v3'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v4'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v5'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="s" style="color: #d14;">'v6'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">})</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">shadow_prices</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Series</span><span class="p">({</span><span class="s" style="color: #d14;">'b1'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'b2'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'b3'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v1'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="s" style="color: #d14;">'v2'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v3'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v4'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v5'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="s" style="color: #d14;">'v6'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">})</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Solution</span><span class="p">(</span><span class="n" style="color: #333;">objective_value</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">5.000</span><span class="p">,</span> <span class="n" style="color: #333;">status</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'optimal'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">fluxes</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fluxes</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">reduced_costs</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reduced_costs</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">shadow_prices</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shadow_prices</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sol</span></span></pre>
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<li id="121889f974f95fa5481a2f1e6357be8434245e1e">
<a href="https://salsa.debian.org/med-team/python-cobra/compare/fff89040cdb873308a398a97bc8a778b455ced12...11d80fce5d66886597adffefca19de87bde01fd2#121889f974f95fa5481a2f1e6357be8434245e1e"><strong>cobra/test/test_flux_analysis/test_deletion.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># -*- coding: utf-8 -*-</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">"""Test functionalities of reaction and gene deletions."""</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">absolute_import</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">math</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pandas</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Series</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">six</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">iteritems</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.flux_analysis.deletion</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">double_gene_deletion</span><span class="p">,</span> <span class="n" style="color: #333;">double_reaction_deletion</span><span class="p">,</span> <span class="n" style="color: #333;">single_gene_deletion</span><span class="p">,</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">single_reaction_deletion</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.flux_analysis.room</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">add_room</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Single gene deletion FBA</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_gene_deletion_fba_benchmark</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">all_solvers</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="s" style="color: #d14;">"""Benchmark single gene deletion using FBA."""</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_solvers</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="n" style="color: #333;">single_gene_deletion</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_gene_deletion_fba</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test single gene deletion using FBA."""</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># expected knockouts for textbook model</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_solvers</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">growth_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"b0008"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.87</span><span class="p">,</span> <span class="s" style="color: #d14;">"b0114"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.80</span><span class="p">,</span> <span class="s" style="color: #d14;">"b0116"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.78</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="s" style="color: #d14;">"b2276"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.21</span><span class="p">,</span> <span class="s" style="color: #d14;">"b1779"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.00</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">single_gene_deletion</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">model</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">gene_list</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">growth_dict</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"fba"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="p">)[</span><span class="s" style="color: #d14;">"growth"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">gene</span><span class="p">,</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iteritems</span><span class="p">(</span><span class="n" style="color: #333;">growth_dict</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">[</span><span class="nb" style="color: #0086b3;">frozenset</span><span class="p">([</span><span class="n" style="color: #333;">gene</span><span class="p">])],</span> <span class="n" style="color: #333;">value</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1E-02</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Singe gene deletion MOMA</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_gene_deletion_moma_benchmark</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">qp_solvers</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="s" style="color: #d14;">"""Benchmark single gene deletion using MOMA."""</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qp_solvers</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'b0008'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b0114'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b2276'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b1779'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="n" style="color: #333;">single_gene_deletion</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">gene_list</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">genes</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"moma"</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_gene_deletion_moma</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">qp_solvers</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test single gene deletion using MOMA."""</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qp_solvers</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># expected knockouts for textbook model</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">growth_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"b0008"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.87</span><span class="p">,</span> <span class="s" style="color: #d14;">"b0114"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.71</span><span class="p">,</span> <span class="s" style="color: #d14;">"b0116"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.56</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="s" style="color: #d14;">"b2276"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.11</span><span class="p">,</span> <span class="s" style="color: #d14;">"b1779"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.00</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">single_gene_deletion</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">model</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">gene_list</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">growth_dict</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"moma"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="p">)[</span><span class="s" style="color: #d14;">"growth"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">gene</span><span class="p">,</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iteritems</span><span class="p">(</span><span class="n" style="color: #333;">growth_dict</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">[</span><span class="nb" style="color: #0086b3;">frozenset</span><span class="p">([</span><span class="n" style="color: #333;">gene</span><span class="p">])],</span> <span class="n" style="color: #333;">value</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1E-02</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_gene_deletion_moma_reference</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">qp_solvers</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test single gene deletion using MOMA (reference solution)."""</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qp_solvers</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># expected knockouts for textbook model</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">growth_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"b0008"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.87</span><span class="p">,</span> <span class="s" style="color: #d14;">"b0114"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.71</span><span class="p">,</span> <span class="s" style="color: #d14;">"b0116"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.56</span><span class="p">,</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="s" style="color: #d14;">"b2276"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.11</span><span class="p">,</span> <span class="s" style="color: #d14;">"b1779"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.00</span><span class="p">}</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">single_gene_deletion</span><span class="p">(</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">model</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">gene_list</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">growth_dict</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"moma"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sol</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="p">)[</span><span class="s" style="color: #d14;">"growth"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">gene</span><span class="p">,</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iteritems</span><span class="p">(</span><span class="n" style="color: #333;">growth_dict</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">[</span><span class="nb" style="color: #0086b3;">frozenset</span><span class="p">([</span><span class="n" style="color: #333;">gene</span><span class="p">])],</span> <span class="n" style="color: #333;">value</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1E-02</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Single gene deletion linear MOMA</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_gene_deletion_linear_moma_benchmark</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="s" style="color: #d14;">"""Benchmark single gene deletion using linear MOMA."""</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_solvers</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'b0008'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b0114'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b2276'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b1779'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="n" style="color: #333;">single_gene_deletion</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">gene_list</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">genes</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"linear moma"</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_gene_deletion_linear_moma</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test single gene deletion using linear MOMA (reference solution)."""</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_solvers</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># expected knockouts for textbook model</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">growth_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"b0008"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.87</span><span class="p">,</span> <span class="s" style="color: #d14;">"b0114"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.76</span><span class="p">,</span> <span class="s" style="color: #d14;">"b0116"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.65</span><span class="p">,</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="s" style="color: #d14;">"b2276"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.08</span><span class="p">,</span> <span class="s" style="color: #d14;">"b1779"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.00</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">single_gene_deletion</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">model</span><span class="p">,</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">gene_list</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">growth_dict</span><span class="p">),</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"linear moma"</span><span class="p">,</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sol</span><span class="p">,</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="p">)[</span><span class="s" style="color: #d14;">"growth"</span><span class="p">]</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">gene</span><span class="p">,</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iteritems</span><span class="p">(</span><span class="n" style="color: #333;">growth_dict</span><span class="p">):</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">[</span><span class="nb" style="color: #0086b3;">frozenset</span><span class="p">([</span><span class="n" style="color: #333;">gene</span><span class="p">])],</span> <span class="n" style="color: #333;">value</span><span class="p">,</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1E-02</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Single gene deletion ROOM</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_gene_deletion_room_benchmark</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">,</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="n" style="color: #333;">all_solvers</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="s" style="color: #d14;">"""Benchmark single gene deletion using ROOM."""</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">all_solvers</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"glpk"</span><span class="p">:</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">skip</span><span class="p">(</span><span class="s" style="color: #d14;">"GLPK is too slow to run ROOM."</span><span class="p">)</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_solvers</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'b0008'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b0114'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b2276'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b1779'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="n" style="color: #333;">single_gene_deletion</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">gene_list</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">genes</span><span class="p">,</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"room"</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Single gene deletion linear ROOM</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_gene_deletion_linear_room_benchmark</span><span class="p">(</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">):</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="s" style="color: #d14;">"""Benchmark single gene deletion using linear ROOM."""</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_solvers</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'b0008'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b0114'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b2276'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b1779'</span><span class="p">]</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="n" style="color: #333;">single_gene_deletion</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">gene_list</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">genes</span><span class="p">,</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"linear room"</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Single reaction deletion</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_reaction_deletion_benchmark</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">all_solvers</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="s" style="color: #d14;">"""Benchmark single reaction deletion."""</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_solvers</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="n" style="color: #333;">single_reaction_deletion</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_reaction_deletion</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test single reaction deletion."""</span></span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_solvers</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">expected_results</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'FBA'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.70404</span><span class="p">,</span> <span class="s" style="color: #d14;">'FBP'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.87392</span><span class="p">,</span> <span class="s" style="color: #d14;">'CS'</span><span class="p">:</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="s" style="color: #d14;">'FUM'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.81430</span><span class="p">,</span> <span class="s" style="color: #d14;">'GAPD'</span><span class="p">:</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">'GLUDy'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.85139</span><span class="p">}</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">single_reaction_deletion</span><span class="p">(</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">model</span><span class="p">,</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"> <span class="n" style="color: #333;">reaction_list</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">expected_results</span><span class="p">),</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="p">)[</span><span class="s" style="color: #d14;">'growth'</span><span class="p">]</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">reaction</span><span class="p">,</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iteritems</span><span class="p">(</span><span class="n" style="color: #333;">expected_results</span><span class="p">):</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">[</span><span class="nb" style="color: #0086b3;">frozenset</span><span class="p">([</span><span class="n" style="color: #333;">reaction</span><span class="p">])],</span> <span class="n" style="color: #333;">value</span><span class="p">,</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1E-05</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Single reaction deletion ROOM</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_reaction_deletion_room</span><span class="p">(</span><span class="n" style="color: #333;">room_model</span><span class="p">,</span> <span class="n" style="color: #333;">room_solution</span><span class="p">,</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="n" style="color: #333;">all_solvers</span><span class="p">):</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test single reaction deletion using ROOM."""</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="n" style="color: #333;">room_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_solvers</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Series</span><span class="p">({</span><span class="s" style="color: #d14;">'v1'</span><span class="p">:</span> <span class="mf" style="color: #099;">10.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v2'</span><span class="p">:</span> <span class="mf" style="color: #099;">5.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v3'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v4'</span><span class="p">:</span> <span class="mf" style="color: #099;">5.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="s" style="color: #d14;">'v5'</span><span class="p">:</span> <span class="mf" style="color: #099;">5.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v6'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'b1'</span><span class="p">:</span> <span class="mf" style="color: #099;">10.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'b2'</span><span class="p">:</span> <span class="mf" style="color: #099;">5.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="s" style="color: #d14;">'b3'</span><span class="p">:</span> <span class="mf" style="color: #099;">5.0</span><span class="p">},</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'v1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'v2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'v3'</span><span class="p">,</span> <span class="s" style="color: #d14;">'v4'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="s" style="color: #d14;">'v5'</span><span class="p">,</span> <span class="s" style="color: #d14;">'v6'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b2'</span><span class="p">,</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="s" style="color: #d14;">'b3'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">room_model</span><span class="p">:</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="n" style="color: #333;">room_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">v6</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">knock_out</span><span class="p">()</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="n" style="color: #333;">add_room</span><span class="p">(</span><span class="n" style="color: #333;">room_model</span><span class="p">,</span> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">room_solution</span><span class="p">,</span> <span class="n" style="color: #333;">delta</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="n" style="color: #333;">epsilon</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">)</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">room_sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">room_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">allclose</span><span class="p">(</span><span class="n" style="color: #333;">room_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">)</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Single reaction deletion linear ROOM</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_reaction_deletion_linear_room</span><span class="p">(</span><span class="n" style="color: #333;">room_model</span><span class="p">,</span> <span class="n" style="color: #333;">room_solution</span><span class="p">,</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">all_solvers</span><span class="p">):</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test single reaction deletion using linear ROOM."""</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">room_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_solvers</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Series</span><span class="p">({</span><span class="s" style="color: #d14;">'v1'</span><span class="p">:</span> <span class="mf" style="color: #099;">10.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v2'</span><span class="p">:</span> <span class="mf" style="color: #099;">5.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v3'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v4'</span><span class="p">:</span> <span class="mf" style="color: #099;">5.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <span class="s" style="color: #d14;">'v5'</span><span class="p">:</span> <span class="mf" style="color: #099;">5.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v6'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'b1'</span><span class="p">:</span> <span class="mf" style="color: #099;">10.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'b2'</span><span class="p">:</span> <span class="mf" style="color: #099;">5.0</span><span class="p">,</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="s" style="color: #d14;">'b3'</span><span class="p">:</span> <span class="mf" style="color: #099;">5.0</span><span class="p">},</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'v1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'v2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'v3'</span><span class="p">,</span> <span class="s" style="color: #d14;">'v4'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="s" style="color: #d14;">'v5'</span><span class="p">,</span> <span class="s" style="color: #d14;">'v6'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b2'</span><span class="p">,</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"> <span class="s" style="color: #d14;">'b3'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">room_model</span><span class="p">:</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"> <span class="n" style="color: #333;">room_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">v6</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">knock_out</span><span class="p">()</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">add_room</span><span class="p">(</span><span class="n" style="color: #333;">room_model</span><span class="p">,</span> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">room_solution</span><span class="p">,</span> <span class="n" style="color: #333;">delta</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="n" style="color: #333;">epsilon</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">linear</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">linear_room_sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">room_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">allclose</span><span class="p">(</span><span class="n" style="color: #333;">linear_room_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Double gene deletion</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_double_gene_deletion_benchmark</span><span class="p">(</span><span class="n" style="color: #333;">large_model</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="s" style="color: #d14;">"""Benchmark double gene deletion."""</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"b0726"</span><span class="p">,</span> <span class="s" style="color: #d14;">"b4025"</span><span class="p">,</span> <span class="s" style="color: #d14;">"b0724"</span><span class="p">,</span> <span class="s" style="color: #d14;">"b0720"</span><span class="p">,</span> <span class="s" style="color: #d14;">"b2935"</span><span class="p">,</span> <span class="s" style="color: #d14;">"b2935"</span><span class="p">,</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="s" style="color: #d14;">"b1276"</span><span class="p">,</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="s" style="color: #d14;">"b1241"</span><span class="p">]</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="n" style="color: #333;">double_gene_deletion</span><span class="p">,</span> <span class="n" style="color: #333;">large_model</span><span class="p">,</span> <span class="n" style="color: #333;">gene_list1</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">genes</span><span class="p">,</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_double_gene_deletion</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test double gene deletion."""</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"> <span class="n" style="color: #333;">genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"b0726"</span><span class="p">,</span> <span class="s" style="color: #d14;">"b4025"</span><span class="p">,</span> <span class="s" style="color: #d14;">"b0724"</span><span class="p">,</span> <span class="s" style="color: #d14;">"b0720"</span><span class="p">,</span> <span class="s" style="color: #d14;">"b2935"</span><span class="p">,</span> <span class="s" style="color: #d14;">"b2935"</span><span class="p">,</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="s" style="color: #d14;">"b1276"</span><span class="p">,</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"> <span class="s" style="color: #d14;">"b1241"</span><span class="p">]</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="n" style="color: #333;">growth_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'b0720'</span><span class="p">:</span> <span class="p">{</span><span class="s" style="color: #d14;">'b0720'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"> <span class="s" style="color: #d14;">'b0724'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="s" style="color: #d14;">'b0726'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"> <span class="s" style="color: #d14;">'b1241'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"> <span class="s" style="color: #d14;">'b1276'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"> <span class="s" style="color: #d14;">'b2935'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"> <span class="s" style="color: #d14;">'b4025'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"> <span class="s" style="color: #d14;">'b0724'</span><span class="p">:</span> <span class="p">{</span><span class="s" style="color: #d14;">'b0720'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="s" style="color: #d14;">'b0724'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.814</span><span class="p">,</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python"> <span class="s" style="color: #d14;">'b0726'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.814</span><span class="p">,</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"> <span class="s" style="color: #d14;">'b1241'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.814</span><span class="p">,</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"> <span class="s" style="color: #d14;">'b1276'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.814</span><span class="p">,</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="python"> <span class="s" style="color: #d14;">'b2935'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.814</span><span class="p">,</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"> <span class="s" style="color: #d14;">'b4025'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.739</span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"> <span class="s" style="color: #d14;">'b0726'</span><span class="p">:</span> <span class="p">{</span><span class="s" style="color: #d14;">'b0720'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"> <span class="s" style="color: #d14;">'b0724'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.814</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"> <span class="s" style="color: #d14;">'b0726'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.858</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <span class="s" style="color: #d14;">'b1241'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.858</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"> <span class="s" style="color: #d14;">'b1276'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.858</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"> <span class="s" style="color: #d14;">'b2935'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.858</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"> <span class="s" style="color: #d14;">'b4025'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.857</span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"> <span class="s" style="color: #d14;">'b1241'</span><span class="p">:</span> <span class="p">{</span><span class="s" style="color: #d14;">'b0720'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"> <span class="s" style="color: #d14;">'b0724'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.814</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"> <span class="s" style="color: #d14;">'b0726'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.858</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python"> <span class="s" style="color: #d14;">'b1241'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.874</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"> <span class="s" style="color: #d14;">'b1276'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.874</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"> <span class="s" style="color: #d14;">'b2935'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.874</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="s" style="color: #d14;">'b4025'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.863</span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"> <span class="s" style="color: #d14;">'b1276'</span><span class="p">:</span> <span class="p">{</span><span class="s" style="color: #d14;">'b0720'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"> <span class="s" style="color: #d14;">'b0724'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.814</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"> <span class="s" style="color: #d14;">'b0726'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.858</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"> <span class="s" style="color: #d14;">'b1241'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.874</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"> <span class="s" style="color: #d14;">'b1276'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.874</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="s" style="color: #d14;">'b2935'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.874</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="s" style="color: #d14;">'b4025'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.863</span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"> <span class="s" style="color: #d14;">'b2935'</span><span class="p">:</span> <span class="p">{</span><span class="s" style="color: #d14;">'b0720'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="python"> <span class="s" style="color: #d14;">'b0724'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.814</span><span class="p">,</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="python"> <span class="s" style="color: #d14;">'b0726'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.858</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="python"> <span class="s" style="color: #d14;">'b1241'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.874</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="python"> <span class="s" style="color: #d14;">'b1276'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.874</span><span class="p">,</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python"> <span class="s" style="color: #d14;">'b2935'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.874</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="python"> <span class="s" style="color: #d14;">'b4025'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.863</span><span class="p">},</span></span>
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<td class="diff-line-num new new_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="python"> <span class="s" style="color: #d14;">'b4025'</span><span class="p">:</span> <span class="p">{</span><span class="s" style="color: #d14;">'b0720'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="python"> <span class="s" style="color: #d14;">'b0724'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.739</span><span class="p">,</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="python"> <span class="s" style="color: #d14;">'b0726'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.857</span><span class="p">,</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="python"> <span class="s" style="color: #d14;">'b1241'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.863</span><span class="p">,</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"> <span class="s" style="color: #d14;">'b1276'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.863</span><span class="p">,</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="python"> <span class="s" style="color: #d14;">'b2935'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.863</span><span class="p">,</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="python"> <span class="s" style="color: #d14;">'b4025'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.863</span><span class="p">}}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python"> <span class="n" style="color: #333;">solution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">double_gene_deletion</span><span class="p">(</span></span>
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<td class="diff-line-num new new_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">gene_list1</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">genes</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)[</span><span class="s" style="color: #d14;">'growth'</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="python"> <span class="n" style="color: #333;">solution_one_process</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">double_gene_deletion</span><span class="p">(</span></span>
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<td class="diff-line-num new new_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">gene_list1</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">genes</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)[</span><span class="s" style="color: #d14;">'growth'</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">rxn_a</span><span class="p">,</span> <span class="n" style="color: #333;">sub</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iteritems</span><span class="p">(</span><span class="n" style="color: #333;">growth_dict</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">rxn_b</span><span class="p">,</span> <span class="n" style="color: #333;">growth</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iteritems</span><span class="p">(</span><span class="n" style="color: #333;">sub</span><span class="p">):</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python"> <span class="n" style="color: #333;">sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solution</span><span class="p">[</span><span class="nb" style="color: #0086b3;">frozenset</span><span class="p">([</span><span class="n" style="color: #333;">rxn_a</span><span class="p">,</span> <span class="n" style="color: #333;">rxn_b</span><span class="p">])]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="python"> <span class="n" style="color: #333;">sol_one</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solution_one_process</span><span class="p">[</span><span class="nb" style="color: #0086b3;">frozenset</span><span class="p">([</span><span class="n" style="color: #333;">rxn_a</span><span class="p">,</span> <span class="n" style="color: #333;">rxn_b</span><span class="p">])]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">sol</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">growth</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">sol_one</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">growth</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Double reaction deletion</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_double_reaction_deletion_benchmark</span><span class="p">(</span><span class="n" style="color: #333;">large_model</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">):</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="python"> <span class="s" style="color: #d14;">"""Benchmark double reaction deletion."""</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="python"> <span class="n" style="color: #333;">reactions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">large_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">::</span><span class="mi" style="color: #099;">100</span><span class="p">]</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="n" style="color: #333;">double_reaction_deletion</span><span class="p">,</span> <span class="n" style="color: #333;">large_model</span><span class="p">,</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python"> <span class="n" style="color: #333;">reaction_list1</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reactions</span><span class="p">)</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="python"></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_double_reaction_deletion</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test double reaction deletion."""</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="python"> <span class="n" style="color: #333;">reactions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'FBA'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ATPS4r'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ENO'</span><span class="p">,</span> <span class="s" style="color: #d14;">'FRUpts2'</span><span class="p">]</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="python"> <span class="n" style="color: #333;">growth_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="python"> <span class="s" style="color: #d14;">"FBA"</span><span class="p">:</span> <span class="p">{</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="python"> <span class="s" style="color: #d14;">"ATPS4r"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.135</span><span class="p">,</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="python"> <span class="s" style="color: #d14;">"ENO"</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="s" style="color: #d14;">'nan'</span><span class="p">),</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="python"> <span class="s" style="color: #d14;">"FRUpts2"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.704</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="python"> <span class="p">},</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="python"> <span class="s" style="color: #d14;">"ATPS4r"</span><span class="p">:</span> <span class="p">{</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="python"> <span class="s" style="color: #d14;">"ENO"</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="s" style="color: #d14;">'nan'</span><span class="p">),</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python"> <span class="s" style="color: #d14;">"FRUpts2"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.374</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python"> <span class="p">},</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="python"> <span class="s" style="color: #d14;">"ENO"</span><span class="p">:</span> <span class="p">{</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="python"> <span class="s" style="color: #d14;">"FRUpts2"</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="python"> <span class="p">},</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="python"> <span class="p">}</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="python"></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="python"> <span class="n" style="color: #333;">solution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">double_reaction_deletion</span><span class="p">(</span></span>
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<td class="diff-line-num new new_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">reaction_list1</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reactions</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)[</span><span class="s" style="color: #d14;">'growth'</span><span class="p">]</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="python"> <span class="n" style="color: #333;">solution_one_process</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">double_reaction_deletion</span><span class="p">(</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">reaction_list1</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reactions</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)[</span><span class="s" style="color: #d14;">'growth'</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">rxn_a</span><span class="p">,</span> <span class="n" style="color: #333;">sub</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iteritems</span><span class="p">(</span><span class="n" style="color: #333;">growth_dict</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">rxn_b</span><span class="p">,</span> <span class="n" style="color: #333;">growth</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iteritems</span><span class="p">(</span><span class="n" style="color: #333;">sub</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="python"> <span class="n" style="color: #333;">sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solution</span><span class="p">[</span><span class="nb" style="color: #0086b3;">frozenset</span><span class="p">([</span><span class="n" style="color: #333;">rxn_a</span><span class="p">,</span> <span class="n" style="color: #333;">rxn_b</span><span class="p">])]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="python"> <span class="n" style="color: #333;">sol_one</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solution_one_process</span><span class="p">[</span><span class="nb" style="color: #0086b3;">frozenset</span><span class="p">([</span><span class="n" style="color: #333;">rxn_a</span><span class="p">,</span> <span class="n" style="color: #333;">rxn_b</span><span class="p">])]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">math</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isnan</span><span class="p">(</span><span class="n" style="color: #333;">growth</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">math</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isnan</span><span class="p">(</span><span class="n" style="color: #333;">sol</span><span class="p">)</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">math</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isnan</span><span class="p">(</span><span class="n" style="color: #333;">sol_one</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">sol</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">growth</span></span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">sol_one</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">growth</span></span></pre>
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<li id="f2400d8661a976763e581e66d5c0245618c4618d">
<a href="https://salsa.debian.org/med-team/python-cobra/compare/fff89040cdb873308a398a97bc8a778b455ced12...11d80fce5d66886597adffefca19de87bde01fd2#f2400d8661a976763e581e66d5c0245618c4618d"><strong>cobra/test/test_flux_analysis/test_gapfilling.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># -*- coding: utf-8 -*-</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">"""Test functionalities of gapfilling."""</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">absolute_import</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.core</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Metabolite</span><span class="p">,</span> <span class="n" style="color: #333;">Model</span><span class="p">,</span> <span class="n" style="color: #333;">Reaction</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.flux_analysis.gapfilling</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">GapFiller</span><span class="p">,</span> <span class="n" style="color: #333;">gapfill</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_gapfilling</span><span class="p">(</span><span class="n" style="color: #333;">salmonella</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test Gapfilling."""</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Model</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">([</span><span class="n" style="color: #333;">Metabolite</span><span class="p">(</span><span class="n" style="color: #333;">m_id</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">m_id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"b"</span><span class="p">,</span> <span class="s" style="color: #d14;">"c"</span><span class="p">]])</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">exa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"EX_a"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">exa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">})</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">b2c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"b2c"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">b2c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">b</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">c</span><span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">})</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">dmc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"DM_c"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">dmc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">c</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">})</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_reactions</span><span class="p">([</span><span class="n" style="color: #333;">exa</span><span class="p">,</span> <span class="n" style="color: #333;">b2c</span><span class="p">,</span> <span class="n" style="color: #333;">dmc</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'DM_c'</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">universal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Model</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">a2b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"a2b"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">a2d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"a2d"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">universal</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_reactions</span><span class="p">([</span><span class="n" style="color: #333;">a2b</span><span class="p">,</span> <span class="n" style="color: #333;">a2d</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">a2b</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">build_reaction_from_string</span><span class="p">(</span><span class="s" style="color: #d14;">"a --> b"</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">a2d</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">build_reaction_from_string</span><span class="p">(</span><span class="s" style="color: #d14;">"a --> d"</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># # GrowMatch</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># result = gapfilling.growMatch(m, universal)[0]</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapfill</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">universal</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"a2b"</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># # SMILEY</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># result = gapfilling.SMILEY(m, "b", universal)[0]</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">m</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_boundary</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'demand'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapfill</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">universal</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"a2b"</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># # 2 rounds of GrowMatch with exchange reactions</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># result = gapfilling.growMatch(m, None, ex_rxns=True, iterations=2)</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapfill</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">exchange_reactions</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">iterations</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">{</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">result</span><span class="p">}</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span><span class="s" style="color: #d14;">"EX_b"</span><span class="p">,</span> <span class="s" style="color: #d14;">"EX_c"</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># somewhat bigger model</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">universal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Model</span><span class="p">(</span><span class="s" style="color: #d14;">"universal_reactions"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">salmonella</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">f6p_c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="p">]:</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">reaction</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_by_id</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">universal</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_reactions</span><span class="p">([</span><span class="n" style="color: #333;">reaction</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">()])</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove_reactions</span><span class="p">([</span><span class="n" style="color: #333;">reaction</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">gf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GapFiller</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">universal</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">penalties</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'TKT2'</span><span class="p">:</span> <span class="mf" style="color: #099;">1e3</span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">demand_reactions</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">solution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fill</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">'TKT2'</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">{</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">solution</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]}</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">gf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">(</span><span class="n" style="color: #333;">solution</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span></pre>
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<li id="2b7222305e740818e905d4627ce0736497cfe1d9">
<a href="https://salsa.debian.org/med-team/python-cobra/compare/fff89040cdb873308a398a97bc8a778b455ced12...11d80fce5d66886597adffefca19de87bde01fd2#2b7222305e740818e905d4627ce0736497cfe1d9"><strong>cobra/test/test_flux_analysis/test_geometric.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># -*- coding: utf-8 -*-</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">"""Test functionalities of Geometric FBA."""</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">absolute_import</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pandas</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Series</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.core</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Metabolite</span><span class="p">,</span> <span class="n" style="color: #333;">Model</span><span class="p">,</span> <span class="n" style="color: #333;">Reaction</span><span class="p">,</span> <span class="n" style="color: #333;">Solution</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.flux_analysis</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">geometric_fba</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="nd">@pytest.fixture</span><span class="p">(</span><span class="n" style="color: #333;">scope</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"module"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">geometric_fba_model</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="s" style="color: #d14;"> Generate geometric FBA model as described in [1]_</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="s" style="color: #d14;"> References</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="s" style="color: #d14;"> ----------</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="s" style="color: #d14;"> .. [1] Smallbone, Kieran & Simeonidis, Vangelis. (2009).</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="s" style="color: #d14;"> Flux balance analysis: A geometric perspective.</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="s" style="color: #d14;"> Journal of theoretical biology.258. 311-5.</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"><span class="s" style="color: #d14;"> 10.1016/j.jtbi.2009.01.027.</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Model</span><span class="p">(</span><span class="s" style="color: #d14;">'geometric_fba_paper_model'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">(</span><span class="n" style="color: #333;">Metabolite</span><span class="p">(</span><span class="s" style="color: #d14;">'A'</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">(</span><span class="n" style="color: #333;">Metabolite</span><span class="p">(</span><span class="s" style="color: #d14;">'B'</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">v_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">'v1'</span><span class="p">,</span> <span class="n" style="color: #333;">upper_bound</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1.0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">v_1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">A</span><span class="p">:</span> <span class="mf" style="color: #099;">1.0</span><span class="p">})</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">v_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">'v2'</span><span class="p">,</span> <span class="n" style="color: #333;">lower_bound</span><span class="o" style="font-weight: 600;">=-</span><span class="mf" style="color: #099;">1000.0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">v_2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">A</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">B</span><span class="p">:</span> <span class="mf" style="color: #099;">1.0</span><span class="p">})</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">v_3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">'v3'</span><span class="p">,</span> <span class="n" style="color: #333;">lower_bound</span><span class="o" style="font-weight: 600;">=-</span><span class="mf" style="color: #099;">1000.0</span><span class="p">)</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">v_3</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">A</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">B</span><span class="p">:</span> <span class="mf" style="color: #099;">1.0</span><span class="p">})</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">v_4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">'v4'</span><span class="p">,</span> <span class="n" style="color: #333;">lower_bound</span><span class="o" style="font-weight: 600;">=-</span><span class="mf" style="color: #099;">1000.0</span><span class="p">)</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">v_4</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">A</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">B</span><span class="p">:</span> <span class="mf" style="color: #099;">1.0</span><span class="p">})</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">v_5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">'v5'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">v_5</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">A</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">B</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span><span class="p">})</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_reactions</span><span class="p">([</span><span class="n" style="color: #333;">v_1</span><span class="p">,</span> <span class="n" style="color: #333;">v_2</span><span class="p">,</span> <span class="n" style="color: #333;">v_3</span><span class="p">,</span> <span class="n" style="color: #333;">v_4</span><span class="p">,</span> <span class="n" style="color: #333;">v_5</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'v5'</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">test_model</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_geometric_fba_benchmark</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="s" style="color: #d14;">"""Benchmark geometric_fba."""</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_solvers</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="n" style="color: #333;">geometric_fba</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_geometric_fba</span><span class="p">(</span><span class="n" style="color: #333;">geometric_fba_model</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test geometric_fba."""</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">geometric_fba_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_solvers</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">geometric_fba_sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">geometric_fba</span><span class="p">(</span><span class="n" style="color: #333;">geometric_fba_model</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Series</span><span class="p">({</span><span class="s" style="color: #d14;">'v1'</span><span class="p">:</span> <span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="s" style="color: #d14;">'v2'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.33</span><span class="p">,</span> <span class="s" style="color: #d14;">'v3'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.33</span><span class="p">,</span> <span class="s" style="color: #d14;">'v4'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.33</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="s" style="color: #d14;">'v5'</span><span class="p">:</span> <span class="mf" style="color: #099;">1.0</span><span class="p">},</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'v1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'v2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'v3'</span><span class="p">,</span> <span class="s" style="color: #d14;">'v4'</span><span class="p">,</span> <span class="s" style="color: #d14;">'v5'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">allclose</span><span class="p">(</span><span class="n" style="color: #333;">geometric_fba_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">,</span> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1E-02</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-cobra/compare/fff89040cdb873308a398a97bc8a778b455ced12...11d80fce5d66886597adffefca19de87bde01fd2#1782e05f588cbb67bfb9f7fcadb7850a3bcf8a6f"><strong>cobra/test/test_flux_analysis/test_loopless.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># -*- coding: utf-8 -*-</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">"""Test functionalities of loopless.py"""</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">absolute_import</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">optlang.interface</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">INFEASIBLE</span><span class="p">,</span> <span class="n" style="color: #333;">OPTIMAL</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">cobra.util.solver</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">sutil</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.core</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Metabolite</span><span class="p">,</span> <span class="n" style="color: #333;">Model</span><span class="p">,</span> <span class="n" style="color: #333;">Reaction</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.flux_analysis.loopless</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">add_loopless</span><span class="p">,</span> <span class="n" style="color: #333;">loopless_solution</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">construct_ll_test_model</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="s" style="color: #d14;">"""Construct test model."""</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Model</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">(</span><span class="n" style="color: #333;">Metabolite</span><span class="p">(</span><span class="s" style="color: #d14;">"A"</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">(</span><span class="n" style="color: #333;">Metabolite</span><span class="p">(</span><span class="s" style="color: #d14;">"B"</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">(</span><span class="n" style="color: #333;">Metabolite</span><span class="p">(</span><span class="s" style="color: #d14;">"C"</span><span class="p">))</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">EX_A</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"EX_A"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">EX_A</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">A</span><span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">})</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">DM_C</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"DM_C"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">DM_C</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">C</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">})</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">v1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"v1"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">v1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">A</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">B</span><span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">})</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">v2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"v2"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">v2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">B</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">C</span><span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">})</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">v3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">"v3"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">v3</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">C</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">A</span><span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">})</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_reactions</span><span class="p">([</span><span class="n" style="color: #333;">EX_A</span><span class="p">,</span> <span class="n" style="color: #333;">DM_C</span><span class="p">,</span> <span class="n" style="color: #333;">v1</span><span class="p">,</span> <span class="n" style="color: #333;">v2</span><span class="p">,</span> <span class="n" style="color: #333;">v3</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">DM_C</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective_coefficient</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">test_model</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"><span class="nd">@pytest.fixture</span><span class="p">(</span><span class="n" style="color: #333;">scope</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"function"</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">s</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"glpk"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cplex"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="s" style="color: #d14;">"gurobi"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solvers</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">ll_test_model</span><span class="p">(</span><span class="n" style="color: #333;">request</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="s" style="color: #d14;">"""Return test model set with different solvers."""</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">construct_ll_test_model</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">request</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">param</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">test_model</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_loopless_benchmark_before</span><span class="p">(</span><span class="n" style="color: #333;">benchmark</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="s" style="color: #d14;">"""Benchmark initial condition."""</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">construct_ll_test_model</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">test_model</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">add_loopless</span><span class="p">(</span><span class="n" style="color: #333;">test_model</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="n" style="color: #333;">_</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_loopless_benchmark_after</span><span class="p">(</span><span class="n" style="color: #333;">benchmark</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="s" style="color: #d14;">"""Benchmark final condition."""</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">test_model</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">construct_ll_test_model</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="n" style="color: #333;">loopless_solution</span><span class="p">,</span> <span class="n" style="color: #333;">test_model</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_loopless_solution</span><span class="p">(</span><span class="n" style="color: #333;">ll_test_model</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test loopless_solution()."""</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">solution_feasible</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loopless_solution</span><span class="p">(</span><span class="n" style="color: #333;">ll_test_model</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">ll_test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">v3</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower_bound</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">ll_test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">solution_infeasible</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loopless_solution</span><span class="p">(</span><span class="n" style="color: #333;">ll_test_model</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">solution_feasible</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">[</span><span class="s" style="color: #d14;">"v3"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mf" style="color: #099;">0.0</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">solution_infeasible</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">[</span><span class="s" style="color: #d14;">"v3"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mf" style="color: #099;">1.0</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_loopless_solution_fluxes</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test fluxes of loopless_solution()"""</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">fluxes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">ll_solution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loopless_solution</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">fluxes</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fluxes</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">ll_solution</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_add_loopless</span><span class="p">(</span><span class="n" style="color: #333;">ll_test_model</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test add_loopless()."""</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">add_loopless</span><span class="p">(</span><span class="n" style="color: #333;">ll_test_model</span><span class="p">)</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">feasible_status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ll_test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">status</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">ll_test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">v3</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower_bound</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">ll_test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">slim_optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">infeasible_status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ll_test_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">status</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">feasible_status</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">OPTIMAL</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">infeasible_status</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">INFEASIBLE</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-cobra/compare/fff89040cdb873308a398a97bc8a778b455ced12...11d80fce5d66886597adffefca19de87bde01fd2#21245091a074c7a40fb0311655c410596a121bff"><strong>cobra/test/test_flux_analysis/test_moma.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># -*- coding: utf-8 -*-</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">"""Test functionalities of MOMA."""</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">absolute_import</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.flux_analysis.moma</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">add_moma</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_moma_sanity</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">qp_solvers</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test optimization criterion and optimality for MOMA."""</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qp_solvers</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PFK</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">knock_out</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">knock_sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">ssq</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">knock_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">pow</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">add_moma</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">linear</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PFK</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">knock_out</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">moma_sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">moma_ssq</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">moma_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">pow</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Use normal FBA as reference solution.</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">add_moma</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sol</span><span class="p">,</span> <span class="n" style="color: #333;">linear</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PFK</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">knock_out</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">moma_ref_sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">moma_ref_ssq</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">moma_ref_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">pow</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">moma_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective_value</span><span class="p">,</span> <span class="n" style="color: #333;">moma_ssq</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">moma_ssq</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">ssq</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">moma_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective_value</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">moma_ref_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective_value</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">moma_ssq</span><span class="p">,</span> <span class="n" style="color: #333;">moma_ref_ssq</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_linear_moma_sanity</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test optimization criterion and optimality for linear MOMA."""</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_solvers</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PFK</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">knock_out</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">knock_sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">sabs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">knock_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">add_moma</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">linear</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PFK</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">knock_out</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">moma_sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">moma_sabs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">moma_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Use normal FBA as reference solution.</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">add_moma</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sol</span><span class="p">,</span> <span class="n" style="color: #333;">linear</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PFK</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">knock_out</span><span class="p">()</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">moma_ref_sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">moma_ref_sabs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">moma_ref_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">allclose</span><span class="p">(</span><span class="n" style="color: #333;">moma_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective_value</span><span class="p">,</span> <span class="n" style="color: #333;">moma_sabs</span><span class="p">)</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">moma_sabs</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">sabs</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">moma_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective_value</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">moma_ref_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective_value</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">moma_sabs</span><span class="p">,</span> <span class="n" style="color: #333;">moma_ref_sabs</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">add_moma</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">linear</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">add_moma</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-cobra/compare/fff89040cdb873308a398a97bc8a778b455ced12...11d80fce5d66886597adffefca19de87bde01fd2#98c2acd17c81ed11626f76acd1e725ef7666e4c3"><strong>cobra/test/test_flux_analysis/test_parsimonious.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># -*- coding: utf-8 -*-</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">"""Test functionalities of pFBA."""</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">warnings</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.exceptions</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Infeasible</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.flux_analysis.parsimonious</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">add_pfba</span><span class="p">,</span> <span class="n" style="color: #333;">pfba</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_pfba_benchmark</span><span class="p">(</span><span class="n" style="color: #333;">large_model</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="s" style="color: #d14;">"""Benchmark pFBA functionality."""</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">large_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_solvers</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="n" style="color: #333;">pfba</span><span class="p">,</span> <span class="n" style="color: #333;">large_model</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_pfba</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test pFBA functionality."""</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_solvers</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">add_pfba</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">add_pfba</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">expression</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">expression</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">n_constraints</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">constraints</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">solution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pfba</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"optimal"</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">x_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"Biomass_Ecoli_core"</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="mf" style="color: #099;">0.8739</span><span class="p">,</span> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1e-4</span><span class="p">,</span> <span class="n" style="color: #333;">rtol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">abs_x</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">x</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">abs_x</span><span class="p">),</span> <span class="mf" style="color: #099;">518.4221</span><span class="p">,</span> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1e-4</span><span class="p">,</span> <span class="n" style="color: #333;">rtol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># test changes to model reverted</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expression</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">expression</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">constraints</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">n_constraints</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># needed?</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Test desired_objective_value</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># desired_objective = 0.8</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># pfba(model, solver=solver,</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># desired_objective_value=desired_objective)</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># abs_x = [abs(i) for i in model.solution.x]</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># assert model.solution.status == "optimal"</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># assert abs(model.solution.f - desired_objective) < 0.001</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># assert abs(sum(abs_x) - 476.1594) < 0.001</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># TODO: parametrize fraction (DRY it up)</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Test fraction_of_optimum</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">solution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pfba</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">fraction_of_optimum</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.95</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"optimal"</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">x_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"Biomass_Ecoli_core"</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="mf" style="color: #099;">0.95</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">0.8739</span><span class="p">,</span> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1e-4</span><span class="p">,</span> <span class="n" style="color: #333;">rtol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">abs_x</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">x</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">abs_x</span><span class="p">),</span> <span class="mf" style="color: #099;">493.4400</span><span class="p">,</span> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1e-4</span><span class="p">,</span> <span class="n" style="color: #333;">rtol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Infeasible solution</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ATPM</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower_bound</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">500</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">catch_warnings</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">simplefilter</span><span class="p">(</span><span class="s" style="color: #d14;">"error"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">UserWarning</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">((</span><span class="nb" style="color: #0086b3;">UserWarning</span><span class="p">,</span> <span class="n" style="color: #333;">Infeasible</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">)):</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">pfba</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">)</span></span></pre>
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<li id="e9f1e74b89eaf3ff93dd4fa111fbde3189bc4fa1">
<a href="https://salsa.debian.org/med-team/python-cobra/compare/fff89040cdb873308a398a97bc8a778b455ced12...11d80fce5d66886597adffefca19de87bde01fd2#e9f1e74b89eaf3ff93dd4fa111fbde3189bc4fa1"><strong>cobra/test/test_flux_analysis/test_phenotype_phase_plane.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># -*- coding: utf-8 -*-</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">"""Test functionalities of Phenotype Phase Plane Analysis."""</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">absolute_import</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.flux_analysis.phenotype_phase_plane</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">production_envelope</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_envelope_one</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test flux of production envelope."""</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">production_envelope</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"EX_o2_e"</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"flux_maximum"</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(),</span> <span class="mf" style="color: #099;">9.342</span><span class="p">,</span> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1e-3</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_envelope_multi_reaction_objective</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test production of multiple objectives."""</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">obj</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">EX_ac_e</span><span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">EX_co2_e</span><span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">production_envelope</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="s" style="color: #d14;">"EX_o2_e"</span><span class="p">,</span> <span class="n" style="color: #333;">obj</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"><span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"variables, num"</span><span class="p">,</span> <span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="p">([</span><span class="s" style="color: #d14;">"EX_glc__D_e"</span><span class="p">],</span> <span class="mi" style="color: #099;">30</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="p">([</span><span class="s" style="color: #d14;">"EX_glc__D_e"</span><span class="p">,</span> <span class="s" style="color: #d14;">"EX_o2_e"</span><span class="p">],</span> <span class="mi" style="color: #099;">20</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="p">([</span><span class="s" style="color: #d14;">"EX_glc__D_e"</span><span class="p">,</span> <span class="s" style="color: #d14;">"EX_o2_e"</span><span class="p">,</span> <span class="s" style="color: #d14;">"EX_ac_e"</span><span class="p">],</span> <span class="mi" style="color: #099;">10</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_multi_variable_envelope</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">variables</span><span class="p">,</span> <span class="n" style="color: #333;">num</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test production of envelope (multiple variable)."""</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">production_envelope</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">variables</span><span class="p">,</span> <span class="n" style="color: #333;">points</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">num</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">num</span> <span class="o" style="font-weight: 600;">**</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">variables</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_envelope_two</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test production of envelope."""</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">production_envelope</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"EX_glc__D_e"</span><span class="p">,</span> <span class="s" style="color: #d14;">"EX_o2_e"</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">objective</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"EX_ac_e"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"flux_maximum"</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(),</span> <span class="mf" style="color: #099;">1737.466</span><span class="p">,</span> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1e-3</span><span class="p">)</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"carbon_yield_maximum"</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(),</span> <span class="mf" style="color: #099;">83.579</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1e-3</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"mass_yield_maximum"</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(),</span> <span class="mf" style="color: #099;">82.176</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1e-3</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-cobra/compare/fff89040cdb873308a398a97bc8a778b455ced12...11d80fce5d66886597adffefca19de87bde01fd2#2999679307f1fe43dc278fdd8d2de577ece4ddec"><strong>cobra/test/test_flux_analysis/test_reaction.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># -*- coding: utf-8 -*-</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">"""Test _assess functions in reaction.py"""</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">absolute_import</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.core</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Metabolite</span><span class="p">,</span> <span class="n" style="color: #333;">Reaction</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.flux_analysis.reaction</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">assess</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_assess</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test assess functions."""</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">assess</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">GLCpts</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">solver</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">all_solvers</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">pyr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pyr_c</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Metabolite</span><span class="p">(</span><span class="s" style="color: #d14;">'a'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Metabolite</span><span class="p">(</span><span class="s" style="color: #d14;">'b'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">([</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">pyr_a2b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">'pyr_a2b'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">pyr_a2b</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">pyr</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">a</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">})</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_reactions</span><span class="p">([</span><span class="n" style="color: #333;">pyr_a2b</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">assess</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">pyr_a2b</span><span class="p">,</span> <span class="mf" style="color: #099;">0.01</span><span class="p">,</span> <span class="n" style="color: #333;">solver</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">all_solvers</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="s" style="color: #d14;">'precursors'</span><span class="p">:</span> <span class="p">{</span><span class="n" style="color: #333;">a</span><span class="p">:</span> <span class="p">{</span><span class="s" style="color: #d14;">'required'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.01</span><span class="p">,</span> <span class="s" style="color: #d14;">'produced'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">}},</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="s" style="color: #d14;">'products'</span><span class="p">:</span> <span class="p">{</span><span class="n" style="color: #333;">b</span><span class="p">:</span> <span class="p">{</span><span class="s" style="color: #d14;">'required'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.01</span><span class="p">,</span> <span class="s" style="color: #d14;">'capacity'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.0</span><span class="p">}}}</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected</span></span></pre>
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<li id="d5bcd065287a3ee1181ca39399fbd58b9942ccbd">
<a href="https://salsa.debian.org/med-team/python-cobra/compare/fff89040cdb873308a398a97bc8a778b455ced12...11d80fce5d66886597adffefca19de87bde01fd2#d5bcd065287a3ee1181ca39399fbd58b9942ccbd"><strong>cobra/test/test_flux_analysis/test_room.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># -*- coding: utf-8 -*-</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">"""Test functionalities of ROOM."""</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">absolute_import</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.flux_analysis.room</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">add_room</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_room_sanity</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test optimization criterion and optimality for ROOM."""</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_solvers</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PYK</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">knock_out</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">knock_sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Internally uses pFBA as reference solution.</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">add_room</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PYK</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">knock_out</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">room_sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Use FBA as reference solution.</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">add_room</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sol</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PYK</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">knock_out</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">room_sol_ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">flux_change</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">knock_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">flux_change_room</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">room_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">flux_change_room_ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">room_sol_ref</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Expect the ROOM solution to have smaller flux changes in</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># reactions compared to a normal FBA.</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">flux_change_room</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">flux_change</span> <span class="ow" style="font-weight: 600;">or</span> \</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">flux_change_room</span><span class="p">,</span> <span class="n" style="color: #333;">flux_change</span><span class="p">,</span> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1E-06</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Expect the FBA-based reference to have less change in</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># flux distribution.</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">flux_change_room_ref</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">flux_change_room</span> <span class="ow" style="font-weight: 600;">or</span> \</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">flux_change_room_ref</span><span class="p">,</span> <span class="n" style="color: #333;">flux_change_room</span><span class="p">,</span> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1E-06</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_linear_room_sanity</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test optimization criterion and optimality for linear ROOM."""</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_solvers</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PYK</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">knock_out</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">knock_sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Internally uses pFBA as reference solution.</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">add_room</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">linear</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PYK</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">knock_out</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">room_sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">model</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Use FBA as reference solution.</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">add_room</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sol</span><span class="p">,</span> <span class="n" style="color: #333;">linear</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PYK</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">knock_out</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">room_sol_ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">flux_change</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">knock_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">flux_change_room</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">room_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">flux_change_room_ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">room_sol_ref</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Expect the ROOM solution to have smaller flux changes in</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># reactions compared to a normal FBA.</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">flux_change_room</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">flux_change</span> <span class="ow" style="font-weight: 600;">or</span> \</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">flux_change_room</span><span class="p">,</span> <span class="n" style="color: #333;">flux_change</span><span class="p">,</span> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1E-06</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Expect the FBA-based reference to have less change in</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># flux distribution.</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">flux_change_room_ref</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">flux_change_room</span> <span class="ow" style="font-weight: 600;">or</span> \</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isclose</span><span class="p">(</span><span class="n" style="color: #333;">flux_change_room_ref</span><span class="p">,</span> <span class="n" style="color: #333;">flux_change_room</span><span class="p">,</span> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1E-06</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-cobra/compare/fff89040cdb873308a398a97bc8a778b455ced12...11d80fce5d66886597adffefca19de87bde01fd2#81680109a2b2fea49bc17acccbbff5bf506af90f"><strong>cobra/test/test_flux_analysis/test_sampling.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># -*- coding: utf-8 -*-</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">"""Test functionalities of flux sampling methods."""</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">absolute_import</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.core</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Metabolite</span><span class="p">,</span> <span class="n" style="color: #333;">Model</span><span class="p">,</span> <span class="n" style="color: #333;">Reaction</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.flux_analysis.parsimonious</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">pfba</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.flux_analysis.sampling</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ACHRSampler</span><span class="p">,</span> <span class="n" style="color: #333;">OptGPSampler</span><span class="p">,</span> <span class="n" style="color: #333;">sample</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="nd">@pytest.fixture</span><span class="p">(</span><span class="n" style="color: #333;">scope</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"function"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">achr</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="s" style="color: #d14;">"""Return ACHRSampler instance for tests."""</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">sampler</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ACHRSampler</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">thinning</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">((</span><span class="n" style="color: #333;">sampler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">n_warmup</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">sampler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">n_warmup</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">variables</span><span class="p">)))</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">sampler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">(</span><span class="n" style="color: #333;">sampler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warmup</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"v"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sampler</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"><span class="nd">@pytest.fixture</span><span class="p">(</span><span class="n" style="color: #333;">scope</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"function"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">optgp</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="s" style="color: #d14;">"""Return OptGPSampler instance for tests."""</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">sampler</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OptGPSampler</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">thinning</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">((</span><span class="n" style="color: #333;">sampler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">n_warmup</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">sampler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">n_warmup</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">variables</span><span class="p">)))</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">sampler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">(</span><span class="n" style="color: #333;">sampler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warmup</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"v"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sampler</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Benchmarks</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_achr_init_benchmark</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="s" style="color: #d14;">"""Benchmark inital ACHR sampling."""</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span><span class="p">:</span> <span class="n" style="color: #333;">ACHRSampler</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_optgp_init_benchmark</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="s" style="color: #d14;">"""Benchmark inital OptGP sampling."""</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span><span class="p">:</span> <span class="n" style="color: #333;">OptGPSampler</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_achr_sample_benchmark</span><span class="p">(</span><span class="n" style="color: #333;">achr</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="s" style="color: #d14;">"""Benchmark ACHR sampling."""</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="n" style="color: #333;">achr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_optgp_sample_benchmark</span><span class="p">(</span><span class="n" style="color: #333;">optgp</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="s" style="color: #d14;">"""Benchmark OptGP sampling."""</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Tests</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_achr</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test ACHR sampling (one sample)."""</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"achr"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shape</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_optgp</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test OptGP sampling (one sample)."""</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shape</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_multi_optgp</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test OptGP sampling (multi sample)."""</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shape</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_wrong_method</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test method intake sanity."""</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">):</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"schwupdiwupp"</span><span class="p">)</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_validate_wrong_sample</span><span class="p">(</span><span class="n" style="color: #333;">achr</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test sample correctness."""</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">achr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">)</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="s" style="color: #d14;">"hello"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">achr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fixed_seed</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test result of fixed seed for sampling."""</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">seed</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">42</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">allclose</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TPI</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="mf" style="color: #099;">9.12037487</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_equality_constraint</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test equality constraint."""</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ACALD</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.5</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">)</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">allclose</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ACALD</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.5</span><span class="p">,</span> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1e-6</span><span class="p">,</span> <span class="n" style="color: #333;">rtol</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"achr"</span><span class="p">)</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">allclose</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ACALD</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.5</span><span class="p">,</span> <span class="n" style="color: #333;">atol</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1e-6</span><span class="p">,</span> <span class="n" style="color: #333;">rtol</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_inequality_constraint</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test inequality constraint."""</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">co</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">problem</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Constraint</span><span class="p">(</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ACALD</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">flux_expression</span><span class="p">,</span> <span class="n" style="color: #333;">lb</span><span class="o" style="font-weight: 600;">=-</span><span class="mf" style="color: #099;">0.5</span><span class="p">)</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_cons_vars</span><span class="p">(</span><span class="n" style="color: #333;">co</span><span class="p">)</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">)</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ACALD</span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">0.5</span> <span class="o" style="font-weight: 600;">-</span> <span class="mf" style="color: #099;">1e-6</span><span class="p">)</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"achr"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ACALD</span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">0.5</span> <span class="o" style="font-weight: 600;">-</span> <span class="mf" style="color: #099;">1e-6</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_sampling</span><span class="p">(</span><span class="n" style="color: #333;">achr</span><span class="p">,</span> <span class="n" style="color: #333;">optgp</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test sampling."""</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">achr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">)</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">achr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"v"</span><span class="p">)</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"v"</span><span class="p">)</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_batch_sampling</span><span class="p">(</span><span class="n" style="color: #333;">achr</span><span class="p">,</span> <span class="n" style="color: #333;">optgp</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test batch sampling."""</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">b</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">achr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">batch</span><span class="p">(</span><span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">achr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"v"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">b</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">batch</span><span class="p">(</span><span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"v"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_variables_samples</span><span class="p">(</span><span class="n" style="color: #333;">achr</span><span class="p">,</span> <span class="n" style="color: #333;">optgp</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test variable samples."""</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">vnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">achr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">variables</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">achr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">fluxes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shape</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">achr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warmup</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shape</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">columns</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">vnames</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">all</span><span class="p">()</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="n" style="color: #333;">achr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"v"</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">all</span><span class="p">()</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">fluxes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shape</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warmup</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shape</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">columns</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">vnames</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">all</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"v"</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">all</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_inhomogeneous_sanity</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test whether inhomogeneous sampling gives approximately the same</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"><span class="s" style="color: #d14;"> standard deviation as a homogeneous version."""</span></span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ACALD</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.5</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">s_inhom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;">64</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ACALD</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.5</span> <span class="o" style="font-weight: 600;">-</span> <span class="mf" style="color: #099;">1e-3</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.5</span> <span class="o" style="font-weight: 600;">+</span> <span class="mf" style="color: #099;">1e-3</span><span class="p">)</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">s_hom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;">64</span><span class="p">)</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">relative_diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">s_inhom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">std</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mf" style="color: #099;">1e-12</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">s_hom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">std</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mf" style="color: #099;">1e-12</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="mf" style="color: #099;">0.5</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">relative_diff</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mean</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span></span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ACALD</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.5</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.5</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"> <span class="n" style="color: #333;">s_inhom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;">64</span><span class="p">,</span> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"achr"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ACALD</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.5</span> <span class="o" style="font-weight: 600;">-</span> <span class="mf" style="color: #099;">1e-3</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.5</span> <span class="o" style="font-weight: 600;">+</span> <span class="mf" style="color: #099;">1e-3</span><span class="p">)</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="n" style="color: #333;">s_hom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;">64</span><span class="p">,</span> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"achr"</span><span class="p">)</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">relative_diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">s_inhom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">std</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mf" style="color: #099;">1e-12</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">s_hom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">std</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mf" style="color: #099;">1e-12</span><span class="p">)</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="mf" style="color: #099;">0.5</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">relative_diff</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mean</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_reproject</span><span class="p">(</span><span class="n" style="color: #333;">optgp</span><span class="p">):</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test reprojection of sampling."""</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">fluxes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="n" style="color: #333;">proj</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">apply_along_axis</span><span class="p">(</span><span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_reproject</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">)</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">(</span><span class="n" style="color: #333;">proj</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"v"</span><span class="p">)</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">random</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rand</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warmup</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shape</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="n" style="color: #333;">proj</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">apply_along_axis</span><span class="p">(</span><span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_reproject</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">)</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">(</span><span class="n" style="color: #333;">proj</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"v"</span><span class="p">)</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_complicated_model</span><span class="p">():</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test a complicated model.</span></span>
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"><span class="s" style="color: #d14;"> Difficult model since the online mean calculation is numerically</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"><span class="s" style="color: #d14;"> unstable so many samples weakly violate the equality constraints.</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="n" style="color: #333;">model</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Model</span><span class="p">(</span><span class="s" style="color: #d14;">'flux_split'</span><span class="p">)</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="n" style="color: #333;">reaction1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">'V1'</span><span class="p">)</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">reaction2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">'V2'</span><span class="p">)</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">reaction3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Reaction</span><span class="p">(</span><span class="s" style="color: #d14;">'V3'</span><span class="p">)</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">reaction1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">)</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">reaction2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">)</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="n" style="color: #333;">reaction3</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">)</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">A</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Metabolite</span><span class="p">(</span><span class="s" style="color: #d14;">'A'</span><span class="p">)</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">reaction1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">A</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">})</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">reaction2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">A</span><span class="p">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">})</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">reaction3</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_metabolites</span><span class="p">({</span><span class="n" style="color: #333;">A</span><span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">})</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_reactions</span><span class="p">([</span><span class="n" style="color: #333;">reaction1</span><span class="p">,</span> <span class="n" style="color: #333;">reaction2</span><span class="p">,</span> <span class="n" style="color: #333;">reaction3</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="n" style="color: #333;">optgp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OptGPSampler</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">seed</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">42</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="n" style="color: #333;">achr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ACHRSampler</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">seed</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">42</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">optgp_samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="mi" style="color: #099;">100</span><span class="p">)</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">achr_samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">achr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="mi" style="color: #099;">100</span><span class="p">)</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">(</span><span class="n" style="color: #333;">optgp_samples</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">corr</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">1.0</span><span class="p">)</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">(</span><span class="n" style="color: #333;">achr_samples</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">corr</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">1.0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># > 95% are valid</span></span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">optgp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">(</span><span class="n" style="color: #333;">optgp_samples</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"v"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">95</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">achr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">validate</span><span class="p">(</span><span class="n" style="color: #333;">achr_samples</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"v"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">95</span></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_point_space</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test the reduction of the sampling space to one point."""</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"> <span class="n" style="color: #333;">pfba_sol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pfba</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">)</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="n" style="color: #333;">pfba_const</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">problem</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Constraint</span><span class="p">(</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">variables</span><span class="p">),</span> <span class="n" style="color: #333;">ub</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">pfba_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective_value</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_cons_vars</span><span class="p">(</span><span class="n" style="color: #333;">pfba_const</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Biomass_Ecoli_core</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower_bound</span> <span class="o" style="font-weight: 600;">=</span> \</span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"> <span class="n" style="color: #333;">pfba_sol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Biomass_Ecoli_core</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">):</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span></pre>
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<li id="1a0dab7c7f6e65b77584a60e96eafe7a7ff8ba8f">
<a href="https://salsa.debian.org/med-team/python-cobra/compare/fff89040cdb873308a398a97bc8a778b455ced12...11d80fce5d66886597adffefca19de87bde01fd2#1a0dab7c7f6e65b77584a60e96eafe7a7ff8ba8f"><strong>cobra/test/test_flux_analysis/test_summary.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># -*- coding: utf-8 -*-</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">"""Test functionalities of summary methods."""</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">absolute_import</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">contextlib</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">contextmanager</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">six</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">StringIO</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.flux_analysis.parsimonious</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">pfba</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="nd">@contextmanager</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">captured_output</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="s" style="color: #d14;">"""A context manager to test the IO summary methods."""</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">new_out</span><span class="p">,</span> <span class="n" style="color: #333;">new_err</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StringIO</span><span class="p">(),</span> <span class="n" style="color: #333;">StringIO</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">old_out</span><span class="p">,</span> <span class="n" style="color: #333;">old_err</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_out</span><span class="p">,</span> <span class="n" style="color: #333;">new_err</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">finally</span><span class="p">:</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">old_out</span><span class="p">,</span> <span class="n" style="color: #333;">old_err</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">check_line</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="n" style="color: #333;">expected_entries</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">pattern</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;">r"\s"</span><span class="p">)):</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="s" style="color: #d14;">"""Ensure each expected entry is in the output."""</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">output_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">pattern</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sub</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitlines</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">elem</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">expected_entries</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">pattern</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sub</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">elem</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">output_set</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">check_in_line</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="n" style="color: #333;">expected_entries</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">pattern</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;">r"\s"</span><span class="p">)):</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="s" style="color: #d14;">"""Ensure each expected entry is contained in the output."""</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">output_strip</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">pattern</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sub</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitlines</span><span class="p">()]</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">elem</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">expected_entries</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">pattern</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sub</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">elem</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">output_strip</span><span class="p">),</span> \</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="s" style="color: #d14;">"Not found: {} in:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">{}"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format</span><span class="p">(</span><span class="n" style="color: #333;">pattern</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sub</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">elem</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">output_strip</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"><span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"names"</span><span class="p">,</span> <span class="p">[</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_model_summary_previous_solution</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">opt_solver</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test summary of previous solution."""</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt_solver</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">solution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">rxn_test</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exchanges</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">names</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">met_test</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">rxn_test</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">())[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">met_test</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">rxn_test</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">())[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fluxes</span><span class="p">[</span><span class="n" style="color: #333;">rxn_test</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">321</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">captured_output</span><span class="p">()</span> <span class="k" style="font-weight: 600;">as</span> <span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">_</span><span class="p">):</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">summary</span><span class="p">(</span><span class="n" style="color: #333;">solution</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">names</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">check_in_line</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getvalue</span><span class="p">(),</span> <span class="p">[</span><span class="n" style="color: #333;">met_test</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'321'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"><span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"names"</span><span class="p">,</span> <span class="p">[</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_model_summary</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">opt_solver</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test model summary."""</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt_solver</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># test non-fva version (these should be fixed for textbook model)</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">names</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">expected_entries</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="s" style="color: #d14;">'O2 21.8'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="s" style="color: #d14;">'D-Glucose 10'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="s" style="color: #d14;">'Ammonium 4.77'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="s" style="color: #d14;">'Phosphate 3.21'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="s" style="color: #d14;">'H2O 29.2'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="s" style="color: #d14;">'CO2 22.8'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="s" style="color: #d14;">'H+ 17.5'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="s" style="color: #d14;">'Biomass_Ecol... 0.874'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">expected_entries</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="s" style="color: #d14;">'o2_e 21.8'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="s" style="color: #d14;">'glc__D_e 10'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="s" style="color: #d14;">'nh4_e 4.77'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="s" style="color: #d14;">'pi_e 3.21'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="s" style="color: #d14;">'h2o_e 29.2'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="s" style="color: #d14;">'co2_e 22.8'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="s" style="color: #d14;">'h_e 17.5'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="s" style="color: #d14;">'Biomass_Ecol... 0.874'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Need to use a different method here because</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># there are multiple entries per line.</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">captured_output</span><span class="p">()</span> <span class="k" style="font-weight: 600;">as</span> <span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">_</span><span class="p">):</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">summary</span><span class="p">(</span><span class="n" style="color: #333;">names</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">names</span><span class="p">)</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">check_in_line</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getvalue</span><span class="p">(),</span> <span class="n" style="color: #333;">expected_entries</span><span class="p">)</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># with model:</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># model.objective = model.exchanges[0]</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># model.summary()</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"><span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"fraction"</span><span class="p">,</span> <span class="p">[</span><span class="mf" style="color: #099;">0.95</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_model_summary_with_fva</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">opt_solver</span><span class="p">,</span> <span class="n" style="color: #333;">fraction</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test model summary (using FVA)."""</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opt_solver</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"optlang-gurobi"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">xfail</span><span class="p">(</span><span class="s" style="color: #d14;">"FVA currently buggy"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># test non-fva version (these should be fixed for textbook model</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">expected_entries</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="s" style="color: #d14;">'idFluxRangeidFluxRangeBiomass_Ecol...0.874'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="s" style="color: #d14;">'o2_e 21.8 [19.9, 23.7]'</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="s" style="color: #d14;">'h2o_e 29.2 [25, 30.7]'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="s" style="color: #d14;">'glc__D_e 10 [9.52, 10]'</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="s" style="color: #d14;">'co2_e 22.8 [18.9, 24.7]'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="s" style="color: #d14;">'nh4_e 4.77 [4.53, 5.16]'</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="s" style="color: #d14;">'h_e 17.5 [16.7, 22.4]'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="s" style="color: #d14;">'pi_e 3.21 [3.05, 3.21]'</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"> <span class="s" style="color: #d14;">'for_e 0 [0, 5.72]'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="s" style="color: #d14;">'ac_e 0 [0, 1.91]'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="s" style="color: #d14;">'pyr_e 0 [0, 1.27]'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="s" style="color: #d14;">'lac__D_e 0 [0, 1.07]'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="s" style="color: #d14;">'succ_e 0 [0, 0.837]'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="s" style="color: #d14;">'glu__L_e 0 [0, 0.636]'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="s" style="color: #d14;">'akg_e 0 [0, 0.715]'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="s" style="color: #d14;">'etoh_e 0 [0, 1.11]'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="s" style="color: #d14;">'acald_e 0 [0, 1.27]'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="p">]</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Need to use a different method here because</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># there are multiple entries per line.</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt_solver</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">solution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">captured_output</span><span class="p">()</span> <span class="k" style="font-weight: 600;">as</span> <span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">_</span><span class="p">):</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">summary</span><span class="p">(</span><span class="n" style="color: #333;">solution</span><span class="p">,</span> <span class="n" style="color: #333;">fva</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fraction</span><span class="p">)</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">check_in_line</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getvalue</span><span class="p">(),</span> <span class="n" style="color: #333;">expected_entries</span><span class="p">)</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"><span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"met"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"q8_c"</span><span class="p">])</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_metabolite_summary_previous_solution</span><span class="p">(</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">opt_solver</span><span class="p">,</span> <span class="n" style="color: #333;">met</span><span class="p">):</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test metabolite summary of previous solution."""</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt_solver</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">solution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pfba</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_by_id</span><span class="p">(</span><span class="n" style="color: #333;">met</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">summary</span><span class="p">(</span><span class="n" style="color: #333;">solution</span><span class="p">)</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"><span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"met, names"</span><span class="p">,</span> <span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"q8_c"</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"q8_c"</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_metabolite_summary</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">opt_solver</span><span class="p">,</span> <span class="n" style="color: #333;">met</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test metabolite summary."""</span></span>
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt_solver</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">captured_output</span><span class="p">()</span> <span class="k" style="font-weight: 600;">as</span> <span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">_</span><span class="p">):</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_by_id</span><span class="p">(</span><span class="n" style="color: #333;">met</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">summary</span><span class="p">(</span><span class="n" style="color: #333;">names</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">names</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">names</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="n" style="color: #333;">expected_entries</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="s" style="color: #d14;">'PRODUCING REACTIONS -- Ubiquinone-8 (q8_c)'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">% </span><span class="s" style="color: #d14;">FLUX RXN ID REACTION'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="s" style="color: #d14;">'100</span><span class="si" style="color: #d14;">% 43.6</span><span class="s" style="color: #d14;"> cytochr... 2.0 H+ + 0.5 O2 + Ubiquinol-8 --> '</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"> <span class="s" style="color: #d14;">'H2O + 2.0 H+ ...'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"> <span class="s" style="color: #d14;">'CONSUMING REACTIONS -- Ubiquinone-8 (q8_c)'</span><span class="p">,</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">% </span><span class="s" style="color: #d14;">FLUX RXN ID REACTION'</span><span class="p">,</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="s" style="color: #d14;">'88</span><span class="si" style="color: #d14;">% 38.5</span><span class="s" style="color: #d14;"> NADH de... 4.0 H+ + Nicotinamide adenine '</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="s" style="color: #d14;">'dinucleotide - re...'</span><span class="p">,</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="s" style="color: #d14;">'12</span><span class="si" style="color: #d14;">% 5.06</span><span class="s" style="color: #d14;"> succina... Ubiquinone-8 + Succinate --> '</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="s" style="color: #d14;">'Fumarate + Ubiquin...'</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="p">]</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="n" style="color: #333;">expected_entries</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="s" style="color: #d14;">'PRODUCING REACTIONS -- Ubiquinone-8 (q8_c)'</span><span class="p">,</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">% </span><span class="s" style="color: #d14;">FLUX RXN ID REACTION'</span><span class="p">,</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="s" style="color: #d14;">'100</span><span class="si" style="color: #d14;">% 43.6</span><span class="s" style="color: #d14;"> CYTBD '</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="s" style="color: #d14;">'2.0 h_c + 0.5 o2_c + q8h2_c --> h2o_c + 2.0 h_e...'</span><span class="p">,</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="s" style="color: #d14;">'CONSUMING REACTIONS -- Ubiquinone-8 (q8_c)'</span><span class="p">,</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">% </span><span class="s" style="color: #d14;">FLUX RXN ID REACTION'</span><span class="p">,</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="s" style="color: #d14;">'88</span><span class="si" style="color: #d14;">% 38.5</span><span class="s" style="color: #d14;"> NADH16 '</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"> <span class="s" style="color: #d14;">'4.0 h_c + nadh_c + q8_c --> 3.0 h_e + nad_c + q...'</span><span class="p">,</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="s" style="color: #d14;">'12</span><span class="si" style="color: #d14;">% 5.06</span><span class="s" style="color: #d14;"> SUCDi q8_c + succ_c --> fum_c + q8h2_c'</span><span class="p">,</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="p">]</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">check_in_line</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getvalue</span><span class="p">(),</span> <span class="n" style="color: #333;">expected_entries</span><span class="p">)</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"><span class="nd">@pytest.mark.parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"fraction, met"</span><span class="p">,</span> <span class="p">[(</span><span class="mf" style="color: #099;">0.99</span><span class="p">,</span> <span class="s" style="color: #d14;">"fdp_c"</span><span class="p">)])</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_metabolite_summary_with_fva</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">opt_solver</span><span class="p">,</span> <span class="n" style="color: #333;">fraction</span><span class="p">,</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">met</span><span class="p">):</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test metabolite summary (using FVA)."""</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># pytest.xfail("FVA currently buggy")</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt_solver</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimize</span><span class="p">()</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">captured_output</span><span class="p">()</span> <span class="k" style="font-weight: 600;">as</span> <span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">_</span><span class="p">):</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metabolites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_by_id</span><span class="p">(</span><span class="n" style="color: #333;">met</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">summary</span><span class="p">(</span><span class="n" style="color: #333;">fva</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fraction</span><span class="p">)</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">expected_entries</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="s" style="color: #d14;">'PRODUCING REACTIONS -- D-Fructose 1,6-bisphosphate (fdp_c)'</span><span class="p">,</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">% </span><span class="s" style="color: #d14;">FLUX RANGE RXN ID REACTION'</span><span class="p">,</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="s" style="color: #d14;">'100</span><span class="si" style="color: #d14;">% 7.48</span><span class="s" style="color: #d14;"> [6.17, 9.26] PFK '</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="s" style="color: #d14;">'atp_c + f6p_c --> adp_c + fdp_c + h_c'</span><span class="p">,</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="s" style="color: #d14;">'CONSUMING REACTIONS -- D-Fructose 1,6-bisphosphate (fdp_c)'</span><span class="p">,</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">% </span><span class="s" style="color: #d14;">FLUX RANGE RXN ID REACTION'</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="s" style="color: #d14;">'100</span><span class="si" style="color: #d14;">% 7.48</span><span class="s" style="color: #d14;"> [6.17, 8.92] FBA fdp_c <=> dhap_c + g3p_c'</span><span class="p">,</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="s" style="color: #d14;">'0</span><span class="si" style="color: #d14;">% 0 </span><span class="s" style="color: #d14;">[0, 1.72] FBP '</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="s" style="color: #d14;">'fdp_c + h2o_c --> f6p_c + pi_c'</span><span class="p">,</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="p">]</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"> <span class="n" style="color: #333;">check_line</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getvalue</span><span class="p">(),</span> <span class="n" style="color: #333;">expected_entries</span><span class="p">)</span></span></pre>
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<li id="5ef71f2d44a76eab71809b92e11f592193d42137">
<a href="https://salsa.debian.org/med-team/python-cobra/compare/fff89040cdb873308a398a97bc8a778b455ced12...11d80fce5d66886597adffefca19de87bde01fd2#5ef71f2d44a76eab71809b92e11f592193d42137"><strong>cobra/test/test_flux_analysis/test_variability.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># -*- coding: utf-8 -*-</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">"""Test functionalities of Flux Variability Analysis."""</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">absolute_import</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">six</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">iteritems</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.exceptions</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Infeasible</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra.flux_analysis.variability</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">find_blocked_reactions</span><span class="p">,</span> <span class="n" style="color: #333;">find_essential_genes</span><span class="p">,</span> <span class="n" style="color: #333;">find_essential_reactions</span><span class="p">,</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">flux_variability_analysis</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># FVA</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_flux_variability_benchmark</span><span class="p">(</span><span class="n" style="color: #333;">large_model</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">,</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">all_solvers</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">"""Benchmark FVA."""</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">large_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_solvers</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="n" style="color: #333;">flux_variability_analysis</span><span class="p">,</span> <span class="n" style="color: #333;">large_model</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">reaction_list</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">large_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">::</span><span class="mi" style="color: #099;">3</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_pfba_flux_variability</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">pfba_fva_results</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">fva_results</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test FVA using pFBA."""</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_solvers</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warns</span><span class="p">(</span><span class="nb" style="color: #0086b3;">UserWarning</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">flux_variability_analysis</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">pfba_factor</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.1</span><span class="p">,</span> <span class="n" style="color: #333;">reaction_list</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">::</span><span class="mi" style="color: #099;">3</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">fva_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flux_variability_analysis</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">pfba_factor</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1.1</span><span class="p">,</span> <span class="n" style="color: #333;">reaction_list</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">result</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iteritems</span><span class="p">(</span><span class="n" style="color: #333;">fva_out</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">T</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iteritems</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">pfba_fva_results</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">][</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">v</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">0.00001</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">pfba_fva_results</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">][</span><span class="n" style="color: #333;">name</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><=</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">fva_results</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">][</span><span class="n" style="color: #333;">name</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">loop_reactions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_by_id</span><span class="p">(</span><span class="n" style="color: #333;">rid</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">rid</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">"FRD7"</span><span class="p">,</span> <span class="s" style="color: #d14;">"SUCDi"</span><span class="p">)]</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">fva_loopless</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flux_variability_analysis</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">pfba_factor</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1.1</span><span class="p">,</span> <span class="n" style="color: #333;">reaction_list</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">loop_reactions</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">loopless</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">allclose</span><span class="p">(</span><span class="n" style="color: #333;">fva_loopless</span><span class="p">[</span><span class="s" style="color: #d14;">"maximum"</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">fva_loopless</span><span class="p">[</span><span class="s" style="color: #d14;">"minimum"</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_flux_variability</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">fva_results</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test FVA."""</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_solvers</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">fva_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flux_variability_analysis</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">reaction_list</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">result</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iteritems</span><span class="p">(</span><span class="n" style="color: #333;">fva_out</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">T</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iteritems</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">fva_results</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">][</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">v</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">0.00001</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Loopless FVA</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_flux_variability_loopless_benchmark</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">benchmark</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">all_solvers</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="s" style="color: #d14;">"""Benchmark loopless FVA."""</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_solvers</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">benchmark</span><span class="p">(</span><span class="n" style="color: #333;">flux_variability_analysis</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">loopless</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">reaction_list</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">::</span><span class="mi" style="color: #099;">3</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_flux_variability_loopless</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test loopless FVA."""</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_solvers</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">loop_reactions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_by_id</span><span class="p">(</span><span class="n" style="color: #333;">rid</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">rid</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">"FRD7"</span><span class="p">,</span> <span class="s" style="color: #d14;">"SUCDi"</span><span class="p">)]</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">fva_normal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flux_variability_analysis</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">reaction_list</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">loop_reactions</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">fva_loopless</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flux_variability_analysis</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">reaction_list</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">loop_reactions</span><span class="p">,</span> <span class="n" style="color: #333;">loopless</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">allclose</span><span class="p">(</span><span class="n" style="color: #333;">fva_normal</span><span class="p">[</span><span class="s" style="color: #d14;">"maximum"</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">fva_normal</span><span class="p">[</span><span class="s" style="color: #d14;">"minimum"</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">allclose</span><span class="p">(</span><span class="n" style="color: #333;">fva_loopless</span><span class="p">[</span><span class="s" style="color: #d14;">"maximum"</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">fva_loopless</span><span class="p">[</span><span class="s" style="color: #d14;">"minimum"</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Internals (essentiality, blocked reactions)</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fva_data_frame</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test DataFrame obtained from FVA."""</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flux_variability_analysis</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">all</span><span class="p">([</span><span class="n" style="color: #333;">df</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">'minimum'</span><span class="p">,</span> <span class="s" style="color: #d14;">'maximum'</span><span class="p">]])</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fva_infeasible</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test FVA infeasibility."""</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">infeasible_model</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">infeasible_model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_by_id</span><span class="p">(</span><span class="s" style="color: #d14;">"EX_glc__D_e"</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower_bound</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># ensure that an infeasible model does not run FVA</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">Infeasible</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">flux_variability_analysis</span><span class="p">(</span><span class="n" style="color: #333;">infeasible_model</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fva_minimization</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test minimization using FVA."""</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">EX_glc__D_e</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">objective_direction</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'min'</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">solution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flux_variability_analysis</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">fraction_of_optimum</span><span class="o" style="font-weight: 600;">=.</span><span class="mi" style="color: #099;">95</span><span class="p">)</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">at</span><span class="p">[</span><span class="s" style="color: #d14;">'EX_glc__D_e'</span><span class="p">,</span> <span class="s" style="color: #d14;">'minimum'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">10.0</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">at</span><span class="p">[</span><span class="s" style="color: #d14;">'EX_glc__D_e'</span><span class="p">,</span> <span class="s" style="color: #d14;">'maximum'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">9.5</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_find_blocked_reactions_solver_none</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test find_blocked_reactions() [no specific solver]."""</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">find_blocked_reactions</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="p">[</span><span class="mi" style="color: #099;">40</span><span class="p">:</span><span class="mi" style="color: #099;">46</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">'FRUpts2'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_essential_genes</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test find_essential_genes()."""</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="n" style="color: #333;">essential_genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'b2779'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b1779'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b0720'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b2416'</span><span class="p">,</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="s" style="color: #d14;">'b2926'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b1136'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b2415'</span><span class="p">}</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">observed_essential_genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">g</span> <span class="ow" style="font-weight: 600;">in</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">find_essential_genes</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">)}</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">observed_essential_genes</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">essential_genes</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_essential_reactions</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">):</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test find_blocked_reactions()."""</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">essential_reactions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'GLNS'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Biomass_Ecoli_core'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PIt2r'</span><span class="p">,</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="s" style="color: #d14;">'GAPD'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="s" style="color: #d14;">'ACONTb'</span><span class="p">,</span> <span class="s" style="color: #d14;">'EX_nh4_e'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ENO'</span><span class="p">,</span> <span class="s" style="color: #d14;">'EX_h_e'</span><span class="p">,</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="s" style="color: #d14;">'EX_glc__D_e'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ICDHyr'</span><span class="p">,</span> <span class="s" style="color: #d14;">'CS'</span><span class="p">,</span> <span class="s" style="color: #d14;">'NH4t'</span><span class="p">,</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="s" style="color: #d14;">'GLCpts'</span><span class="p">,</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="s" style="color: #d14;">'PGM'</span><span class="p">,</span> <span class="s" style="color: #d14;">'EX_pi_e'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PGK'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RPI'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ACONTa'</span><span class="p">}</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">observed_essential_reactions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">find_essential_reactions</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">)}</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">observed_essential_reactions</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">essential_reactions</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_find_blocked_reactions</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">all_solvers</span><span class="p">):</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test find_blocked_reactions()."""</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">solver</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_solvers</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">find_blocked_reactions</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="p">[</span><span class="mi" style="color: #099;">40</span><span class="p">:</span><span class="mi" style="color: #099;">46</span><span class="p">])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">'FRUpts2'</span><span class="p">]</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">find_blocked_reactions</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="p">[</span><span class="mi" style="color: #099;">42</span><span class="p">:</span><span class="mi" style="color: #099;">48</span><span class="p">])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span><span class="s" style="color: #d14;">'FUMt2_2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'FRUpts2'</span><span class="p">}</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">find_blocked_reactions</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reactions</span><span class="p">[</span><span class="mi" style="color: #099;">30</span><span class="p">:</span><span class="mi" style="color: #099;">50</span><span class="p">],</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">open_exchanges</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[]</span></span></pre>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">python-cobra (0.13.<span class="idiff left right">3-1) UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-cobra (0.13.<span class="idiff left right">4-1) unstable</span>; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> [ Afif Elghraoui ]</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> Closes: #904709</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> * Update dependencies</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * Refresh patch</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Drop obsolete patch</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,17 +13,19 @@ python-cobra (0.13.3-1) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> * Standards-Version: 4.2.1</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> * Point Vcs-fields to Salsa</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> * debhelper 11</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> * cme fix dpkg-control</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> * Build-Depends: python*-requests, python*-pip</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> * Drop failing test TestCobraFluxSampling.test_fixed_seed</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> * Rename debian/tests/control to control.autodep8</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> * Testsuite: autopkgtest-pkg-python</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> * Drop Python2 package since it has no reverse dependencies</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> (as well as autopkgtest of Python2 version)</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> * Build-Depends: python3-depinfo, python3-pipdeptree</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> * Drop failing test: test_show_versions (needs further investigation</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> with upstream)</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> <span class="idiff left right">TODO: Wait until ftpmaster accepted python3-depinfo</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> <span class="idiff left right">* Silence lintian about wrong Python version of data file</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Sat, 28 Apr 2018 22:36:04</span> +0200</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Wed, 17 Oct 2018 21:31:48</span> +0200</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">python-cobra (0.5.9-1) unstable; urgency=medium</span>
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<a href="https://salsa.debian.org/med-team/python-cobra/compare/fff89040cdb873308a398a97bc8a778b455ced12...11d80fce5d66886597adffefca19de87bde01fd2#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,29 +4,28 @@ Uploaders: Afif Elghraoui <afif@debian.org></td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: python</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Testsuite: autopkgtest-pkg-python</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Build-Depends:</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> debhelper (>= 11~),</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> libglpk-dev,</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> python3-all,</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> python3-all-dev,</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> python3-setuptools,</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> python3-depinfo,</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> python3-future,</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> python3-numpy (>= 1.6),</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> python3-optlang,,</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> python3-ruamel.yaml,</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> python3-pandas (>= 0.17.0),</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> python3-pip,</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> python3-pipdeptree,</span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> python3-requests,</span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> python3-swiglpk,</span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> python3-tabulate,</span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> cython3,</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~),</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> dh-python,</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> libglpk-dev,</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> python3-all,</span>
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<td class="diff-line-num new old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> python3-all-dev,</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> python3-setuptools,</span>
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<td class="diff-line-num new old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> python3-depinfo,</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> python3-future,</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> python3-numpy,</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> python3-optlang,</span>
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<td class="diff-line-num new old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> python3-ruamel.yaml,</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> python3-pandas (>= 0.17.0),</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> python3-pip,</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> python3-pipdeptree,</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> python3-requests,</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> python3-swiglpk,</span>
</pre>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> python3-tabulate,</span>
</pre>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> cython3,</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
26
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"># Test-Depends:</span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"><span class="idiff left right"> </span>python3-pytest,</span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"><span class="idiff left right"> </span>python3-pytest-benchmark,</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"><span class="idiff left right"> </span>python3-jsonschema (>> 2.5.0)</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"><span class="idiff left right"> </span>python3-pytest,</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"><span class="idiff left right"> </span>python3-pytest-benchmark,</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"><span class="idiff left right"> </span>python3-jsonschema (>> 2.5.0)</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">Standards-Version: 4.2.1</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/python-cobra</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/python-cobra.git</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -34,14 +33,12 @@ Homepage: http://opencobra.github.io/cobrapy/</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">Package: python3-cobra</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext">Depends:</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext"> ${shlibs:Depends},</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"> ${python3:Depends},</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext"> python-cobra-data (= ${source:Version}),</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">Suggests:</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"> python3-matplotlib,</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext"> qsopt-ex,</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> ${python3:Depends},</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> python-cobra-data (= ${source:Version})</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">Suggests: python3-matplotlib,</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> qsopt-ex</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">Description: constraint-based modeling of biological networks with Python 3</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"> COnstraint-Based Reconstruction and Analysis (COBRA) methods are widely</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> used for genome-scale modeling of metabolic networks in both prokaryotes</span>
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<a href="https://salsa.debian.org/med-team/python-cobra/compare/fff89040cdb873308a398a97bc8a778b455ced12...11d80fce5d66886597adffefca19de87bde01fd2#e1b8252b3d9de521fcfa9547cf7a0bf98adeb786"><strong>debian/patches/drop_failing_test.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Description: Drop failing test TestCobraFluxSampling.test_fixed_seed</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">Last-Update: Sat, 28 Apr 2018 22:36:04 +0200</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/cobra/test/test_flux_analysis.py</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/cobra/test/test_flux_analysis.py</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1025,9 +1025,9 @@ class TestCobraFluxSampling:</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> with pytest.raises(ValueError):</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> self.achr.validate(s)</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def test_fixed_seed(self, model):</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- s = sample(model, 1, seed=42)</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- assert numpy.allclose(s.TPI[0], 9.12037487)</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# def test_fixed_seed(self, model):</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# s = sample(model, 1, seed=42)</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# assert numpy.allclose(s.TPI[0], 9.12037487)</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> def test_equality_constraint(self, model):</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> model.reactions.ACALD.bounds = (-1.5, -1.5)</span></pre>
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<a href="https://salsa.debian.org/med-team/python-cobra/compare/fff89040cdb873308a398a97bc8a778b455ced12...11d80fce5d66886597adffefca19de87bde01fd2#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">mathjax.patch</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">drop_failing_test.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">drop_failing_test2.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/python-cobra/compare/fff89040cdb873308a398a97bc8a778b455ced12...11d80fce5d66886597adffefca19de87bde01fd2#b23d92f5a77e25540a4fc42a41dbafb232cc71c2"><strong>debian/patches/testsuite-check-jsonschema.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Description: Disable jsonschema requirement for test-suite</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"> The python{3}-jsonschema packages are not yet available in Debian unstable</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"> for the version required by this package. The test suite is not appropriately</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> configured to skip the tests that require this package. The patches here</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"> fix that.</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">Author: Afif Elghraoui <afif@ghraoui.name></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff">Forwarded: no</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff">Last-Update: 2015-08-10</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-cobra.orig/cobra/test/io_tests.py</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-cobra/cobra/test/io_tests.py</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -164,7 +164,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> # MAT does not store gene names</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> None</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+@skipIf(not jsonschema, "jsonschema required")</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> class TestCobraIOjson(TestCase, TestCobraIO):</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> def setUp(self):</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> self.test_model = mini_model</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-cobra.orig/setup.py</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-cobra/setup.py</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -164,7 +164,6 @@</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"> packages=find_packages(exclude=['cobra.oven', 'cobra.oven*']),</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> setup_requires=[],</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> install_requires=["six"],</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tests_require=["jsonschema > 2.5"],</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"> extras_require=extras,</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"> ext_modules=ext_modules,</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/python-cobra/compare/fff89040cdb873308a398a97bc8a778b455ced12...11d80fce5d66886597adffefca19de87bde01fd2#acdb87288c45d89620490f6861d4c545259be6c6"><strong>debian/python3-cobra.lintian-overrides</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># The data file is for both Python versions</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">python3-cobra: python-package-depends-on-package-from-other-python-variant Depends: python-cobra-data</span></pre>
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<a href="https://salsa.debian.org/med-team/python-cobra/compare/fff89040cdb873308a398a97bc8a778b455ced12...11d80fce5d66886597adffefca19de87bde01fd2#36d9f10c399cace22f9ea6e1cdd8d797af0bcf57"><strong>debian/tests/Makefile</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="make"><span class="nl">.ONESHELL</span><span class="o" style="font-weight: 600;">:</span></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="make"><span class="nl">all</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">py<span class="idiff left right">2-test py</span>3-test</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="make"><span class="nl">all</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">py3-test</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="make"><span class="nl">py2-test</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">SHELL=python2</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="make"><span class="nl">py3-test</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">SHELL=python3</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="make"><span class="nl">%-test</span><span class="o" style="font-weight: 600;">:</span></span>
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<a href="https://salsa.debian.org/med-team/python-cobra/compare/fff89040cdb873308a398a97bc8a778b455ced12...11d80fce5d66886597adffefca19de87bde01fd2#b4050d1f9b649372e9a774473db2bfeae3683f6d"><strong>debian/tests/control.autodep8</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Test-Command:</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> export MAKEFILES="$PWD/debian/tests/Makefile";</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> cd $ADTTMP && make py2-test</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">Depends:</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> make,</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> python-cobra,</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> python-pytest,</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> python-jsonschema,</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"># We could have avoided retyping these by adding the "needs-recommends" restriction, but doing that would also cause matplotlib to be pulled in.</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"># The tests involving matplotlib fail on debci from trying to do graphical operations on a headless server.</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> python-sbml,</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> python-scipy,</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> python-numpy,</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> python-pandas,</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">Restrictions: allow-stderr</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"></span>
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17
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Test-Command:</span>
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18
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"> export MAKEFILES="$PWD/debian/tests/Makefile";</span>
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19
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> cd $ADTTMP && make py3-test</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -26,4 +10,6 @@ Depends:</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> python3-scipy,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> python3-numpy,</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> python3-pandas,</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> # Python2 test also contained python-sbml. Once python3-sbml might exist this should be probably added here</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> # python3-sbml</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<a href="https://salsa.debian.org/med-team/python-cobra/compare/fff89040cdb873308a398a97bc8a778b455ced12...11d80fce5d66886597adffefca19de87bde01fd2#bf2c65c12ea72838ebea674a20f020795f52b698"><strong>release-notes/0.13.4.md</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Release notes for cobrapy 0.13.4</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Fixes</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p">*</span> Internal re-organization of the test suite.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="p">*</span> Upgrade the <span class="sb" style="color: #d14;">`ruamel.yaml`</span> version making it compatible with Python 3.7.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="p">*</span> Fix a bug with a regular expression in the Matlab interface.</span></pre>
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<a href="https://salsa.debian.org/med-team/python-cobra/compare/fff89040cdb873308a398a97bc8a778b455ced12...11d80fce5d66886597adffefca19de87bde01fd2#8c91c0296909b5ea3c496fde69e9dc44a6c6ae5f"><strong>setup.cfg</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">[bumpversion]</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">current_version = 0.13.<span class="idiff left right">3</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">current_version = 0.13.<span class="idiff left right">4</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">commit = True</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">tag = True</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">parse = (?P<major>\d+)</span>
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<a href="https://salsa.debian.org/med-team/python-cobra/compare/fff89040cdb873308a398a97bc8a778b455ced12...11d80fce5d66886597adffefca19de87bde01fd2#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -37,14 +37,14 @@ except IOError:</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"__main__"</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">setup</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"cobra"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"0.13.<span class="idiff left right">3</span>"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"0.13.<span class="idiff left right">4</span>"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">packages</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">find_packages</span><span class="p">(),</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">setup_requires</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">setup_requirements</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="s" style="color: #d14;">"six"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="s" style="color: #d14;">"future"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="s" style="color: #d14;">"swiglpk"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="s" style="color: #d14;">"ruamel.yaml<span class="idiff left right"><</span>0.15"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="s" style="color: #d14;">"ruamel.yaml<span class="idiff left right">>=</span>0.15"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="s" style="color: #d14;">"numpy>=1.13"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="s" style="color: #d14;">"pandas>=0.17.0"</span><span class="p">,</span></span>
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"> <span class="s" style="color: #d14;">"optlang>=1.4.2"</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -88,6 +88,7 @@ if __name__ == "__main__":</td>
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="s" style="color: #d14;">'Programming Language :: Python :: 3.4'</span><span class="p">,</span></span>
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"> <span class="s" style="color: #d14;">'Programming Language :: Python :: 3.5'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"> <span class="s" style="color: #d14;">'Programming Language :: Python :: 3.6'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="s" style="color: #d14;">'Programming Language :: Python :: 3.7'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"> <span class="s" style="color: #d14;">'Programming Language :: Python :: Implementation :: CPython'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"> <span class="s" style="color: #d14;">'Topic :: Scientific/Engineering'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python"> <span class="s" style="color: #d14;">'Topic :: Scientific/Engineering :: Bio-Informatics'</span></span>
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<a href="https://salsa.debian.org/med-team/python-cobra/compare/fff89040cdb873308a398a97bc8a778b455ced12...11d80fce5d66886597adffefca19de87bde01fd2#61be067c7cf3bdbf8a6b021a2b5167eb30612d0c"><strong>tox.ini</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="ini"><span class="nn" style="color: #555;">[tox]</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="ini"><span class="py">envlist</span> <span class="p">=</span> <span class="s" style="color: #d14;">pep8, py27, py34, py35, py36, sbml, array</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="ini"><span class="py">envlist</span> <span class="p">=</span> <span class="s" style="color: #d14;">pep8, py27, py34, py35, py36, <span class="idiff left right">py37, </span>sbml, array</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="ini"></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="ini"><span class="nn" style="color: #555;">[testenv]</span></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="ini"><span class="py">passenv</span> <span class="p">=</span></span>
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