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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/python-cobra">Debian Med / python-cobra</a>
</h3>
<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/python-cobra/-/commit/40bd941368a727d29c8d1e507168842db3ae3468">40bd9413</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-08-08T12:04:12+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.18.1</pre>
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<h4>5 changed files:</h4>
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<a href="#2562dc47c12586d518db2b6ce12e991436fe5c6a">
cobra/__init__.py
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<li class="file-stats">
<a href="#269c10fb5fe09fcf23a28ded4c81358f922f06a6">
cobra/io/sbml.py
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<a href="#69e2939e4a9c46ae71bbd717f20c647d33302b34">
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+
release-notes/0.18.1.md
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<li class="file-stats">
<a href="#8c91c0296909b5ea3c496fde69e9dc44a6c6ae5f">
setup.cfg
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<h4>Changes:</h4>
<li id="2562dc47c12586d518db2b6ce12e991436fe5c6a">
<a href="https://salsa.debian.org/med-team/python-cobra/-/commit/40bd941368a727d29c8d1e507168842db3ae3468#2562dc47c12586d518db2b6ce12e991436fe5c6a"><strong>cobra/__init__.py</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -41,4 +41,4 @@ from cobra import io</td>
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cobra</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">sampling</span></span>
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42
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<pre style="margin: 0;"> <span id="LC42" 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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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"></span>
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44
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<pre style="margin: 0;">-<span id="LC44" 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;">"0.18.<span class="idiff left right">0</span>"</span></span></pre>
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44
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<pre style="margin: 0;">+<span id="LC44" 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;">"0.18.<span class="idiff left right">1</span>"</span></span></pre>
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<li id="269c10fb5fe09fcf23a28ded4c81358f922f06a6">
<a href="https://salsa.debian.org/med-team/python-cobra/-/commit/40bd941368a727d29c8d1e507168842db3ae3468#269c10fb5fe09fcf23a28ded4c81358f922f06a6"><strong>cobra/io/sbml.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1003" 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="1003" 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">@@ -1003,9 +1003,9 @@ def _model_to_sbml(cobra_model, f_replace=None, units=True):</td>
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1003
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1003
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<pre style="margin: 0;"> <span id="LC1003" class="line" lang="python"> <span class="n" style="color: #333;">_create_parameter</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">pid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ZERO_BOUND_ID</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="1004" 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">
1004
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<td class="diff-line-num new_line" data-linenumber="1004" 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">
1004
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<pre style="margin: 0;"> <span id="LC1004" class="line" lang="python"> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">sbo</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">SBO_DEFAULT_FLUX_BOUND</span><span class="p">)</span></span>
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1005
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1005
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<pre style="margin: 0;"> <span id="LC1005" class="line" lang="python"> <span class="n" style="color: #333;">_create_parameter</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">pid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">BOUND_MINUS_INF</span><span class="p">,</span></span>
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1006
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<pre style="margin: 0;">-<span id="LC1006" class="line" lang="python"> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">=-</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="s" style="color: #d14;">"Inf"</span><span class="p">),</span> <span class="n" style="color: #333;">sbo</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">SBO_FLUX_BOUND</span><span class="p">)</span></span>
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1006
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<pre style="margin: 0;">+<span id="LC1006" class="line" lang="python"> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">=-</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="s" style="color: #d14;">"Inf"</span><span class="p">),</span> <span class="n" style="color: #333;">sbo</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">SBO_<span class="idiff left right">DEFAULT_</span>FLUX_BOUND</span><span class="p">)</span></span>
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1007
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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;">_create_parameter</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">pid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">BOUND_PLUS_INF</span><span class="p">,</span></span>
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1008
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<td class="diff-line-num new_line old" data-linenumber="1008" 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="LC1008" class="line" lang="python"> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="s" style="color: #d14;">"Inf"</span><span class="p">),</span> <span class="n" style="color: #333;">sbo</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">SBO_FLUX_BOUND</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="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="s" style="color: #d14;">"Inf"</span><span class="p">),</span> <span class="n" style="color: #333;">sbo</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">SBO_<span class="idiff left right">DEFAULT_</span>FLUX_BOUND</span><span class="p">)</span></span>
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1009
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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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1010
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<pre style="margin: 0;"> <span id="LC1010" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Compartments</span></span>
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1011
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1011
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<pre style="margin: 0;"> <span id="LC1011" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># FIXME: use first class compartment model (and write notes & annotations)</span></span>
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<a href="https://salsa.debian.org/med-team/python-cobra/-/commit/40bd941368a727d29c8d1e507168842db3ae3468#69e2939e4a9c46ae71bbd717f20c647d33302b34"><strong>release-notes/0.18.1.md</strong></a>
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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 0.18.1</span></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> Use the correct SBO term for unbounded (infinite bounds) reactions.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Other</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">*</span> Pin dependency on python-libsbml-experimental 5.18.1.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"></span></pre>
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<a href="https://salsa.debian.org/med-team/python-cobra/-/commit/40bd941368a727d29c8d1e507168842db3ae3468#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 = 0.18.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">current_version = 0.18.<span class="idiff left right">1</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/-/commit/40bd941368a727d29c8d1e507168842db3ae3468#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">@@ -38,7 +38,7 @@ except IOError:</td>
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<pre style="margin: 0;"> <span id="LC38" 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="LC39" 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="LC40" 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="LC41" 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;">"0.18.<span class="idiff left right">0</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;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"0.18.<span class="idiff left right">1</span>"</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;">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="LC43" 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="LC44" 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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -50,7 +50,7 @@ if __name__ == "__main__":</td>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"> <span class="s" style="color: #d14;">"pandas>=0.17.0"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"> <span class="s" style="color: #d14;">"optlang>=1.4.2"</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;">"depinfo"</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;">"python-libsbml-experimental==5.18.<span class="idiff left right">0</span>"</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;">"python-libsbml-experimental==5.18.<span class="idiff left right">1</span>"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <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;">tests_require</span><span class="o" style="font-weight: 600;">=</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;">"jsonschema > 2.5"</span><span class="p">,</span></span>
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