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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-ruffus">Debian Med / python-ruffus</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-ruffus/-/commit/1227e611533af86a7fa3086e2657c27a5e5dda31">1227e611</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-06-10T01:49:34+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-ruffus/-/commit/33017e96cb944a2b0c618fea8567077cb8ec5f60">33017e96</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-06-10T01:49:35+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.8.4</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-ruffus/-/commit/524f7b8900b3ce0d146d1d6847ae455431de2ea7">524f7b89</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-06-10T01:50:01+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.8.4'
Update to upstream version '2.8.4'
with Debian dir 3d1e70f29798d47e8ffce04e2dbd05c2cd0ca6bb</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-ruffus/-/commit/86707c1a2f77aa9ed730adcef7273fcc65ec8a5f">86707c1a</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-06-10T01:50:01+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-ruffus/-/commit/8ec04769d23f33ee21578015f8c1e7a9a8b36a97">8ec04769</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-06-10T01:50:01+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-ruffus/-/commit/50e7a92a2cd70b0c7dca55fcfb58319c02911993">50e7a92a</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-06-10T01:59:25+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload.
</pre>
</li>
</ul>
<h4>22 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
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<li class="file-stats">
<a href="#561b88e19de321ca62c7590bbb350765fb110905">
README.rst
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#b46d29336084baa469c9a38cc2012f37c6a81b88">
<span class="deleted-file">
−
debian/patches/privacy.patch
</span>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#a4234da9cc78d3002106fe922234840556d0ebca">
doc/_templates/index.html
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<li class="file-stats">
<a href="#df0576cbb783bc50b36e1efa3cbe0564a26c8295">
doc/conf.py
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<li class="file-stats">
<a href="#8ecf3e586f6ea9e26bfdbf0b845f82f0e4ba6f96">
doc/contents.rst
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<li class="file-stats">
<a href="#9bb0d91e64a1bceb6971734f19c76c7ac195de27">
<span class="new-file">
+
doc/contributing.rst
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<li class="file-stats">
<a href="#3a02212ac350fb6ea2a2adb215a7964cc4d79bc9">
doc/global.inc
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<li class="file-stats">
<a href="#f86456c11071a3e3c905f4ffce635aa11f60ddd4">
doc/history.rst
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<li class="file-stats">
<a href="#6677207c6fa30ac9cec19ad036ae842582159ecb">
doc/installation.rst
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<li class="file-stats">
<a href="#3fde0b6affdde9e1563e335095509d690ada8729">
doc/release.rst
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<li class="file-stats">
<a href="#f5fa6835fe9f2151b6d2ff119a3394759e3303a0">
ruffus/file_name_parameters.py
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<li class="file-stats">
<a href="#70d4ac283e821a092fc491d0b0b3a1166608efd9">
ruffus/ruffus_utility.py
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<li class="file-stats">
<a href="#282fffd5824d7005fdb581654578b3626c1c4d02">
ruffus/ruffus_version.py
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<li class="file-stats">
<a href="#9a51c336c0f56509ea7be1eb6b75f9c5f7cf5c71">
ruffus/task.py
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<li class="file-stats">
<a href="#f4a26c15b587fe217799af494d7c695e3aeaf273">
ruffus/test/Makefile
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<li class="file-stats">
<a href="#50554ba19f0d467432195b287c0ed97d7e509203">
ruffus/test/test_drmaa_wrapper_run_job_locally.py
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<h4>Changes:</h4>
<li id="a5cc2925ca8258af241be7e5b0381edf30266302">
<a href="https://salsa.debian.org/med-team/python-ruffus/-/compare/aa0328fe78135954f0c81d6724ab696f51ce8db6...50e7a92a2cd70b0c7dca55fcfb58319c02911993#a5cc2925ca8258af241be7e5b0381edf30266302"><strong>.gitignore</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6" 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">@@ -6,4 +6,10 @@ build</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">_build</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">doc/hosted_site.cmd</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">.ruffus_history.sqlite</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">ruffus_development.*</span></pre>
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<td class="new_line diff-line-num" 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">\ No newline at end of file</td>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">ruffus_development.*</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"># Vim auxiliary files</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">*~</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">*.swp</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">*.time</span></pre>
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<a href="https://salsa.debian.org/med-team/python-ruffus/-/compare/aa0328fe78135954f0c81d6724ab696f51ce8db6...50e7a92a2cd70b0c7dca55fcfb58319c02911993#561b88e19de321ca62c7590bbb350765fb110905"><strong>README.rst</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">===========</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">CGAT-ruffus</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">===========</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"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">***************************************</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Overview</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">***************************************</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">@@ -14,15 +19,20 @@ Each python function can be called in parallel to run multiple **jobs**.</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Ruffus was originally designed for use in bioinformatics to analyse multiple genome</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">data sets.</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">More recently, we have extended the functionality of CGAT-ruffus to incude cluster integration (Currently</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">support SGE, SLURM and PBS-pro/Torque), paramaterisation, logging, database integration</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">and conda environment switching. `CGAT-core <https://github.com/cgat-developers/cgat-core>`_ code and `documentation <https://cgat-core.readthedocs.io/en/latest/>`_.</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">***************************************</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">Documentation</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">***************************************</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="LC21" class="line" lang="plaintext">Ruffus documentation can be found `here <http://www.ruffus.org.uk/>`_ ,</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">with `installation notes <http://www.ruffus.org.uk/installation.html>`_ ,</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">a `short tutorial <http://www.ruffus.org.uk/tutorials/simple_tutorial/simple_tutorial.html>`_ and</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">an `in-depth manual <http://www.ruffus.org.uk/tutorials/manual/manual_introduction.html>`_ .</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Ruffus documentation can be found `here <https://cgat-ruffus.readthedocs.io/en/latest/>`_ ,</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">with `installation notes <https://cgat-ruffus.readthedocs.io/en/latest/installation.html>`_ , and</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">an `in-depth manual <https://cgat-ruffus.readthedocs.io/en/latest/tutorials/new_tutorial/manual_contents.html>`_ .</span>
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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">However, to utilise the full power of this workflow management system we recomend</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">using `CGAT-core <https://github.com/cgat-developers/cgat-core>`_ (`documentation <https://cgat-core.readthedocs.io/en/latest/>`_).</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">***************************************</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">Background</span>
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<a href="https://salsa.debian.org/med-team/python-ruffus/-/compare/aa0328fe78135954f0c81d6724ab696f51ce8db6...50e7a92a2cd70b0c7dca55fcfb58319c02911993#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-ruffus (2.8.4-1) unstable; 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"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.5.0 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Wed, 10 Jun 2020 01:49:34 +0200</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">python-ruffus (2.8.1-6) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * Test-Depend: s/python-pytest/python3-pytest/</span>
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<a href="https://salsa.debian.org/med-team/python-ruffus/-/compare/aa0328fe78135954f0c81d6724ab696f51ce8db6...50e7a92a2cd70b0c7dca55fcfb58319c02911993#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">@@ -4,7 +4,7 @@ Uploaders: Andreas Tille <tille@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: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python3-all,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> python3-setuptools,</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">@@ -12,15 +12,14 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> python3-sphinx-rtd-theme,</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> python3-pytest,</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> graphviz</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4.1</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5.0</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/python-ruffus</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/python-ruffus.git</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Homepage: http://www.ruffus.org.uk/</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Package: python3-ruffus</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> ${python3:Depends},</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> graphviz</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Description: Python3 computation pipeline library widely used in bioinformatics</span>
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<li id="b46d29336084baa469c9a38cc2012f37c6a81b88">
<a href="https://salsa.debian.org/med-team/python-ruffus/-/compare/aa0328fe78135954f0c81d6724ab696f51ce8db6...50e7a92a2cd70b0c7dca55fcfb58319c02911993#b46d29336084baa469c9a38cc2012f37c6a81b88"><strong>debian/patches/privacy.patch</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Wed, 11 Jul 2018 11:21:00 +0200</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Description: Avoid privacy issue</span></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">--- a/doc/_templates/index.html</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/doc/_templates/index.html</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -153,8 +153,7 @@</span> The very latest (in development) code ca</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> <form action="http://groups.google.com/group/ruffus_discuss/boxsubscribe"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> Email: <input type=text name=email></span></pre>
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<a href="https://salsa.debian.org/med-team/python-ruffus/-/compare/aa0328fe78135954f0c81d6724ab696f51ce8db6...50e7a92a2cd70b0c7dca55fcfb58319c02911993#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">use_libjs-mathjax.patch</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">#use_png_instead_of_jpg.patch</span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">#fix_test.patch</span></pre>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">privacy.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/python-ruffus/-/compare/aa0328fe78135954f0c81d6724ab696f51ce8db6...50e7a92a2cd70b0c7dca55fcfb58319c02911993#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -54,6 +54,8 @@ override_dh_auto_clean:</td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext"> doc/_build/doctrees \</span>
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55
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext"> ruffus/test/*.log \</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext"> .ruffus_history.sqlite</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> rm -f ruffus.egg-info/PKG-INFO ruffus.egg-info/SOURCES.txt ruffus.egg-info/dependency_links.txt ruffus.egg-info/top_level.txt</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext">override_dh_install:</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext"> dh_install</span>
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<a href="https://salsa.debian.org/med-team/python-ruffus/-/compare/aa0328fe78135954f0c81d6724ab696f51ce8db6...50e7a92a2cd70b0c7dca55fcfb58319c02911993#a4234da9cc78d3002106fe922234840556d0ebca"><strong>doc/_templates/index.html</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">@@ -11,7 +11,7 @@</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="html"><span class="nt" style="color: #000080;"><meta</span> <span class="na" style="color: #008080;">content=</span><span class="s" style="color: #d14;">'index, follow'</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">'robots'</span><span class="nt" style="color: #000080;">/></span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="html"><span class="nt" style="color: #000080;"><meta</span> <span class="na" style="color: #008080;">content=</span><span class="s" style="color: #d14;">'en-uk'</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">'language'</span><span class="nt" style="color: #000080;">/></span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="html"><span class="nt" style="color: #000080;"><meta</span> <span class="na" style="color: #008080;">content=</span><span class="s" style="color: #d14;">'United Kingdom'</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">'country'</span><span class="nt" style="color: #000080;">/></span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="html"><span class="nt" style="color: #000080;"><meta</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">'copyright'</span> <span class="na" style="color: #008080;">content=</span><span class="s" style="color: #d14;">'<span class="idiff left right">cgat-developers</span>'</span><span class="nt" style="color: #000080;">/></span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="html">{% endblock %}</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="html"></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">@@ -120,62 +120,36 @@ Please cite <I>Ruffus</I> as:<br/></td>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="html"></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="html"></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span><span class="idiff left right">Get</span> <span class="nt" style="color: #000080;"><I></span>Ruffus<span class="nt" style="color: #000080;"></I></h2></span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="html"><span class="nt" style="color: #000080;"><h2></span><span class="idiff left right">Install</span> <span class="nt" style="color: #000080;"><I></span>Ruffus<span class="nt" style="color: #000080;"></I></h2></span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="html"></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="html"> <span class="nt" style="color: #000080;"><i></span>Ruffus<span class="nt" style="color: #000080;"></i></span> is available as a<span class="idiff left right">n</span> <span class="nt" style="color: #000080;"><a</span> </span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="html"> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"<span class="idiff left">http://peak.telecommunity.com/DevCenter/EasyInstall"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff right">easy-install</span><span class="nt" style="color: #000080;"></a></span>able package on the <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://pypi.python.org/pypi/ruffus"</span><span class="nt" style="color: #000080;">></span>Python Package</span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="html"> <span class="nt" style="color: #000080;"><i></span>Ruffus<span class="nt" style="color: #000080;"></i></span> is available as a<span class="idiff left right"> </span> <span class="nt" style="color: #000080;"><a</span> </span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="html"> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"<span class="idiff left">"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff right">conda package</span><span class="nt" style="color: #000080;"></a></span>able package on the <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://pypi.python.org/pypi/ruffus"</span><span class="nt" style="color: #000080;">></span>Python Package</span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="html"> Index<span class="nt" style="color: #000080;"></a></span>.</span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="html"> <span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="html">Just run:</span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">style=</span><span class="s" style="color: #d14;">"margin-left: 30px"</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"highlight-python"</span><span class="nt" style="color: #000080;">><pre></span><span class="idiff left">sudo pip install ruffus --upgrade</span><span class="nt" style="color: #000080;"><span class="idiff"></pre></span></span><span class="idiff right"> or</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">style=</span><span class="s" style="color: #d14;">"margin-left: 30px"</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"highlight-python"</span><span class="nt" style="color: #000080;">><pre></span><span class="idiff left">conda install -c bioconda ruffus</span><span class="nt" style="color: #000080;"><span class="idiff"></pre></span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="html">or</span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">style=</span><span class="s" style="color: #d14;">"margin-left: 30px"</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"highlight-python"</span><span class="nt" style="color: #000080;">><pre></span>easy_install -U ruffus<span class="nt" style="color: #000080;"></pre></span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">style=</span><span class="s" style="color: #d14;">"margin-left: 30px"</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"highlight-python"</span><span class="nt" style="color: #000080;">><pre></span>pip install ruffus<span class="nt" style="color: #000080;"></pre></span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="html"> </span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="html"><span class="nt" style="color: #000080;"><br></span> </span>
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="html">The very latest (in development) code can be obtained via <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://code.google.com/p/ruffus/source/checkout"</span><span class="nt" style="color: #000080;">></span> git <span class="nt" style="color: #000080;"></a></span>:</span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="html"> <span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">style=</span><span class="s" style="color: #d14;">"color: #ff0000"</span> <span class="nt" style="color: #000080;">></span></span>
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143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="html"> <span class="nt" style="color: #000080;"><pre></span>git clone https://bunbun68@code.google.com/p/ruffus/<span class="nt" style="color: #000080;"></pre></span></span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="html">The very latest (in development) code can be obtained via <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://github.com/cgat-developers/ruffus"</span><span class="nt" style="color: #000080;">></span> git <span class="nt" style="color: #000080;"></a></span>:</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">style=</span><span class="s" style="color: #d14;">"margin-left: 30px"</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"highlight-python"</span><span class="nt" style="color: #000080;">><pre></span>git clone https://github.com/cgat-developers/ruffus.git<span class="nt" style="color: #000080;"></pre></span> </span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
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147
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="html"><span class="nt" style="color: #000080;"><h1></span>Feedback and Getting Involved:<span class="nt" style="color: #000080;"></h1></span></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="html"><span class="nt" style="color: #000080;"><ul></span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="html"> <span class="nt" style="color: #000080;"><li></span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="html"> The <span class="nt" style="color: #000080;"><I></span>Ruffus<span class="nt" style="color: #000080;"></I></span> project is hosted with <span class="nt" style="color: #000080;"><b><a</span> </span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="html"> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://code.google.com/p/ruffus"</span><span class="nt" style="color: #000080;">></span>Google </span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="html"> Code here.<span class="nt" style="color: #000080;"></a></b><br><br></span></span>
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="html"> <span class="na" style="color: #008080;">height=</span><span class="s" style="color: #d14;">30</span> <span class="na" style="color: #008080;">alt=</span><span class="s" style="color: #d14;">"Google Groups"</span><span class="nt" style="color: #000080;">></span> <span class="nt" style="color: #000080;"><b></span>Subscribe to the <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://groups.google.com/forum/#!forum/ruffus_discuss"</span><span class="nt" style="color: #000080;">><i></span>ruffus_discuss<span class="nt" style="color: #000080;"></i></span> mailing list <span class="nt" style="color: #000080;"></a></b></span></span>
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="html"> Email: <span class="nt" style="color: #000080;"><input</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">text</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">email</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="html"> <span class="nt" style="color: #000080;"><input</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">submit</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"sub"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"Subscribe"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>We would love your input and involvment. If you find a bug or would like to request an improvement</span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="html">please raise a github issue. for more information on how to contribute code please see the</span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="html"> <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"contributing.html"</span><span class="nt" style="color: #000080;">></span> contributing <span class="nt" style="color: #000080;"></a></span> section for more information on how to</span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="html">contribute to the project<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="html">{% endblock %}</span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="html"></span></pre>
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<a href="https://salsa.debian.org/med-team/python-ruffus/-/compare/aa0328fe78135954f0c81d6724ab696f51ce8db6...50e7a92a2cd70b0c7dca55fcfb58319c02911993#df0576cbb783bc50b36e1efa3cbe0564a26c8295"><strong>doc/conf.py</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff left right"></span></span><span class="c1" style="color: #998; font-style: italic;"># -*- coding: utf-8 -*-</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" 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 class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ruffus documentation build configuration file, created by</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># sphinx-quickstart on Tue Apr 21 16:55:56 2009.</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">@@ -10,10 +10,11 @@</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># All configuration values have a default; values that are commented out</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># serve to show the default.</span></span>
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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;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</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 class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span><span class="p">,</span> <span class="n" style="color: #333;">os</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;">sys</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">".."</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;">print</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">sys</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">path</span></span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">sys</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">path</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">ruffus</span><span class="p">,</span> <span class="n" style="color: #333;">ruffus</span><span class="p">.</span><span class="n" style="color: #333;">task</span><span class="p">,</span> <span class="n" style="color: #333;">ruffus</span><span class="p">.</span><span class="n" style="color: #333;">ruffus_version</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>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="52" 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="53" 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">@@ -52,7 +53,7 @@ master_doc = 'contents'</td>
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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="c1" style="color: #998; font-style: italic;"># General information about the project.</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"><span class="n" style="color: #333;">project</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">u'ruffus'</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"><span class="n" style="color: #333;">copyright</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">u'2009-201<span class="idiff left right">5 Leo Goodstadt</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"><span class="n" style="color: #333;">copyright</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">u'2009-201<span class="idiff left right">9 cgat-developers</span>'</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="c1" style="color: #998; font-style: italic;"># The version info for the project you're documenting, acts as replacement for</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># |version| and |release|, also used in various other places throughout the</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">@@ -63,7 +64,7 @@ version=ruffus.ruffus_version.__version #major.minor[.patch[.sub]]</td>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The full version, without betaincluding alpha/beta/rc tags.</span></span>
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<pre style="margin: 0;"> <span id="LC65" 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="LC66" class="line" lang="python"><span class="n" style="color: #333;">release</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="n" style="color: #333;">subn</span><span class="p">(</span><span class="s" style="color: #d14;">"([\d\.]+).*"</span><span class="p">,</span> <span class="s" style="color: #d14;">r"\1"</span><span class="p">,</span> <span class="n" style="color: #333;">version</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;">print</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">version</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">release</span></span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">version</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">release</span></span><span class="p"><span class="idiff right">)</span></span></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>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The language for content autogenerated by Sphinx. Refer to documentation</span></span>
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<a href="https://salsa.debian.org/med-team/python-ruffus/-/compare/aa0328fe78135954f0c81d6724ab696f51ce8db6...50e7a92a2cd70b0c7dca55fcfb58319c02911993#8ecf3e586f6ea9e26bfdbf0b845f82f0e4ba6f96"><strong>doc/contents.rst</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">@@ -12,14 +12,15 @@ Start Here:</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> :caption: Introduction</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> :name: introduction_toc</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> index.html</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> installation.rst</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> history.rst</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> tutorials/new_tutorial/manual_contents.rst</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> tutorials/new_syntax.rst</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> Future plans<span class="idiff left right"> <todo></span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> Future plans</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> faq.rst</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> gallery.rst</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> why_ruffus.rst</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> tutorials/new_tutorial/manual_contents.rst</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> release.rst</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">@@ -61,11 +62,15 @@ Quick Reference:</td>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext"> print_dependencies.rst</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext"> adjacent_pairs_iterate.rst</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">.. toctree::</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> :maxdepth: 1</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> :caption: Contributing</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> :name: contributing_toc</span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext">=====================</span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext">Indices and tables</span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext">=====================</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> contributing.rst</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">=======</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">Indices</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">=======</span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext">* :ref:`genindex`</span></pre>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext">* :ref:`modindex`</span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext">* :ref:`search`</span></pre>
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<a href="https://salsa.debian.org/med-team/python-ruffus/-/compare/aa0328fe78135954f0c81d6724ab696f51ce8db6...50e7a92a2cd70b0c7dca55fcfb58319c02911993#9bb0d91e64a1bceb6971734f19c76c7ac195de27"><strong>doc/contributing.rst</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.. _contribute:</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">============</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Contributing</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">============</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Contributions are very much encouraged and we greatly appreciate the time and effort people make to help maintain and support out tools. Every contribution helps, please dont be shy, we dont bite.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">You can contribute to the development of our software in a number of different ways:</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">-------------------</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Reporting bug fixes</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">-------------------</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Bugs are annoying and reporting them will help us to fix your issue.</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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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Bugs can be reported using the issue section in `github <https://github.com/cgat-developers/ruffus/issues>`_</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">When reporting issues, please include:</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">- Steps in your code/command that led to the bug so it can be reproduced.</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">- The error message from the log message.</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">- Any other helpful info, such as the system/cluster engine or version information.</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">-----------------------------------</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">Proposing a new feature/enhancement</span>
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27
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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="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">If you wish to contribute a new feature to the CGAT-ruffus repository then the best way is to raise this as an issue and label it as an enhancement in `github <https://github.com/cgat-developers/ruffus/issues>`_</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">If you propose a new feature then please:</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">- Explain how your enhancement will work</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">- Describe as best as you can how you plan to implement this.</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">- If you dont think you have the necessary skills to implement this on your own then please say and we will try our best to help (or implement this for you). However, please be aware that this is a community developed software and our volunteers have other jobs. Therefore, we may not be able to work as fast as you hoped.</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">-----------------------</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">Pull Request Guidelines</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">-----------------------</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">Why not contribute to our project, its a great way of making the project better, your help is always welcome. We follow the fork/pull request `model <https://guides.github.com/activities/forking>`_. To update our documentation, fix bugs or add extra enhancements you will need to create a pull request through github.</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">To create a pull request perform these steps:</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">1. Create a github account.</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">2. Create a personal fork of the project on github.</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">3. Clone the fork onto your local machine. Your remote repo on github is called ``origin``.</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">4. Add the orginal repository as a remote called ``upstream``.</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">5. If you made the fork a while ago then please make sure you ``git pull upstream`` to keep your repository up to date</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">6. Create a new branch to work on! We usually name our branches with capital first and last followed by a dash and something unique. For example: ``git checkout -b AC-new_doc``.</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">7. Impliment your fix/enhancement and make sure your code is effectively documented.</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">8. Our code has tests and these will be ran when a pull request is submitted, however you can run our tests before you make the pull request, we have a number written in the ``ruffus/test/`` directory. To run all test run: `cd ruffus/test && /bin/bash run_all_unit_tests.cmd`.</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">9. Add or change our documentation in the ``docs/`` directory.</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">10. Squash all of your commits into a single commit with git `interactive rebase <https://help.github.com/articles/about-git-rebase/>`_.</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">11. Push your branch to your fork on github ``git push origin``</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">12. From your fork in github.com, open a pull request in the correct branch.</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">13. ... This is where someone will review your changes and modify them or approve them ...</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">14. Once the pull request is approved and merged you can pull the changes from the ``upstream`` to your local repo and delete your branch.</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">.. note:: Always write your commit messages in the present tense. Your commit messages should describe what the commit does to the code and not what you did to the code.</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/python-ruffus/-/compare/aa0328fe78135954f0c81d6724ab696f51ce8db6...50e7a92a2cd70b0c7dca55fcfb58319c02911993#3a02212ac350fb6ea2a2adb215a7964cc4d79bc9"><strong>doc/global.inc</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">@@ -6,8 +6,7 @@</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="php"> <span class="o" style="font-weight: 600;">:</span><span class="nx">keywords</span><span class="o" style="font-weight: 600;">:</span> <span class="nx">python</span><span class="p">,</span> <span class="nx">pipeline</span><span class="p">,</span> <span class="nx">computation</span><span class="p">,</span> <span class="nx">cluster</span><span class="p">,</span> <span class="nx">Ruffus</span><span class="p">,</span> <span class="nx">bioinformatics</span><span class="p">,</span> <span class="nx">parallel</span><span class="s1" style="color: #d14;">' name='</span><span class="nx">keywords</span></span>
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7
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<td class="diff-line-num new_line" data-linenumber="7" 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="LC7" class="line" lang="php"> <span class="o" style="font-weight: 600;">:</span><span class="nx">Author</span><span class="o" style="font-weight: 600;">:</span> <span class="nx">Leo</span> <span class="nx">Goodstadt</span></span>
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<td class="diff-line-num old_line" data-linenumber="8" 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">
8
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<td class="diff-line-num new_line" data-linenumber="8" 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">
8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="php"> <span class="o" style="font-weight: 600;">:</span><span class="nx">Publisher</span><span class="o" style="font-weight: 600;">:</span> <span class="nx">Leo</span> <span class="nx">Goodstadt</span></span>
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<td class="diff-line-num old old_line" data-linenumber="9" 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">
9
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<td class="diff-line-num new_line old" data-linenumber="9" 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="LC9" class="line" lang="php"> <span class="o" style="font-weight: 600;">:</span><span class="nx">Email</span><span class="o" style="font-weight: 600;">:</span> <span class="nx">ruffus</span><span class="o" style="font-weight: 600;">@</span><span class="nx">llew</span><span class="o" style="font-weight: 600;">.</span><span class="nx">org</span><span class="o" style="font-weight: 600;">.</span><span class="nx">uk</span></span>
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10
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<td class="diff-line-num new_line" data-linenumber="9" 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">
9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="php"> <span class="o" style="font-weight: 600;">:</span><span class="nx">robots</span><span class="o" style="font-weight: 600;">:</span> <span class="nx">index</span><span class="p">,</span> <span class="nx">follow</span></span>
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<td class="diff-line-num old_line" data-linenumber="11" 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">
11
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<td class="diff-line-num 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">
10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="php"> <span class="o" style="font-weight: 600;">:</span><span class="nx">language</span><span class="o" style="font-weight: 600;">:</span> <span class="nx">en</span><span class="o" style="font-weight: 600;">-</span><span class="nx">uk</span></span>
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12
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<td class="diff-line-num new_line" data-linenumber="11" 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">
11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="php"> <span class="o" style="font-weight: 600;">:</span><span class="nx">country</span><span class="o" style="font-weight: 600;">:</span> <span class="nx">United</span> <span class="nx">Kingdom</span></span>
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13
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<td class="diff-line-num new_line old" data-linenumber="12" 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="LC13" class="line" lang="php"> <span class="o" style="font-weight: 600;">:</span><span class="nx">copyright</span><span class="o" style="font-weight: 600;">:</span> <span class="nx"><span class="idiff left">Leo</span></span><span class="idiff"> </span><span class="nx"><span class="idiff">Goodstadt</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2009</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">2014</span></span></span></pre>
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<td class="diff-line-num new new_line" data-linenumber="12" 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">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="php"> <span class="o" style="font-weight: 600;">:</span><span class="nx">copyright</span><span class="o" style="font-weight: 600;">:</span> <span class="nx"><span class="idiff left">cgat</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="nx"><span class="idiff">developers</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2009</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">2019</span></span></span></pre>
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<li id="f86456c11071a3e3c905f4ffce635aa11f60ddd4">
<a href="https://salsa.debian.org/med-team/python-ruffus/-/compare/aa0328fe78135954f0c81d6724ab696f51ce8db6...50e7a92a2cd70b0c7dca55fcfb58319c02911993#f86456c11071a3e3c905f4ffce635aa11f60ddd4"><strong>doc/history.rst</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" 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>
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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">@@ -18,6 +18,20 @@ Major Features added to Ruffus</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> See :ref:`To do list <todo>` for future enhancements to Ruffus</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">********************************************************************</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">version 2.8.1</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">********************************************************************</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">* compatibility with gevent >= 1.2</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="LC28" class="line" lang="plaintext">********************************************************************</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">version 2.8.1</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">********************************************************************</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">* Ctrl-C will kill drmaa jobs</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">* python3.7 compatibility, thanks to @jbarlow83, @QuLogic</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">********************************************************************</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">version 2.6.3</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">********************************************************************</span>
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<a href="https://salsa.debian.org/med-team/python-ruffus/-/compare/aa0328fe78135954f0c81d6724ab696f51ce8db6...50e7a92a2cd70b0c7dca55fcfb58319c02911993#6677207c6fa30ac9cec19ad036ae842582159ecb"><strong>doc/installation.rst</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">@@ -9,99 +9,45 @@ Installation</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">.. note ::</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> Ruffus requires Python <span class="idiff left right">2.6 or higher or Python 3.0 or higher</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> Ruffus requires Python <span class="idiff left right">3.0 or higher, python 2 is no longer supported but older versions will still be python 2 compatible.</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">==============================================================================</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"><span class="idiff left right">The easy way</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"><span class="idiff left right">conda installation</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">==============================================================================</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"><span class="idiff left right"> *Ruffus* is available as an</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"><span class="idiff left right"> `easy-install <http://peak.telecommunity.com/DevCenter/EasyInstall>`_ -able package</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"><span class="idiff left right"> on the `Python Package Index <http://pypi.python.org/pypi/Sphinx>`_</span>.</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"><span class="idiff left right">The recomended method for installing CGAT-ruffus is to install using `conda <https://conda.io/en/latest/>`_ through</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"><span class="idiff left right">the `bioconda <https://anaconda.org/bioconda/ruffus>`_ channel. The reson for conda being the prefferred method</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"><span class="idiff left right">is that the dependancied are taken care of</span>.</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> ::</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> sudo pip install ruffus --upgrade</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="LC28" class="line" lang="plaintext"> This may also work for older installations::</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"> easy_install -U ruffus</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> See below if ``eady_install`` is missing</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext">==============================================================================</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext">The most up-to-date code:</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext">==============================================================================</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext"> * `Download the latest sources <https://pypi.python.org/pypi/ruffus>`_ or</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext"> * Check out the latest code from Google using git::</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"> git clone https://bunbun68@code.google.com/p/ruffus/ .</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext"> * Bleeding edge Ruffus development takes place on github::</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext"></span>
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47
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext"> git clone git@github.com:bunbun/ruffus.git .</span>
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48
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"></span>
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49
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext"></span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext"> * To install after downloading, change to the , type::</span>
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51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"></span>
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52
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext"> python ./setup.py install</span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext"></span>
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54
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext">======================</span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext">Prequisites</span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext">======================</span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext">==============================================================================</span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext">Installing easy_install</span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext">==============================================================================</span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext"></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext"> If your system doesn't have ``easy_install``, you can `install <ubuntu/linux mint>`__ one using a package manager, for example::</span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext"></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext"> # ubuntu/linux mint</span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext"> $ sudo apt-get install python-setuptools</span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext"> $ or sudo yum install python-setuptools</span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext"></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext"> or manually::</span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext"></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext"> sudo curl http://peak.telecommunity.com/dist/ez_setup.py | python</span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext"></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext"> or manually::</span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext"> wget peak.telecommunity.com/dist/ez_setup.py</span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext"> sudo python ez_setup.py</span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> conda install -c bioconda ruffus</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="LC28" class="line" lang="plaintext">==============================================================================</span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext"><span class="idiff left right">Installing pip</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"><span class="idiff left right">pip installation</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">==============================================================================</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext"> <span class="idiff left right">If Pip is missing::</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> <span class="idiff left right">*Ruffus* is also available on `pypi <https://pypi.org/project/ruffus/>`_.</span></span>
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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="LC84" class="line" lang="plaintext"> <span class="idiff left right"> $ sudo easy_install -U pip</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> <span class="idiff left right">::</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> pip install ruffus</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">==============================================================================</span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="plaintext"><span class="idiff left right"> Graphical flowcharts The most up-to-date code:</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"><span class="idiff left right">Manual installation</span></span>
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89
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">==============================================================================</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="plaintext"> **Ruffus** relies on the ``dot`` programme from `Graphviz <http://www.graphviz.org/>`_</span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext"> ("Graph visualisation") to make pretty flowchart representations of your pipelines in multiple</span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="plaintext"> graphical formats (e.g. ``png``, ``jpg``). The crossplatform Graphviz package can be</span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="plaintext"> `downloaded here <http://www.graphviz.org/Download.php>`_ for Windows,</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">To obtain the latest code, check it out from `github <https://github.com/cgat-developers/ruffus>`_ and activate it.</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="plaintext"> Linux, Macs and Solaris. For Fedora, try</span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="plaintext"> ::</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> ::</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="plaintext"> yum list 'graphviz*'</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> git clone https://github.com/cgat-developers/ruffus.git</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> cd ruffus</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> python setup.py install</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="plaintext"> For ubuntu / Debian, try</span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="plaintext"> ::</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="plaintext"> sudo apt-get install graphviz</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/python-ruffus/-/compare/aa0328fe78135954f0c81d6724ab696f51ce8db6...50e7a92a2cd70b0c7dca55fcfb58319c02911993#3fde0b6affdde9e1563e335095509d690ada8729"><strong>doc/release.rst</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">@@ -2,6 +2,18 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Release notes</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">*************</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">=============</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Release 2.8.3</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">=============</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">* add missing import</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">=============</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Release 2.8.2</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">=============</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">* implement retry behaviour for input file check.</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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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">=============</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Release 2.8.1</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">=============</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="21" 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>
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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">@@ -21,3 +33,23 @@ Release 2.8.0</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">* [#86] use pytest for testing</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">* python3.7 compatibility, thanks to @jbarlow83, @QuLogic</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">=============</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">Release 2.6.3</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">=============</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">* @transform works even when the ouput has more than one file.</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">* @subdivide works in exactly the same way as @transform.</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">* ruffus.drmaa_wrapper.run_job() works with python3 `(github) Fixed issue with byte and text streams.</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">* ruffus.drmaa.wrapper.run_job() allows env (environment) to be set for jobs run locally as well as those on the cluster.</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">* New object-orientated style syntax works seamlessly with Ruffus command line support. </span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">=============</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">Release 2.6.2</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">=============</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">* pipeline_printout_graph()` incompatibility with python3 fixed.</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">* checkpointing did not work correctly with @split and @subdivide.</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">* @transoform has easier to understand syntax and takes care of most common use cases of ruffus (Thanks Milan Simonovic).</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">* @transform takes an optional output_dir. </span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">* Decorators can take named parameters.</span></pre>
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<li id="f5fa6835fe9f2151b6d2ff119a3394759e3303a0">
<a href="https://salsa.debian.org/med-team/python-ruffus/-/compare/aa0328fe78135954f0c81d6724ab696f51ce8db6...50e7a92a2cd70b0c7dca55fcfb58319c02911993#f5fa6835fe9f2151b6d2ff119a3394759e3303a0"><strong>ruffus/file_name_parameters.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">@@ -2,7 +2,7 @@ from __future__ import print_function</td>
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<pre style="margin: 0;"> <span id="LC2" 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="LC3" 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;">dbdict</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.ruffus_utility</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="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.ruffus_utility</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">shorten_filenames_encoder</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;">.ruffus_utility</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">shorten_filenames_encoder</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">FILE_CHECK_RETRY</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">FILE_CHECK_SLEEP</span></span></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;">.ruffus_exceptions</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="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">################################################################################</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">@@ -55,6 +55,7 @@ from .ruffus_exceptions import *</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># 88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;"> <span id="LC57" 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="LC58" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">time</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">glob</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">itertools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">groupby</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">itertools</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">@@ -354,39 +355,43 @@ def needs_update_check_directory_missing(*params, **kwargs):</td>
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="s" style="color: #d14;">": Directories %r is missing"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">missing_directories</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="LC356" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="s" style="color: #d14;">"All directories exist"</span></span>
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># _________________________________________________________________________________________</span></span>
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># check_input_files_exist</span></span>
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">check_input_files_exist</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">params</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="python"> <span class="s" style="color: #d14;">"""If inputs are missing then there is no way a job can run</span></span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="python"><span class="s" style="color: #d14;"> successful. Must throw exception.</span></span>
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># _________________________________________________________________________________________</span></span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="python"><span class="s" style="color: #d14;"> This extra function is a hack to make sure input files exists</span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="python"><span class="s" style="color: #d14;"> right before job is called for better error messages, and to save</span></span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="python"><span class="s" style="color: #d14;"> things from blowing up inside the task function.</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="s" style="color: #d14;"> In practice, we have observed a sporadic time-lag between a task</span></span>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="python"><span class="s" style="color: #d14;"> completing on a remote node and an output file appearing in the</span></span>
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="python"><span class="s" style="color: #d14;"> expected location on the host running the ruffus pipeline. This</span></span>
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="python"><span class="s" style="color: #d14;"> causes a subsequent task to fail with missing input file even</span></span>
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="python"><span class="s" style="color: #d14;"> though the file will appear a few seconds later. It is not clear</span></span>
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="python"><span class="s" style="color: #d14;"> if this is an issue of a poorly configured storage, but a retry</span></span>
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="python"><span class="s" style="color: #d14;"> behaviour has been implemented to work around such issues.</span></span>
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">check_input_files_exist</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">params</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="python"><span class="s" style="color: #d14;"> If inputs are missing then there is no way a job can run successful.</span></span>
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="python"><span class="s" style="color: #d14;"> Must throw exception.</span></span>
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="python"><span class="s" style="color: #d14;"> This extra function is a hack to make sure input files exists right before</span></span>
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="python"><span class="s" style="color: #d14;"> job is called for better error messages, and to save things from blowing</span></span>
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="python"><span class="s" style="color: #d14;"> up inside the task function</span></span>
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="python"><span class="s" style="color: #d14;"> """</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="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">params</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;">input_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">params</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="LC378" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">get_strings_in_flattened_sequence</span><span class="p">(</span><span class="n" style="color: #333;">input_files</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="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">lexists</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">MissingInputFileError</span><span class="p">(</span><span class="s" style="color: #d14;">"No way to run job: "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC379" class="line" lang="python"> <span class="s" style="color: #d14;">"Input file '%s' is a broken symbolic link."</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC380" 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="LC381" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">MissingInputFileError</span><span class="p">(</span><span class="s" style="color: #d14;">"No way to run job: "</span> <span class="o" style="font-weight: 600;">+</span></span>
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382
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="python"> <span class="s" style="color: #d14;">"Input file '%s' does not exist"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># _________________________________________________________________________________________</span></span>
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="python"> <span class="n" style="color: #333;">tries</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FILE_CHECK_RETRY</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">tries</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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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">):</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">lexists</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">):</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">MissingInputFileError</span><span class="p">(</span><span class="s" style="color: #d14;">"No way to run job: "</span> <span class="o" style="font-weight: 600;">+</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="python"> <span class="s" style="color: #d14;">"Input file '%s' is a broken symbolic link."</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">f</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;">tries</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="LC387" class="line" lang="python"> <span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">sleep</span><span class="p">(</span><span class="n" style="color: #333;">FILE_CHECK_SLEEP</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tries</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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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">MissingInputFileError</span><span class="p">(</span><span class="s" style="color: #d14;">"No way to run job: "</span> <span class="o" style="font-weight: 600;">+</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="python"> <span class="s" style="color: #d14;">"Input file '%s' does not exist"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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393
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># needs_update_check_exist</span></span>
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="python"></span>
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389
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># _________________________________________________________________________________________</span></span>
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390
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">needs_update_check_exist</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">params</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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391
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396
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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392
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397
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="python"><span class="s" style="color: #d14;"> Given input and output files, see if all exist</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">@@ -1108,7 +1113,17 @@ def yield_io_params_per_job(input_params,</td>
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<pre style="margin: 0;"> <span id="LC1113" 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="LC1114" class="line" lang="python"> <span class="n" style="color: #333;">input_param</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">orig_input_param</span></span>
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1115
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<pre style="margin: 0;"> <span id="LC1115" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC1111" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># extras</span></span>
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<pre style="margin: 0;">+<span id="LC1116" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># extras - this statement applies transformations on the</span></span>
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<pre style="margin: 0;">+<span id="LC1117" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># extra parameters. It traverses nested data</span></span>
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<pre style="margin: 0;">+<span id="LC1118" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># structures. The transformation forces a copy of each</span></span>
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<pre style="margin: 0;">+<span id="LC1119" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># parameter which causes memory duplication. The memory use</span></span>
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<pre style="margin: 0;">+<span id="LC1120" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># can be significant if extras is large.</span></span>
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<pre style="margin: 0;">+<span id="LC1121" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC1122" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># For example, if extras contains a list of 10000 files,</span></span>
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<pre style="margin: 0;">+<span id="LC1123" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># there will be one copy for each input parameter. If</span></span>
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1124
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<pre style="margin: 0;">+<span id="LC1124" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># there are 1000 input files, this means there will be</span></span>
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1125
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<pre style="margin: 0;">+<span id="LC1125" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># 1000 * 100000 filenames (instead of 1000 references to</span></span>
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<pre style="margin: 0;">+<span id="LC1126" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># the same list containing 10000 strings).</span></span>
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<pre style="margin: 0;"> <span id="LC1127" class="line" lang="python"> <span class="n" style="color: #333;">extra_params</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">file_names_transform</span><span class="p">.</span><span class="n" style="color: #333;">substitute</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC1128" class="line" lang="python"> <span class="n" style="color: #333;">filenames</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">extra_specs</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1129" class="line" lang="python"></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">@@ -105,6 +105,11 @@ CHECKSUM_FUNCTIONS_AND_PARAMS = 3</td>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"><span class="n" style="color: #333;">CHECKSUM_REGENERATE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span> <span class="c1" style="color: #998; font-style: italic;"># regenerate checksums</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="LC108" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># number of times to check if an input file exists</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"><span class="n" style="color: #333;">FILE_CHECK_RETRY</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># number of seconds to sleep before retrying a file check</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"><span class="n" style="color: #333;">FILE_CHECK_SLEEP</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># _________________________________________________________________________________________</span></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="c1" style="color: #998; font-style: italic;"># t_extra_inputs</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">@@ -873,20 +878,29 @@ SUFFIX_SUBSTITUTE = 1</td>
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<pre style="margin: 0;"> <span id="LC878" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC879" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC880" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC876" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">regex_replace</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">regex_str</span><span class="p">,</span> <span class="n" style="color: #333;">compiled_regex</span><span class="p">,</span> <span class="n" style="color: #333;">substitution_patterns</span><span class="p">,</span> <span class="n" style="color: #333;">regex_or_suffix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">REGEX_SUBSTITUTE</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC877" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">apply_func_to_sequence</span><span class="p">(</span><span class="n" style="color: #333;">substitution_patterns</span><span class="p">,</span> <span class="n" style="color: #333;">t_regex_replace</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">regex_str</span><span class="p">,</span> <span class="n" style="color: #333;">compiled_regex</span><span class="p">,</span> <span class="n" style="color: #333;">regex_or_suffix</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">regex_replace</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">regex_str</span><span class="p">,</span> <span class="n" style="color: #333;">compiled_regex</span><span class="p">,</span> <span class="n" style="color: #333;">substitution_patterns</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="python"> <span class="n" style="color: #333;">regex_or_suffix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">REGEX_SUBSTITUTE</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">apply_func_to_sequence</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="python"> <span class="n" style="color: #333;">substitution_patterns</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC885" class="line" lang="python"> <span class="n" style="color: #333;">t_regex_replace</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">regex_str</span><span class="p">,</span> <span class="n" style="color: #333;">compiled_regex</span><span class="p">,</span> <span class="n" style="color: #333;">regex_or_suffix</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC886" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC887" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC888" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">formatter_replace</span><span class="p">(</span><span class="n" style="color: #333;">filenames</span><span class="p">,</span> <span class="n" style="color: #333;">regex_str</span><span class="p">,</span> <span class="n" style="color: #333;">compiled_regex</span><span class="p">,</span> <span class="n" style="color: #333;">substitution_patterns</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC881" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">apply_func_to_sequence</span><span class="p">(</span><span class="n" style="color: #333;">substitution_patterns</span><span class="p">,</span> <span class="n" style="color: #333;">t_formatter_replace</span><span class="p">(</span><span class="n" style="color: #333;">filenames</span><span class="p">,</span> <span class="n" style="color: #333;">regex_str</span><span class="p">,</span> <span class="n" style="color: #333;">compiled_regex</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">apply_func_to_sequence</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="python"> <span class="n" style="color: #333;">substitution_patterns</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="python"> <span class="n" style="color: #333;">t_formatter_replace</span><span class="p">(</span><span class="n" style="color: #333;">filenames</span><span class="p">,</span> <span class="n" style="color: #333;">regex_str</span><span class="p">,</span> <span class="n" style="color: #333;">compiled_regex</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC892" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC893" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC894" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">nested_formatter_replace</span><span class="p">(</span><span class="n" style="color: #333;">filenames</span><span class="p">,</span> <span class="n" style="color: #333;">regex_strings</span><span class="p">,</span> <span class="n" style="color: #333;">compiled_regexes</span><span class="p">,</span> <span class="n" style="color: #333;">substitution_patterns</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC885" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">apply_func_to_sequence</span><span class="p">(</span><span class="n" style="color: #333;">substitution_patterns</span><span class="p">,</span> <span class="n" style="color: #333;">t_nested_formatter_replace</span><span class="p">(</span><span class="n" style="color: #333;">filenames</span><span class="p">,</span> <span class="n" style="color: #333;">regex_strings</span><span class="p">,</span> <span class="n" style="color: #333;">compiled_regexes</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC895" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">apply_func_to_sequence</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC896" class="line" lang="python"> <span class="n" style="color: #333;">substitution_patterns</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="python"> <span class="n" style="color: #333;">t_nested_formatter_replace</span><span class="p">(</span><span class="n" style="color: #333;">filenames</span><span class="p">,</span> <span class="n" style="color: #333;">regex_strings</span><span class="p">,</span> <span class="n" style="color: #333;">compiled_regexes</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC898" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC899" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC900" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">nested_string_replace</span><span class="p">(</span><span class="n" style="color: #333;">prev_str</span><span class="p">,</span> <span class="n" style="color: #333;">new_str</span><span class="p">,</span> <span class="n" style="color: #333;">substitution_patterns</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC889" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">apply_func_to_sequence</span><span class="p">(</span><span class="n" style="color: #333;">substitution_patterns</span><span class="p">,</span> <span class="n" style="color: #333;">t_nested_string_replace</span><span class="p">(</span><span class="n" style="color: #333;">prev_str</span><span class="p">,</span> <span class="n" style="color: #333;">new_str</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC901" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">apply_func_to_sequence</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC902" class="line" lang="python"> <span class="n" style="color: #333;">substitution_patterns</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC903" class="line" lang="python"> <span class="n" style="color: #333;">t_nested_string_replace</span><span class="p">(</span><span class="n" style="color: #333;">prev_str</span><span class="p">,</span> <span class="n" style="color: #333;">new_str</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC904" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC905" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC906" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># _________________________________________________________________________________________</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># THE SOFTWARE.</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#################################################################################</span></span>
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<pre style="margin: 0;">-<span id="LC26" 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;">'2.8.<span class="idiff left right">1</span>'</span></span></pre>
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<pre style="margin: 0;">+<span id="LC26" 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;">'2.8.<span class="idiff left right">4</span>'</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-ruffus/-/compare/aa0328fe78135954f0c81d6724ab696f51ce8db6...50e7a92a2cd70b0c7dca55fcfb58319c02911993#9a51c336c0f56509ea7be1eb6b75f9c5f7cf5c71"><strong>ruffus/task.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">@@ -456,7 +456,8 @@ def generic_job_descriptor(unglobbed_params, verbose_abbreviated_path, runtime_d</td>
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">io_files_job_descriptor</span><span class="p">(</span><span class="n" style="color: #333;">unglobbed_params</span><span class="p">,</span> <span class="n" style="color: #333;">verbose_abbreviated_path</span><span class="p">,</span> <span class="n" style="color: #333;">runtime_data</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC459" class="line" lang="python"> <span class="n" style="color: #333;">extra_param</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">", "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">shorten_filenames_encoder</span><span class="p">(</span><span class="n" style="color: #333;">unglobbed_params</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">:],</span> <span class="n" style="color: #333;">verbose_abbreviated_path</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 class="p">]</span> \</span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="python"> <span class="n" style="color: #333;">extra_param</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">", "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">shorten_filenames_encoder</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">unglobbed_params</span><span class="p">[</span><span class="mi" style="color: #099;">2</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;">verbose_abbreviated_path</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 class="p">]</span> \</span>
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">unglobbed_params</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">2</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">""</span></span>
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="python"> <span class="n" style="color: #333;">out_param</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">shorten_filenames_encoder</span><span class="p">(</span><span class="n" style="color: #333;">unglobbed_params</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">verbose_abbreviated_path</span><span class="p">)</span> \</span>
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">unglobbed_params</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"??"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="873" 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>
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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">@@ -873,10 +874,11 @@ class Pipeline(dict):</td>
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<pre style="margin: 0;"> <span id="LC874" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">task_name</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">task_names</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC875" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;"> <span id="LC876" 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="LC876" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ruffus_exceptions</span><span class="p">.</span><span class="n" style="color: #333;">error_duplicate_task_name</span><span class="p">(</span><span class="s" style="color: #d14;">"The task string '%s' is ambiguous for "</span></span>
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<pre style="margin: 0;">-<span id="LC877" class="line" lang="python"> <span class="s" style="color: #d14;">"Pipeline '%s'. You must disambiguate "</span></span>
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<pre style="margin: 0;">-<span id="LC878" class="line" lang="python"> <span class="s" style="color: #d14;">"explicitly with different task names "</span></span>
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<pre style="margin: 0;">-<span id="LC879" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">task_str</span><span class="p">,</span> <span class="bp" style="color: #999;">self</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="LC877" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ruffus_exceptions</span><span class="p">.</span><span class="n" style="color: #333;">error_duplicate_task_name</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="python"> <span class="s" style="color: #d14;">"The task string '{}' is ambiguous for "</span></span>
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="python"> <span class="s" style="color: #d14;">"Pipeline '{}'. You must disambiguate "</span></span>
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="python"> <span class="s" style="color: #d14;">"explicitly with different task names "</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="python"> <span class="n" style="color: #333;">task_str</span><span class="p">,</span> <span class="bp" style="color: #999;">self</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="LC882" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Task</span><span class="p">(</span><span class="n" style="color: #333;">task_func</span><span class="p">,</span> <span class="n" style="color: #333;">task_name</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="LC883" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC884" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</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">@@ -2342,7 +2344,7 @@ class Task(node):</td>
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<pre style="margin: 0;"> <span id="LC2344" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC2345" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># rethrow exception after adding task name</span></span>
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<pre style="margin: 0;"> <span id="LC2346" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">-<span id="LC2345" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">exceptionType</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">error_task</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC2347" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">exceptionType</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left">ruffus_exceptions</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">error_task</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC2348" class="line" lang="python"> <span class="n" style="color: #333;">exceptionValue</span><span class="p">.</span><span class="n" style="color: #333;">specify</span></span>
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<pre style="margin: 0;"> <span id="LC2349" class="line" lang="python"> <span class="n" style="color: #333;">inst</span><span class="p">.</span><span class="n" style="color: #333;">specify_task</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="s" style="color: #d14;">"Exceptions in dependency checking"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC2350" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</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">@@ -5028,7 +5030,10 @@ def pipeline_run(target_tasks=[],</td>
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5030
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<pre style="margin: 0;"> <span id="LC5030" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">gevent.event</span></span>
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5031
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<pre style="margin: 0;"> <span id="LC5031" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">gevent.queue</span></span>
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5032
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<pre style="margin: 0;"> <span id="LC5032" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">gevent.pool</span></span>
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<pre style="margin: 0;">-<span id="LC5031" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">gevent.signal</span></span>
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5033
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<pre style="margin: 0;">+<span id="LC5033" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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5034
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<pre style="margin: 0;">+<span id="LC5034" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">gevent.signal</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">signal</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">gevent_signal</span></span>
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5035
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<pre style="margin: 0;">+<span id="LC5035" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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5036
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<pre style="margin: 0;">+<span id="LC5036" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">gevent.signal</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">gevent_signal</span></span>
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5032
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5037
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<pre style="margin: 0;"> <span id="LC5037" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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5033
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5038
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<pre style="margin: 0;"> <span id="LC5038" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">gevent.lock</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">gevent_lock</span></span>
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5034
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5039
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<pre style="margin: 0;"> <span id="LC5039" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</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">@@ -5038,9 +5043,9 @@ def pipeline_run(target_tasks=[],</td>
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5043
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<pre style="margin: 0;"> <span id="LC5043" class="line" lang="python"> <span class="n" style="color: #333;">pool_t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gevent</span><span class="p">.</span><span class="n" style="color: #333;">pool</span><span class="p">.</span><span class="n" style="color: #333;">Pool</span></span>
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5039
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5044
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<pre style="margin: 0;"> <span id="LC5044" class="line" lang="python"> <span class="n" style="color: #333;">pool</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pool_t</span><span class="p">(</span><span class="n" style="color: #333;">parallelism</span><span class="p">)</span></span>
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5045
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<pre style="margin: 0;"> <span id="LC5045" class="line" lang="python"> <span class="n" style="color: #333;">queue_t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gevent</span><span class="p">.</span><span class="n" style="color: #333;">queue</span><span class="p">.</span><span class="n" style="color: #333;">Queue</span></span>
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5041
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<pre style="margin: 0;">-<span id="LC5041" class="line" lang="python"> <span class="n" style="color: #333;">gevent</span><span class="p"><span class="idiff left right">.</span></span><span class="n" style="color: #333;">signal</span><span class="p">(</span><span class="n" style="color: #333;">signal</span><span class="p">.</span><span class="n" style="color: #333;">SIGINT</span><span class="p">,</span> <span class="n" style="color: #333;">functools</span><span class="p">.</span><span class="n" style="color: #333;">partial</span><span class="p">(</span><span class="n" style="color: #333;">handle_sigint</span><span class="p">,</span> <span class="n" style="color: #333;">pool</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">pool</span><span class="p">,</span> <span class="n" style="color: #333;">pipeline</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">pipeline</span><span class="p">))</span></span>
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5042
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<pre style="margin: 0;">-<span id="LC5042" class="line" lang="python"> <span class="n" style="color: #333;">gevent</span><span class="p"><span class="idiff left right">.</span></span><span class="n" style="color: #333;">signal</span><span class="p">(</span><span class="n" style="color: #333;">signal</span><span class="p">.</span><span class="n" style="color: #333;">SIGUSR1</span><span class="p">,</span> <span class="n" style="color: #333;">functools</span><span class="p">.</span><span class="n" style="color: #333;">partial</span><span class="p">(</span><span class="n" style="color: #333;">handle_sigusr1</span><span class="p">,</span> <span class="n" style="color: #333;">pool</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">pool</span><span class="p">,</span> <span class="n" style="color: #333;">pipeline</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">pipeline</span><span class="p">))</span></span>
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5043
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<pre style="margin: 0;">-<span id="LC5043" class="line" lang="python"> <span class="n" style="color: #333;">gevent</span><span class="p"><span class="idiff left right">.</span></span><span class="n" style="color: #333;">signal</span><span class="p">(</span><span class="n" style="color: #333;">signal</span><span class="p">.</span><span class="n" style="color: #333;">SIGUSR2</span><span class="p">,</span> <span class="n" style="color: #333;">functools</span><span class="p">.</span><span class="n" style="color: #333;">partial</span><span class="p">(</span><span class="n" style="color: #333;">handle_sigusr2</span><span class="p">,</span> <span class="n" style="color: #333;">pool</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">pool</span><span class="p">,</span> <span class="n" style="color: #333;">pipeline</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">pipeline</span><span class="p">))</span></span>
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5046
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<pre style="margin: 0;">+<span id="LC5046" class="line" lang="python"> <span class="n" style="color: #333;">gevent<span class="idiff left right">_</span>signal</span><span class="p">(</span><span class="n" style="color: #333;">signal</span><span class="p">.</span><span class="n" style="color: #333;">SIGINT</span><span class="p">,</span> <span class="n" style="color: #333;">functools</span><span class="p">.</span><span class="n" style="color: #333;">partial</span><span class="p">(</span><span class="n" style="color: #333;">handle_sigint</span><span class="p">,</span> <span class="n" style="color: #333;">pool</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">pool</span><span class="p">,</span> <span class="n" style="color: #333;">pipeline</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">pipeline</span><span class="p">))</span></span>
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5047
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<pre style="margin: 0;">+<span id="LC5047" class="line" lang="python"> <span class="n" style="color: #333;">gevent<span class="idiff left right">_</span>signal</span><span class="p">(</span><span class="n" style="color: #333;">signal</span><span class="p">.</span><span class="n" style="color: #333;">SIGUSR1</span><span class="p">,</span> <span class="n" style="color: #333;">functools</span><span class="p">.</span><span class="n" style="color: #333;">partial</span><span class="p">(</span><span class="n" style="color: #333;">handle_sigusr1</span><span class="p">,</span> <span class="n" style="color: #333;">pool</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">pool</span><span class="p">,</span> <span class="n" style="color: #333;">pipeline</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">pipeline</span><span class="p">))</span></span>
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5048
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<pre style="margin: 0;">+<span id="LC5048" class="line" lang="python"> <span class="n" style="color: #333;">gevent<span class="idiff left right">_</span>signal</span><span class="p">(</span><span class="n" style="color: #333;">signal</span><span class="p">.</span><span class="n" style="color: #333;">SIGUSR2</span><span class="p">,</span> <span class="n" style="color: #333;">functools</span><span class="p">.</span><span class="n" style="color: #333;">partial</span><span class="p">(</span><span class="n" style="color: #333;">handle_sigusr2</span><span class="p">,</span> <span class="n" style="color: #333;">pool</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">pool</span><span class="p">,</span> <span class="n" style="color: #333;">pipeline</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">pipeline</span><span class="p">))</span></span>
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5044
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<pre style="margin: 0;"> <span id="LC5049" 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="LC5050" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"unknown pool manager '{}'"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">pool_manager</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC5051" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/python-ruffus/-/compare/aa0328fe78135954f0c81d6724ab696f51ce8db6...50e7a92a2cd70b0c7dca55fcfb58319c02911993#f4a26c15b587fe217799af494d7c695e3aeaf273"><strong>ruffus/test/Makefile</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">@@ -17,7 +17,7 @@ NOTEST_RUN=$(NOTEST:%.py=%.run)</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="make"><span class="nl">all</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(PYTEST_RUN) $(NOTEST_RUN)</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="make"><span class="nl">%.pytest</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">%.py</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="make"> pytest <span class="nv" style="color: #008080;">$(PYTEST_OPTIONS)</span> <span class="nv" style="color: #008080;">$<</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="make"> <span class="idiff left">/usr/bin/time </span><span class="nt" style="color: #000080;"><span class="idiff">--output</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="nv" style="color: #008080;"><span class="idiff">$*</span></span><span class="idiff">.time </span><span class="nt" style="color: #000080;"><span class="idiff">-v</span></span><span class="idiff right"> </span>pytest <span class="nv" style="color: #008080;">$(PYTEST_OPTIONS)</span> <span class="nv" style="color: #008080;">$<</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="make"><span class="nl">%.run</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">%.py</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="make"> python <span class="nv" style="color: #008080;">$<</span></span></pre>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="make"> <span class="idiff left">/usr/bin/time </span><span class="nt" style="color: #000080;"><span class="idiff">--output</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="nv" style="color: #008080;"><span class="idiff">$*</span></span><span class="idiff">.time </span><span class="nt" style="color: #000080;"><span class="idiff">-v</span></span><span class="idiff right"> </span>python <span class="nv" style="color: #008080;">$<</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-ruffus/-/compare/aa0328fe78135954f0c81d6724ab696f51ce8db6...50e7a92a2cd70b0c7dca55fcfb58319c02911993#50554ba19f0d467432195b287c0ed97d7e509203"><strong>ruffus/test/test_drmaa_wrapper_run_job_locally.py</strong></a>
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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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -114,14 +114,14 @@ class Test_ruffus(unittest.TestCase):</td>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">environ</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"RUFFUS_HEEHEE"</span><span class="p">:</span> <span class="s" style="color: #d14;">"what?"</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">home_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">expanduser</span><span class="p">(</span><span class="s" style="color: #d14;">"~"</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;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">" Run echoing to screen...</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"> <span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">stderr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ruffus</span><span class="p">.</span><span class="n" style="color: #333;">drmaa_wrapper</span><span class="p">.</span><span class="n" style="color: #333;">run_job</span><span class="p">(</span><span class="n" style="color: #333;">cmd_str</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"<span class="idiff left">python %s/slow_process_for_testing.py"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">script_dir</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">stderr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ruffus</span><span class="p">.</span><span class="n" style="color: #333;">drmaa_wrapper</span><span class="p">.</span><span class="n" style="color: #333;">run_job</span><span class="p">(</span><span class="n" style="color: #333;">cmd_str</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"<span class="idiff left">%s %s/slow_process_for_testing.py"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">sys</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">executable</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">script_dir</span></span><span class="p"><span class="idiff right">)</span>,</span></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">job_environment</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">environ</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">working_directory</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">home_dir</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">run_locally</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="LC121" class="line" lang="python"> <span class="n" style="color: #333;">verbose</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="LC122" class="line" lang="python"> <span class="n" style="color: #333;">local_echo</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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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">" Run silently...</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">stderr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ruffus</span><span class="p">.</span><span class="n" style="color: #333;">drmaa_wrapper</span><span class="p">.</span><span class="n" style="color: #333;">run_job</span><span class="p">(</span><span class="n" style="color: #333;">cmd_str</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"<span class="idiff left">python %s/slow_process_for_testing.py"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">script_dir</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">stderr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ruffus</span><span class="p">.</span><span class="n" style="color: #333;">drmaa_wrapper</span><span class="p">.</span><span class="n" style="color: #333;">run_job</span><span class="p">(</span><span class="n" style="color: #333;">cmd_str</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"<span class="idiff left">%s %s/slow_process_for_testing.py"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">sys</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">executable</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">script_dir</span></span><span class="p"><span class="idiff right">)</span>,</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"> <span class="n" style="color: #333;">job_environment</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">environ</span><span class="p">,</span></span>
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126
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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;">working_directory</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">home_dir</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python"> <span class="n" style="color: #333;">run_locally</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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<li id="8e2edce0d507e1297474f25c00cae94258db38d8">
<a href="https://salsa.debian.org/med-team/python-ruffus/-/compare/aa0328fe78135954f0c81d6724ab696f51ce8db6...50e7a92a2cd70b0c7dca55fcfb58319c02911993#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="152" 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">@@ -152,7 +152,7 @@ Usage</td>
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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="s" style="color: #d14;">"""</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'http://www.ruffus.org.uk'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">download_url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"https://<span class="idiff left right">pypi.python.org/pypi</span>/ruffus"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">download_url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"https://<span class="idiff left right">github.com/cgat-developers</span>/ruffus"</span><span class="p">,</span></span>
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156
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"></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;">install_requires</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">module_dependencies</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">#['multiprocessing>=1.0', 'json' ], #, 'python>=2.5'],</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;">setup_requires</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">module_dependencies</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">#['multiprocessing>=1.0', 'json'], #, 'python>=2.5'],</span></span>
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