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<h3>
Rebecca N. Palmer pushed to branch master
at <a href="https://salsa.debian.org/med-team/snakemake">Debian Med / snakemake</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/snakemake/-/commit/c8348291b8bcbd6cfe979d88c1e54690046a1a65">c8348291</a></strong>
<div>
<span>by Rebecca N. Palmer</span>
<i>at 2020-08-28T07:55:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 5.23.0</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snakemake/-/commit/0ce8679fe4def2f3cf079290183bd7bf9a7384f0">0ce8679f</a></strong>
<div>
<span>by Rebecca N. Palmer</span>
<i>at 2020-08-28T07:55:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/5.23.0'
Update to upstream version '5.23.0'
with Debian dir c2da5c7512d9b4bc66f9609b3bab3c168d6038c4</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snakemake/-/commit/19b324181635fb25322d78deac516018c801f46a">19b32418</a></strong>
<div>
<span>by Rebecca N. Palmer</span>
<i>at 2020-08-28T08:40:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add new dependency python3-pulp.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snakemake/-/commit/a056d4757cee7ceeb9fa894d04268a56381678a2">a056d475</a></strong>
<div>
<span>by Rebecca N. Palmer</span>
<i>at 2020-08-29T11:48:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove unnecessary test skips, and document remaining ones.
</pre>
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</ul>
<h4>24 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#45267e3a9556cafa9cb7b61dab7a3b6659e73aad">
CHANGELOG.rst
</a>
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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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="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<li class="file-stats">
<a href="#3c7246c0b371cfd3a475428be04706178ca01f0f">
docs/project_info/faq.rst
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<li class="file-stats">
<a href="#9b54be2cff8d0de677b1245d0b0dc07cca021923">
docs/snakefiles/configuration.rst
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<li class="file-stats">
<a href="#945ec74fc1c17902d98bca84b7a1f0dfd755c01b">
docs/snakefiles/deployment.rst
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<li class="file-stats">
<a href="#dfeb7b6e739ba66056c1799c63a5a39c7698b59f">
docs/snakefiles/rules.rst
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<li class="file-stats">
<a href="#d366205d7cd679ff6d4a61f70728e92537101763">
snakemake/__init__.py
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<li class="file-stats">
<a href="#5e16cbeea010f59dbef52f8950f4873c94f39c7e">
snakemake/_version.py
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<li class="file-stats">
<a href="#d70c11793454d64a7b2d77ced116226d2f13378e">
snakemake/parser.py
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<li class="file-stats">
<a href="#93a82c4f9627ca07fc8ef809981ab851baae987e">
snakemake/remote/AzBlob.py
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<li class="file-stats">
<a href="#7e910b8868374c8ee0002ac6d034da0012544b27">
snakemake/remote/GS.py
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<li class="file-stats">
<a href="#0ac0ac393192e0b6a8ebf767dd5e206b4afbf3b2">
snakemake/scheduler.py
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<li class="file-stats">
<a href="#cb9e107597e441fb1c0d61663359d9cf1dbfe04d">
snakemake/workflow.py
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<li class="file-stats">
<a href="#d1deee71de70305809d43086b13f7eb407aff6f2">
test-environment.yml
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<li class="file-stats">
<a href="#8170eb84634a720714408bf5991cf0fe862aedc8">
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+
tests/test_peppy/pep/config.yaml
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<li class="file-stats">
<a href="#30236538d99508b82b584f45580c3c0df56c0e7c">
<span class="new-file">
+
tests/test_peppy/pep/sample_table.csv
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<li class="file-stats">
<a href="#bcab5d626d6045306643ffe54e563626806802d8">
<span class="new-file">
+
tests/test_peppy/workflow/Snakefile
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<li class="file-stats">
<a href="#e76fdd319bd72c5dffe8ebaa1ce6374f9188f2b7">
<span class="new-file">
+
tests/test_peppy/workflow/schemas/pep.yaml
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<h4>Changes:</h4>
<li id="45267e3a9556cafa9cb7b61dab7a3b6659e73aad">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/4b95c63220e2d1360913804c11116ddd7a1a7fa6...a056d4757cee7ceeb9fa894d04268a56381678a2#45267e3a9556cafa9cb7b61dab7a3b6659e73aad"><strong>CHANGELOG.rst</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">[5.23.0] - 2020-08-24</span>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">=====================</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Added</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">-----</span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">- Support for workflow configuration via portable encapsulated projects (PEPs, https://pep.databio.org).</span>
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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">- A new ILP based default scheduler now ensures that temporary files are deleted as fast as possible (@FelixMoelder, @johanneskoester).</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Changed</span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">-------</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">- Fixed bug in modification date comparison for files in google storage (@vsoch).</span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">- Various small documentation improvements (@dcroote, @erjel, @dlaehnemann, @goi42).</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"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">[5.22.1] - 2020-08-14</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">Changed</span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/4b95c63220e2d1360913804c11116ddd7a1a7fa6...a056d4757cee7ceeb9fa894d04268a56381678a2#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</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">@@ -6,7 +6,7 @@</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"><span class="gh" style="color: #999;"># Snakemake</span></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/4b95c63220e2d1360913804c11116ddd7a1a7fa6...a056d4757cee7ceeb9fa894d04268a56381678a2#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">snakemake (5.23.0-1) 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"> * New upstream release.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Add new dependency python3-pulp.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Remove unnecessary test skips, and document remaining ones.</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"> -- Rebecca N. Palmer <rebecca_palmer@zoho.com> Sat, 29 Aug 2020 11:46:20 +0100</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">snakemake (5.22.1-1) unstable; urgency=medium</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"> * New upstream release. Refresh patches.</span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/4b95c63220e2d1360913804c11116ddd7a1a7fa6...a056d4757cee7ceeb9fa894d04268a56381678a2#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">@@ -7,6 +7,7 @@ Build-Depends: ca-certificates,</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> cwltool,</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> debhelper-compat (= 13),</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> dh-python,</span>
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<td class="diff-line-num new new_line" data-linenumber="10" 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">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> environment-modules,</span>
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<td class="diff-line-num old_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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<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="plaintext"> imagemagick,</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="12" 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">
12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> python3,</span>
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<td class="diff-line-num old_line" data-linenumber="12" 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">
12
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<td class="diff-line-num new_line" data-linenumber="13" 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">
13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> python3-appdirs,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -26,6 +27,7 @@ Build-Depends: ca-certificates,</td>
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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
26
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<td class="diff-line-num new_line" data-linenumber="27" 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">
27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> python3-pandas,</span>
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<td class="diff-line-num old_line" data-linenumber="27" 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">
27
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<td class="diff-line-num new_line" data-linenumber="28" 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">
28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> python3-pkg-resources,</span>
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<td class="diff-line-num old_line" data-linenumber="28" 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">
28
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<td class="diff-line-num new_line" data-linenumber="29" 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">
29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> python3-psutil,</span>
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<td class="diff-line-num new old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="30" 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">
30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> python3-pulp,</span>
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<td class="diff-line-num old_line" data-linenumber="29" 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">
29
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<td class="diff-line-num new_line" data-linenumber="31" 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">
31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> python3-pygments,</span>
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<td class="diff-line-num old_line" data-linenumber="30" 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">
30
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<td class="diff-line-num new_line" data-linenumber="32" 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">
32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> python3-pygraphviz,</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="31" 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">
31
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<td class="diff-line-num new_line" data-linenumber="33" 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">
33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> python3-pytest,</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="68" 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="70" 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">@@ -68,6 +70,7 @@ Depends: ca-certificates,</td>
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<td class="diff-line-num old_line" data-linenumber="68" 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">
68
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<td class="diff-line-num new_line" data-linenumber="70" 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">
70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext"> python3-nbformat,</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="69" 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">
69
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<td class="diff-line-num new_line" data-linenumber="71" 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">
71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="plaintext"> python3-pkg-resources,</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="70" 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">
70
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<td class="diff-line-num new_line" data-linenumber="72" 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">
72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext"> python3-psutil,</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="73" 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">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> python3-pulp,</span>
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<td class="diff-line-num old_line" data-linenumber="71" 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">
71
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<td class="diff-line-num new_line" data-linenumber="74" 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">
74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext"> python3-ratelimiter,</span>
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<td class="diff-line-num old_line" data-linenumber="72" 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">
72
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<td class="diff-line-num new_line" data-linenumber="75" 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">
75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext"> python3-requests,</span>
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<td class="diff-line-num old_line" data-linenumber="73" 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">
73
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<td class="diff-line-num new_line" data-linenumber="76" 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">
76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext"> python3-toposort,</span>
</pre>
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<br>
</li>
<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/4b95c63220e2d1360913804c11116ddd7a1a7fa6...a056d4757cee7ceeb9fa894d04268a56381678a2#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -6,21 +6,21 @@</td>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">export PYBUILD_NAME=snakemake</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">
7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">export PYBUILD_DESTDIR_python3=debian/snakemake</span>
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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">export PYBUILD_BEFORE_TEST_python3=chmod +x {dir}/bin/snakemake; cp -r {dir}/bin {dir}/tests {build_dir}</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">export PYBUILD_TEST_ARGS=python{version} -m pytest -v tests/test*.py -k 'not <span class="idiff left right">report and not ancient and not test_script and not default_remote and not issue635 and not convert_to_cwl and not issue1083 and not issue1092 and not issue1093 and not test_remote and not test_default_resources and not test_tibanna and not test_github_issue78 and not test_output_file_cache_remote and not test_env_modules and not test_archive and not test_container and not test_jupyter_notebook and not test_conda and not test_upstream_conda and not test_conda_custom_prefix and not test_wrapper</span>'</span>
</pre>
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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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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"># <span class="idiff left right">test_report</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"># <span class="idiff left right">test_ancient</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"># <span class="idiff left right">test_script requires conda; manually disabling conda show the need for the binary 'julia'</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"># <span class="idiff left right">test_default_remote requires network access</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"># <span class="idiff left right">test_issue634 requires conda, but passes when conda is turned off manually</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"># <span class="idiff left right">test_convert_to_cwl tries to build a singularity format software image from docker://quay.io/snakemake/snakemake:v5.5.4</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"><span class="idiff left right"># test_issue1083 tries to build a singularity format software image from docker://bash</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"># <span class="idiff left right">test_issue1093 fails due to conda usage; commenting that out and installing bwa produces a different ordering than desired</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"># <span class="idiff left right">test_default_resources and test_remote needs moto to be packaged https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=777089</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"># <span class="idiff left right">test_env_modules relies on "module load" which is not packaged for Debian</span></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"><span class="idiff left right"># test_archive, test_jupyter_notebook, test_conda, test_upstream_conda, test_conda_custom_prefix use conda</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"># <span class="idiff left right">test_wrapper uses conda and a downloaded file</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"># <span class="idiff left right">test_container uses docker://bash</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">export PYBUILD_TEST_ARGS=python{version} -m pytest -v tests/test*.py -k 'not <span class="idiff left right">test_cwl and not test_cwl_singularity and not test_url_include and not test_wrapper and not test_issue1083 and not test_github_issue78 and not test_container and not test_singularity and not test_singularity_conda and not test_convert_to_cwl and not test_report and not test_report_zip and not test_archive and not test_jupyter_notebook and not test_conda and not test_upstream_conda and not test_conda_custom_prefix and not test_script and not test_issue635 and not test_issue1093 and not test_default_resources and not test_default_remote and not test_remote and not test_output_file_cache_remote and not test_tibanna and not test_ancient</span>'</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 class="idiff left right">Skipped because they download executables (which is forbidden in Debian buildd and debci)</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"># <span class="idiff left right">Snakefile/snakemake-wrapper/CWL scripts: test_cwl, test_cwl_singularity, test_url_include, test_wrapper</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"># <span class="idiff left right">Docker images: test_issue1083, test_github_issue78, test_container, test_singularity, test_singularity_conda, test_cwl_singularity, test_convert_to_cwl, test_report, test_report_zip</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"># <span class="idiff left right">Conda packages: test_archive, test_jupyter_notebook, test_conda, test_upstream_conda, test_conda_custom_prefix, test_wrapper, test_script, test_issue635, test_issue1093, test_singularity_conda, test_report, test_report_zip</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"># <span class="idiff left right">Note that even if conda were added to Debian (ITP #926416), using it normally would still be downloading executables = forbidden</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"># <span class="idiff left right">Modification to run without conda was previously attempted on test_issue635 (succeeded) and test_issue1093 (failed as current bwa gives a different ordering), but is not in current use</span></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"># <span class="idiff left right">Skipped due to not-in-Debian dependencies</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"># <span class="idiff left right">python3-moto (RFP #777089): test_default_resources, test_default_remote, test_remote, test_output_file_cache_remote</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"># <span class="idiff left right">python3-tibanna: test_tibanna</span></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 class="idiff left right">Skipped in build due to network use, but run in autopkgtest: test_ancient</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"># <span class="idiff left right">Tests marked @connected skip themselves in this case</span></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">export PYBUILD_AFTER_TEST_python3=rm -fr {build_dir}/bin {build_dir}/tests {dir}/tests/test_filegraph/.snakemake/ {dir}/tests/linting/*/.snakemake/</span>
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<pre style="margin: 0;"> <span id="LC26" 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">@@ -44,5 +44,6 @@ override_dh_auto_install:</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> find . -name '*.pyc' | xargs rm -Rf</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> find debian -name '.gitignore' | xargs rm -Rf</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"># the modules.sh is a workaround for #928826; putting it in PYBUILD_BEFORE_TEST_python3 doesn't work</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"> PYBUILD_SYSTEM=custom dh_auto_test</span></pre>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> <span class="idiff left right">. /etc/profile.d/modules.sh && </span>PYBUILD_SYSTEM=custom dh_auto_test</span></pre>
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<li id="83223a554d33ba7e1888274ff8ac43adb8147ba0">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/4b95c63220e2d1360913804c11116ddd7a1a7fa6...a056d4757cee7ceeb9fa894d04268a56381678a2#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/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">@@ -5,5 +5,10 @@ Restrictions: allow-stderr</td>
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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"># upstream's tests</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">Depends: snakemake, python3-pandas, python3-pytest, python3-pygraphviz, stress</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Depends: snakemake,</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> environment-modules,</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> python3-pygraphviz,</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> python3-pandas,</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> python3-pytest,</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> stress</span>
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9
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/4b95c63220e2d1360913804c11116ddd7a1a7fa6...a056d4757cee7ceeb9fa894d04268a56381678a2#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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">@@ -17,6 +17,9 @@ cd "${AUTOPKGTEST_TMP}"</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">HOME</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># workaround for #928826</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">.</span> /etc/profile.d/modules.sh</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#See debian/rules for why these are excluded</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell">python3 <span class="nt" style="color: #000080;">-m</span> pytest <span class="nt" style="color: #000080;">-v</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">ROOT</span><span class="k" style="font-weight: 600;">}</span>/tests/test<span class="k" style="font-weight: 600;">*</span>.py <span class="nt" style="color: #000080;">-k</span> <span class="s1" style="color: #d14;">'not <span class="idiff left right">report and not ancient and not test_script and not default_remote and not issue635 and not convert_to_cwl and not issue1083 and not issue1092 and not issue1093 and not test_remote and not test_default_resources and not test_singularity and not test_singularity_conda and not test_cwl_singularity and not test_cwl and not test_url_include and not test_tibanna and not test_github_issue78 and not test_output_file_cache_remote and not test_env_modules and not test_archive and not test_container and not test_jupyter_notebook and not test_conda and not test_upstream_conda and not test_conda_custom_prefix and not test_wrapper</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell">python3 <span class="nt" style="color: #000080;">-m</span> pytest <span class="nt" style="color: #000080;">-v</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">ROOT</span><span class="k" style="font-weight: 600;">}</span>/tests/test<span class="k" style="font-weight: 600;">*</span>.py <span class="nt" style="color: #000080;">-k</span> <span class="s1" style="color: #d14;">'not <span class="idiff left right">test_cwl and not test_cwl_singularity and not test_url_include and not test_wrapper and not test_issue1083 and not test_github_issue78 and not test_container and not test_singularity and not test_singularity_conda and not test_convert_to_cwl and not test_report and not test_report_zip and not test_archive and not test_jupyter_notebook and not test_conda and not test_upstream_conda and not test_conda_custom_prefix and not test_script and not test_issue635 and not test_issue1093 and not test_default_resources and not test_default_remote and not test_remote and not test_output_file_cache_remote and not test_tibanna</span>'</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"></span></pre>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/4b95c63220e2d1360913804c11116ddd7a1a7fa6...a056d4757cee7ceeb9fa894d04268a56381678a2#3c7246c0b371cfd3a475428be04706178ca01f0f"><strong>docs/project_info/faq.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">@@ -515,7 +515,23 @@ If you are just interested in the final summary, you can use the ``--quiet`` fla</td>
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<pre style="margin: 0;"> <span id="LC515" class="line" lang="plaintext">Git is messing up the modification times of my input files, what can I do?</span>
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<pre style="margin: 0;"> <span id="LC516" class="line" lang="plaintext">--------------------------------------------------------------------------</span>
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<pre style="margin: 0;"> <span id="LC517" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC518" class="line" lang="plaintext">When you checkout a git repository, the modification times of updated files are set to the time of the checkout. If you rely on these files as input **and** output files in your workflow, this can cause trouble. For example, Snakemake could think that a certain (git-tracked) output has to be re-executed, just because its input has been checked out a bit later. In such cases, it is advisable to set the file modification dates to the last commit date after an update has been pulled. See `here <https://stackoverflow.com/questions/2458042/restore-files-modification-time-in-git/22638823#22638823>`_ for a solution to achieve this.</span>
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="plaintext">When you checkout a git repository, the modification times of updated files are set to the time of the checkout. If you rely on these files as input **and** output files in your workflow, this can cause trouble. For example, Snakemake could think that a certain (git-tracked) output has to be re-executed, just because its input has been checked out a bit later. In such cases, it is advisable to set the file modification dates to the last commit date after an update has been pulled. One solution is to add the following lines to your ``.bashrc`` (or similar):</span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="plaintext">.. code-block:: bash</span>
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521
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="plaintext"> gitmtim(){</span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="plaintext"> local f</span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="plaintext"> for f; do</span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="plaintext"> touch -d @0`git log --pretty=%at -n1 -- "$f"` "$f"</span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="plaintext"> done</span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="plaintext"> }</span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="plaintext"> gitmodtimes(){</span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="plaintext"> for f in $(git ls-tree -r $(git rev-parse --abbrev-ref HEAD) --name-only); do</span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="plaintext"> gitmtim $f</span>
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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="plaintext"> done</span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="plaintext"> }</span>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="plaintext">(inspired by the answer `here <https://stackoverflow.com/questions/2458042/restore-files-modification-time-in-git/22638823#22638823>`_). You can then run ``gitmodtimes`` to update the modification times of all tracked files on the current branch to their last commit time in git; BE CAREFUL--this does not account for local changes that have not been commited.</span>
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="plaintext">How do I exit a running Snakemake workflow?</span>
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<pre style="margin: 0;"> <span id="LC537" class="line" lang="plaintext">-------------------------------------------</span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/4b95c63220e2d1360913804c11116ddd7a1a7fa6...a056d4757cee7ceeb9fa894d04268a56381678a2#9b54be2cff8d0de677b1245d0b0dc07cca021923"><strong>docs/snakefiles/configuration.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">@@ -158,6 +158,41 @@ the schema for validating the samples data frame looks like this:</td>
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158
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="plaintext">Here, in case the case column is missing, the validate function will</span>
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159
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="plaintext">populate it with True for all entries.</span>
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160
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="plaintext"></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext">.. _snakefiles-peps:</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext"></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext">-------------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext">Configuring scientific experiments via PEPs</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext">-------------------------------------------</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext"></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext">Often scientific experiments consist of a set of samples (with optional subsamples), for which raw data and metainformation is known.</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext">Instead of writing custom sample sheets as shown above, Snakemake allows to use `portable encapsulated project (PEP) <http://pep.databio.org>`_ definitions to configure a workflow.</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext">This is done via a special directive `pepfile`, that can optionally complemented by a schema for validation (which is recommended for production workflows):</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext"></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext">.. code-block:: python</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext"></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext"> pepfile: "pep/config.yaml"</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext"> pepschema: "schemas/pep.yaml"</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext"></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext"> rule all:</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext"> input:</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext"> expand("{sample}.txt", sample=pep.sample_table["sample_name"])</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext"></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext"> rule a:</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext"> output:</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext"> "{sample}.txt"</span>
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<td class="diff-line-num new new_line" data-linenumber="183" 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">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext"> shell:</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext"> "touch {output}"</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext"></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext">Using the ``pepfile`` directive leads to parsing of the provided PEP with `peppy <http://peppy.databio.org>`_.</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext">The resulting project object is made globally available under the name ``pep``.</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext">Here, we use it to aggregate over the set of sample names that is defined in the corresponding PEP.</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext"></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">**Importantly**, note that PEPs are meant to contain sample metadata and any global information about a project or experiment. </span>
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext">They should **not** be used to encode workflow specific configuration options.</span>
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext">For those, one should always complement the pepfile with an ordinary :ref:`config file <snakefiles_standard_configuration>`.</span>
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext">The rationale is that PEPs should be portable between different data analysis workflows (that could be applied to the same data) and even between workflow management systems.</span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext">In other words, a PEP should describe everything needed about the data, while a workflow and its configuration should describe everything needed about the analysis that is applied to it.</span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="plaintext">.. _snakefiles-cluster_configuration:</span>
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="plaintext">----------------------------------</span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/4b95c63220e2d1360913804c11116ddd7a1a7fa6...a056d4757cee7ceeb9fa894d04268a56381678a2#945ec74fc1c17902d98bca84b7a1f0dfd755c01b"><strong>docs/snakefiles/deployment.rst</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="112" 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">@@ -112,7 +112,7 @@ The path to the environment definition is interpreted as **relative to the Snake</td>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="plaintext">Snakemake will store the environment persistently in ``.snakemake/conda/$hash`` with ``$hash`` being the MD5 hash of the environment definition file content. This way, updates to the environment definition are automatically detected.</span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="plaintext">Note that you need to clean up environments manually for now. However, in many cases they are lightweight and consist of symlinks to your central conda installation.</span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="plaintext">Conda deployment also works well for offline or air-gapped environments. Running ``snakemake -<span class="idiff left right">n --use-conda -</span>-create-envs-only`` will only install the required conda environments without running the full workflow. Subsequent runs with ``--use-conda`` will make use of the local environments without requiring internet access.</span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">Conda deployment also works well for offline or air-gapped environments. Running ``snakemake -<span class="idiff left right">-use-conda --conda</span>-create-envs-only`` will only install the required conda environments without running the full workflow. Subsequent runs with ``--use-conda`` will make use of the local environments without requiring internet access.</span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="plaintext">.. _singularity:</span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/4b95c63220e2d1360913804c11116ddd7a1a7fa6...a056d4757cee7ceeb9fa894d04268a56381678a2#dfeb7b6e739ba66056c1799c63a5a39c7698b59f"><strong>docs/snakefiles/rules.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">@@ -263,7 +263,11 @@ In particular, it should be noted that the specified threads have to be seen as</td>
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="plaintext">Hardcoding a particular maximum number of threads like above is useful when a certain tool has a natural maximum beyond which parallelization won't help to further speed it up.</span>
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="plaintext">This is often the case, and should be evaluated carefully for production workflows.</span>
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="plaintext">If it is certain that no such maximum exists for a tool, one can instead define threads as a function of the number of cores given to Snakemake:</span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="plaintext">Also, setting a ``threads:`` maximum is required to achieve parallelism in tools that (often implicitly and without the user knowing) rely on an environment variable for the maximum of cores to use.</span>
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="plaintext">For example, this is the case for many linear algebra libraries and for OpenMP.</span>
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="plaintext">Snakemake limits the respective environment variables to one core by default, to avoid unexpected and unlimited core-grabbing, but will override this with the ``threads:`` you specify in a rule (the parameters set to ``threads:``, or defaulting to ``1``, are: ``OMP_NUM_THREADS``, ``GOTO_NUM_THREADS``, ``OPENBLAS_NUM_THREADS``, ``MKL_NUM_THREADS``, ``VECLIB_MAXIMUM_THREADS``, ``NUMEXPR_NUM_THREADS``).</span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="plaintext">If it is certain that no maximum for efficient parallelism exists for a tool, one can instead define threads as a function of the number of cores given to Snakemake:</span>
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267
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="plaintext"></span>
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268
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272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="plaintext">.. code-block:: python</span>
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269
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273
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="plaintext"></span>
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<li id="8e2edce0d507e1297474f25c00cae94258db38d8">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/4b95c63220e2d1360913804c11116ddd7a1a7fa6...a056d4757cee7ceeb9fa894d04268a56381678a2#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -67,6 +67,7 @@ setup(</td>
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67
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"> <span class="s" style="color: #d14;">"psutil"</span><span class="p">,</span></span>
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68
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"> <span class="s" style="color: #d14;">"nbformat"</span><span class="p">,</span></span>
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69
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="s" style="color: #d14;">"toposort"</span><span class="p">,</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="s" style="color: #d14;">"pulp"</span><span class="p">,</span></span>
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70
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="p">],</span></span>
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71
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">extras_require</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span></span>
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72
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"> <span class="s" style="color: #d14;">"reports"</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">"jinja2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"networkx"</span><span class="p">,</span> <span class="s" style="color: #d14;">"pygments"</span><span class="p">,</span> <span class="s" style="color: #d14;">"pygraphviz"</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">@@ -77,6 +78,10 @@ setup(</td>
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77
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"> <span class="s" style="color: #d14;">"google-api-python-client"</span><span class="p">,</span></span>
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78
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="s" style="color: #d14;">"google-cloud-storage"</span><span class="p">,</span></span>
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79
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"> <span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="s" style="color: #d14;">"pep"</span><span class="p">:</span> <span class="p">[</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="s" style="color: #d14;">"peppy"</span><span class="p">,</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="s" style="color: #d14;">"eido"</span><span class="p">,</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="p">]</span></span>
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"> <span class="p">},</span></span>
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81
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">classifiers</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <span class="s" style="color: #d14;">"Development Status :: 5 - Production/Stable"</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/4b95c63220e2d1360913804c11116ddd7a1a7fa6...a056d4757cee7ceeb9fa894d04268a56381678a2#d366205d7cd679ff6d4a61f70728e92537101763"><strong>snakemake/__init__.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -137,6 +137,7 @@ def snakemake(</td>
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137
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">list_conda_envs</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">singularity_prefix</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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139
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">shadow_prefix</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">scheduler</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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140
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">conda_create_envs_only</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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141
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Mode</span><span class="p">.</span><span class="n" style="color: #333;">default</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">wrapper_prefix</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</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">@@ -276,6 +277,7 @@ def snakemake(</td>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="python"><span class="s" style="color: #d14;"> keep_incomplete (bool): keep incomplete output files of failed jobs</span></span>
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="python"><span class="s" style="color: #d14;"> edit_notebook (object): "notebook.Listen" object to configuring notebook server for interactive editing of a rule notebook. If None, do not edit.</span></span>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="python"><span class="s" style="color: #d14;"> log_handler (list): redirect snakemake output to this list of custom log handler, each a function that takes a log message dictionary (see below) as its only argument (default []). The log message dictionary for the log handler has to following entries:</span></span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="python"><span class="s" style="color: #d14;"> scheduler (str): Select scheduling algorithm (default ilp)</span></span>
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="python"><span class="s" style="color: #d14;"> :level:</span></span>
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="python"><span class="s" style="color: #d14;"> the log level ("info", "error", "debug", "progress", "job_info")</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">@@ -517,6 +519,7 @@ def snakemake(</td>
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517
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<pre style="margin: 0;"> <span id="LC519" class="line" lang="python"> <span class="n" style="color: #333;">singularity_prefix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">singularity_prefix</span><span class="p">,</span></span>
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518
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520
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="python"> <span class="n" style="color: #333;">shadow_prefix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shadow_prefix</span><span class="p">,</span></span>
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519
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521
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<pre style="margin: 0;"> <span id="LC521" class="line" lang="python"> <span class="n" style="color: #333;">singularity_args</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">singularity_args</span><span class="p">,</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="python"> <span class="n" style="color: #333;">scheduler_type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">scheduler</span><span class="p">,</span></span>
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520
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523
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<pre style="margin: 0;"> <span id="LC523" class="line" lang="python"> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">mode</span><span class="p">,</span></span>
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521
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<pre style="margin: 0;"> <span id="LC524" class="line" lang="python"> <span class="n" style="color: #333;">wrapper_prefix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">wrapper_prefix</span><span class="p">,</span></span>
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525
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<pre style="margin: 0;"> <span id="LC525" class="line" lang="python"> <span class="n" style="color: #333;">printshellcmds</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">printshellcmds</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">@@ -605,6 +608,7 @@ def snakemake(</td>
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605
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608
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<pre style="margin: 0;"> <span id="LC608" class="line" lang="python"> <span class="n" style="color: #333;">singularity_prefix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">singularity_prefix</span><span class="p">,</span></span>
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606
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609
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<pre style="margin: 0;"> <span id="LC609" class="line" lang="python"> <span class="n" style="color: #333;">shadow_prefix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shadow_prefix</span><span class="p">,</span></span>
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607
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610
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<pre style="margin: 0;"> <span id="LC610" class="line" lang="python"> <span class="n" style="color: #333;">singularity_args</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">singularity_args</span><span class="p">,</span></span>
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611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="python"> <span class="n" style="color: #333;">scheduler</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">scheduler</span><span class="p">,</span></span>
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608
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612
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<pre style="margin: 0;"> <span id="LC612" class="line" lang="python"> <span class="n" style="color: #333;">list_conda_envs</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">list_conda_envs</span><span class="p">,</span></span>
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609
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613
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<pre style="margin: 0;"> <span id="LC613" class="line" lang="python"> <span class="n" style="color: #333;">kubernetes</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">kubernetes</span><span class="p">,</span></span>
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610
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614
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<pre style="margin: 0;"> <span id="LC614" class="line" lang="python"> <span class="n" style="color: #333;">container_image</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">container_image</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="628" 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="632" 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">@@ -628,6 +632,7 @@ def snakemake(</td>
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628
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632
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<pre style="margin: 0;"> <span id="LC632" class="line" lang="python"> <span class="n" style="color: #333;">targets</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">targets</span><span class="p">,</span></span>
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629
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633
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<pre style="margin: 0;"> <span id="LC633" class="line" lang="python"> <span class="n" style="color: #333;">dryrun</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">dryrun</span><span class="p">,</span></span>
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630
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634
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="python"> <span class="n" style="color: #333;">touch</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">touch</span><span class="p">,</span></span>
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635
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="python"> <span class="n" style="color: #333;">scheduler_type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">scheduler</span><span class="p">,</span></span>
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631
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636
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<pre style="margin: 0;"> <span id="LC636" class="line" lang="python"> <span class="n" style="color: #333;">local_cores</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">local_cores</span><span class="p">,</span></span>
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632
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637
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<pre style="margin: 0;"> <span id="LC637" class="line" lang="python"> <span class="n" style="color: #333;">forcetargets</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">forcetargets</span><span class="p">,</span></span>
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638
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<pre style="margin: 0;"> <span id="LC638" class="line" lang="python"> <span class="n" style="color: #333;">forceall</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">forceall</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">@@ -1147,6 +1152,16 @@ def get_argument_parser(profile=None):</td>
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1147
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1152
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<pre style="margin: 0;"> <span id="LC1152" class="line" lang="python"> <span class="s" style="color: #d14;">"If not supplied, the value is set to the '.snakemake' directory relative "</span></span>
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1153
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<pre style="margin: 0;"> <span id="LC1153" class="line" lang="python"> <span class="s" style="color: #d14;">"to the working directory."</span></span>
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1149
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1154
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<pre style="margin: 0;"> <span id="LC1154" class="line" lang="python"> <span class="p">),</span></span>
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1155
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<pre style="margin: 0;">+<span id="LC1155" class="line" lang="python"> <span class="p">),</span></span>
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1156
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<pre style="margin: 0;">+<span id="LC1156" class="line" lang="python"> <span class="n" style="color: #333;">group_exec</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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1157
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<pre style="margin: 0;">+<span id="LC1157" class="line" lang="python"> <span class="s" style="color: #d14;">"--scheduler"</span><span class="p">,</span></span>
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1158
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<pre style="margin: 0;">+<span id="LC1158" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"ilp"</span><span class="p">,</span></span>
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1159
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<pre style="margin: 0;">+<span id="LC1159" class="line" lang="python"> <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"?"</span><span class="p">,</span></span>
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1160
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<pre style="margin: 0;">+<span id="LC1160" class="line" lang="python"> <span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"ilp"</span><span class="p">,</span> <span class="s" style="color: #d14;">"greedy"</span><span class="p">],</span></span>
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1161
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<pre style="margin: 0;">+<span id="LC1161" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span></span>
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1162
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<pre style="margin: 0;">+<span id="LC1162" class="line" lang="python"> <span class="s" style="color: #d14;">"Specifies if jobs are selected by a greedy algorithm or by solving an ilp. "</span></span>
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1163
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<pre style="margin: 0;">+<span id="LC1163" class="line" lang="python"> <span class="s" style="color: #d14;">"The ilp scheduler aims to reduce runtime and hdd usage by best possible use of resources."</span></span>
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1164
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<pre style="margin: 0;">+<span id="LC1164" class="line" lang="python"> <span class="p">),</span></span>
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1150
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1165
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<pre style="margin: 0;"> <span id="LC1165" class="line" lang="python"> <span class="p">)</span></span>
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1151
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1166
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<pre style="margin: 0;"> <span id="LC1166" class="line" lang="python"></span>
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1152
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1167
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<pre style="margin: 0;"> <span id="LC1167" class="line" lang="python"> <span class="n" style="color: #333;">group_report</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">"REPORTS"</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">@@ -2371,6 +2386,7 @@ def main(argv=None):</td>
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2371
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2386
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<pre style="margin: 0;"> <span id="LC2386" class="line" lang="python"> <span class="n" style="color: #333;">singularity_prefix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">singularity_prefix</span><span class="p">,</span></span>
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2372
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2387
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<pre style="margin: 0;"> <span id="LC2387" class="line" lang="python"> <span class="n" style="color: #333;">shadow_prefix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">shadow_prefix</span><span class="p">,</span></span>
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2373
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2388
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<pre style="margin: 0;"> <span id="LC2388" class="line" lang="python"> <span class="n" style="color: #333;">singularity_args</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">singularity_args</span><span class="p">,</span></span>
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2389
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<pre style="margin: 0;">+<span id="LC2389" class="line" lang="python"> <span class="n" style="color: #333;">scheduler</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">scheduler</span><span class="p">,</span></span>
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2374
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2390
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<pre style="margin: 0;"> <span id="LC2390" class="line" lang="python"> <span class="n" style="color: #333;">conda_create_envs_only</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">conda_create_envs_only</span><span class="p">,</span></span>
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2375
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2391
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<pre style="margin: 0;"> <span id="LC2391" class="line" lang="python"> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">mode</span><span class="p">,</span></span>
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2376
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2392
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<pre style="margin: 0;"> <span id="LC2392" class="line" lang="python"> <span class="n" style="color: #333;">wrapper_prefix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">wrapper_prefix</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/4b95c63220e2d1360913804c11116ddd7a1a7fa6...a056d4757cee7ceeb9fa894d04268a56381678a2#5e16cbeea010f59dbef52f8950f4873c94f39c7e"><strong>snakemake/_version.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">@@ -22,9 +22,9 @@ def get_keywords():</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># setup.py/versioneer.py will grep for the variable names, so they must</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;"># each be defined on a line of their own. _version.py will just call</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;"># get_keywords().</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">git_refnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" (HEAD -> master, tag: v5.2<span class="idiff left right">2.1</span>)"</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">git_full</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">982f1d1f5bb55eda1caa8f15853041922ef4bea</span>0"</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">git_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2020-08-<span class="idiff left right">14 08:41:41</span> +0200"</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">git_refnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" (HEAD -> master, tag: v5.2<span class="idiff left right">3.0</span>)"</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">git_full</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">5c2f2b133fff051a8386625ead1c4a4bf04dbae</span>0"</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">git_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2020-08-<span class="idiff left right">24 15:07:04</span> +0200"</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">keywords</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"refnames"</span><span class="p">:</span> <span class="n" style="color: #333;">git_refnames</span><span class="p">,</span> <span class="s" style="color: #d14;">"full"</span><span class="p">:</span> <span class="n" style="color: #333;">git_full</span><span class="p">,</span> <span class="s" style="color: #d14;">"date"</span><span class="p">:</span> <span class="n" style="color: #333;">git_date</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">keywords</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/4b95c63220e2d1360913804c11116ddd7a1a7fa6...a056d4757cee7ceeb9fa894d04268a56381678a2#d70c11793454d64a7b2d77ced116226d2f13378e"><strong>snakemake/parser.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">@@ -212,9 +212,7 @@ class RuleKeywordState(KeywordState):</td>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="s" style="color: #d14;">"@workflow.{keyword}("</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">keyword</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">keyword</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SubworkflowKeywordState</span><span class="p">(</span><span class="n" style="color: #333;">KeywordState</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Subworkflow"</span></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SectionKeywordState</span><span class="p">(</span><span class="n" style="color: #333;">KeywordState</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">start</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="LC217" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="s" style="color: #d14;">", {keyword}="</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">keyword</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">keyword</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC218" 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">@@ -244,6 +242,17 @@ class Configfile(GlobalKeywordState):</td>
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># PEPs</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Pepfile</span><span class="p">(</span><span class="n" style="color: #333;">GlobalKeywordState</span><span class="p">):</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Pepschema</span><span class="p">(</span><span class="n" style="color: #333;">GlobalKeywordState</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Report</span><span class="p">(</span><span class="n" style="color: #333;">GlobalKeywordState</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="283" 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">@@ -283,6 +292,10 @@ class GlobalContainer(GlobalKeywordState):</td>
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># subworkflows</span></span>
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SubworkflowKeywordState</span><span class="p">(</span><span class="n" style="color: #333;">SectionKeywordState</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="python"> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Subworkflow"</span></span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SubworkflowSnakefile</span><span class="p">(</span><span class="n" style="color: #333;">SubworkflowKeywordState</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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301
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<pre style="margin: 0;"> <span id="LC301" 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">@@ -777,6 +790,8 @@ class Python(TokenAutomaton):</td>
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777
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790
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<pre style="margin: 0;"> <span id="LC790" class="line" lang="python"> <span class="n" style="color: #333;">include</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Include</span><span class="p">,</span></span>
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791
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<pre style="margin: 0;"> <span id="LC791" class="line" lang="python"> <span class="n" style="color: #333;">workdir</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Workdir</span><span class="p">,</span></span>
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779
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792
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<pre style="margin: 0;"> <span id="LC792" class="line" lang="python"> <span class="n" style="color: #333;">configfile</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Configfile</span><span class="p">,</span></span>
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793
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="python"> <span class="n" style="color: #333;">pepfile</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Pepfile</span><span class="p">,</span></span>
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794
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="python"> <span class="n" style="color: #333;">pepschema</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Pepschema</span><span class="p">,</span></span>
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780
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795
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<pre style="margin: 0;"> <span id="LC795" class="line" lang="python"> <span class="n" style="color: #333;">report</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Report</span><span class="p">,</span></span>
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796
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<pre style="margin: 0;"> <span id="LC796" class="line" lang="python"> <span class="n" style="color: #333;">ruleorder</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Ruleorder</span><span class="p">,</span></span>
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797
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<pre style="margin: 0;"> <span id="LC797" class="line" lang="python"> <span class="n" style="color: #333;">rule</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Rule</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/4b95c63220e2d1360913804c11116ddd7a1a7fa6...a056d4757cee7ceeb9fa894d04268a56381678a2#93a82c4f9627ca07fc8ef809981ab851baae987e"><strong>snakemake/remote/AzBlob.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">@@ -292,9 +292,7 @@ class AzureStorageHelper(object):</td>
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292
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># just create an empty file with the right timestamps</span></span>
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293
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python"> <span class="n" style="color: #333;">ts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">get_blob_properties</span><span class="p">().</span><span class="n" style="color: #333;">last_modified</span><span class="p">.</span><span class="n" style="color: #333;">timestamp</span><span class="p">()</span></span>
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294
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">destination_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"wb"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fp</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">utime</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="python"> <span class="n" style="color: #333;">fp</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">ts</span><span class="p">,</span> <span class="n" style="color: #333;">ts</span><span class="p">),</span></span>
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297
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">utime</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">ts</span><span class="p">,</span> <span class="n" style="color: #333;">ts</span><span class="p">))</span></span>
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298
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">destination_path</span></span>
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297
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="python"></span>
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298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">delete_from_container</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">container_name</span><span class="p">,</span> <span class="n" style="color: #333;">blob_name</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/4b95c63220e2d1360913804c11116ddd7a1a7fa6...a056d4757cee7ceeb9fa894d04268a56381678a2#7e910b8868374c8ee0002ac6d034da0012544b27"><strong>snakemake/remote/GS.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">@@ -143,7 +143,7 @@ class RemoteObject(AbstractRemoteObject):</td>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># By way of being listed, it exists. mtime is a datetime object</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"{}/{}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">blob</span><span class="p">.</span><span class="n" style="color: #333;">bucket</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">blob</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="LC145" class="line" lang="python"> <span class="n" style="color: #333;">cache</span><span class="p">.</span><span class="n" style="color: #333;">exists_remote</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">cache</span><span class="p">.</span><span class="n" style="color: #333;">mtime</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">blob</span><span class="p">.</span><span class="n" style="color: #333;">updated</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">cache</span><span class="p">.</span><span class="n" style="color: #333;">mtime</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">blob</span><span class="p">.</span><span class="n" style="color: #333;">updated</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">timestamp</span></span><span class="p"><span class="idiff right">()</span></span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">cache</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">blob</span><span class="p">.</span><span class="n" style="color: #333;">size</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Mark bucket and prefix as having an inventory, such that this method is</span></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/4b95c63220e2d1360913804c11116ddd7a1a7fa6...a056d4757cee7ceeb9fa894d04268a56381678a2#0ac0ac393192e0b6a8ebf767dd5e206b4afbf3b2"><strong>snakemake/scheduler.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">@@ -6,11 +6,14 @@ __license__ = "MIT"</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span><span class="p">,</span> <span class="n" style="color: #333;">signal</span><span class="p">,</span> <span class="n" style="color: #333;">sys</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">threading</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">operator</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">time</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">math</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">functools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">partial</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;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">defaultdict</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">itertools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">chain</span><span class="p">,</span> <span class="n" style="color: #333;">accumulate</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">itertools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">chain</span><span class="p">,</span> <span class="n" style="color: #333;">accumulate</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">product</span></span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">contextlib</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ContextDecorator</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;"><span class="idiff left">import</span></span><span class="idiff"> </span><span class="nn" style="color: #555;"><span class="idiff right">time</span></span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">snakemake.executors</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">DryrunExecutor</span><span class="p">,</span> <span class="n" style="color: #333;">TouchExecutor</span><span class="p">,</span> <span class="n" style="color: #333;">CPUExecutor</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">snakemake.executors</span> <span class="kn" style="font-weight: 600;">import</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">@@ -83,6 +86,7 @@ class JobScheduler:</td>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">force_use_threads</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">assume_shared_fs</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="LC88" class="line" lang="python"> <span class="n" style="color: #333;">keepincomplete</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">scheduler_type</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"> <span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"> <span class="s" style="color: #d14;">""" Create a new instance of KnapsackJobScheduler. """</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">ratelimiter</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">RateLimiter</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="106" 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">@@ -102,6 +106,7 @@ class JobScheduler:</td>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">greediness</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="LC107" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">max_jobs_per_second</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_jobs_per_second</span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">keepincomplete</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">keepincomplete</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">scheduler_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scheduler_type</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">global_resources</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="p">:</span> <span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">maxsize</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">res</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">res</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">@@ -391,7 +396,11 @@ class JobScheduler:</td>
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="python"> <span class="s" style="color: #d14;">"Ready jobs ({}):</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">needrun</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="python"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="n" style="color: #333;">join</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;">needrun</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="python"> <span class="n" style="color: #333;">run</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">job_selector</span><span class="p">(</span><span class="n" style="color: #333;">needrun</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="python"> <span class="n" style="color: #333;">run</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">job_selector_greedy</span><span class="p">(</span><span class="n" style="color: #333;">needrun</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">scheduler_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"greedy"</span></span>
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">job_selector_ilp</span><span class="p">(</span><span class="n" style="color: #333;">needrun</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="python"> <span class="s" style="color: #d14;">"Selected jobs ({}):</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="python"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="n" style="color: #333;">join</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;">run</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">@@ -522,11 +531,98 @@ class JobScheduler:</td>
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<pre style="margin: 0;"> <span id="LC531" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_user_kill</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"graceful"</span></span>
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<pre style="margin: 0;"> <span id="LC532" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_open_jobs</span><span class="p">.</span><span class="n" style="color: #333;">release</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC533" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC525" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">job_selector</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">jobs</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">job_selector_ilp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">jobs</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="python"><span class="s" style="color: #d14;"> Job scheduling by optimization of resource usage by solving ILP using pulp </span></span>
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pulp</span></span>
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pulp</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">lpSum</span></span>
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># assert self.resources["_cores"] > 0</span></span>
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="python"> <span class="n" style="color: #333;">scheduled_jobs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="python"> <span class="n" style="color: #333;">job</span><span class="p">:</span> <span class="n" style="color: #333;">pulp</span><span class="p">.</span><span class="n" style="color: #333;">LpVariable</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="python"> <span class="s" style="color: #d14;">f"job_</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">job</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">_</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">idx</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">lowBound</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">upBound</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">cat</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">pulp</span><span class="p">.</span><span class="n" style="color: #333;">LpInteger</span></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="n" style="color: #333;">job</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">jobs</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="python"> <span class="n" style="color: #333;">temp_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="python"> <span class="n" style="color: #333;">temp_file</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">job</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">jobs</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">temp_file</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;">dag</span><span class="p">.</span><span class="n" style="color: #333;">temp_input</span><span class="p">(</span><span class="n" style="color: #333;">job</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="python"> <span class="n" style="color: #333;">temp_job_improvement</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="python"> <span class="n" style="color: #333;">temp_file</span><span class="p">:</span> <span class="n" style="color: #333;">pulp</span><span class="p">.</span><span class="n" style="color: #333;">LpVariable</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="python"> <span class="n" style="color: #333;">temp_file</span><span class="p">,</span> <span class="n" style="color: #333;">lowBound</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">upBound</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">cat</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Continuous"</span></span>
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">temp_file</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">temp_files</span></span>
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="python"> <span class="n" style="color: #333;">prob</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pulp</span><span class="p">.</span><span class="n" style="color: #333;">LpProblem</span><span class="p">(</span><span class="s" style="color: #d14;">"Job scheduler"</span><span class="p">,</span> <span class="n" style="color: #333;">pulp</span><span class="p">.</span><span class="n" style="color: #333;">LpMaximize</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="python"> <span class="n" style="color: #333;">total_temp_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">([</span><span class="n" style="color: #333;">temp_file</span><span class="p">.</span><span class="n" style="color: #333;">size</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">temp_file</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">temp_files</span><span class="p">]),</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="python"> <span class="n" style="color: #333;">total_core_requirement</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="python"> <span class="p">[</span><span class="n" style="color: #333;">job</span><span class="p">.</span><span class="n" style="color: #333;">resources</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"_cores"</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="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">job</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">jobs</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Objective function</span></span>
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Job priority > Core load</span></span>
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Core load > temp file removal</span></span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Instant removal > temp size</span></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># temp file size > fast removal?!</span></span>
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="python"> <span class="n" style="color: #333;">prob</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="python"> <span class="n" style="color: #333;">total_core_requirement</span></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="python"> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">total_temp_size</span></span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="python"> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lpSum</span><span class="p">([</span><span class="n" style="color: #333;">job</span><span class="p">.</span><span class="n" style="color: #333;">priority</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scheduled_jobs</span><span class="p">[</span><span class="n" style="color: #333;">job</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">job</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">jobs</span><span class="p">])</span></span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="python"> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">total_temp_size</span></span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="python"> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lpSum</span><span class="p">(</span></span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="python"> <span class="p">[</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">job</span><span class="p">.</span><span class="n" style="color: #333;">resources</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"_cores"</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 class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">scheduled_jobs</span><span class="p">[</span><span class="n" style="color: #333;">job</span><span class="p">]</span></span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">job</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">jobs</span></span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="python"> <span class="p">]</span></span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="python"> <span class="p">)</span></span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="python"> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">lpSum</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="python"> <span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="python"> <span class="n" style="color: #333;">temp_job_improvement</span><span class="p">[</span><span class="n" style="color: #333;">temp_file</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">temp_file</span><span class="p">.</span><span class="n" style="color: #333;">size</span></span>
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">temp_file</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">temp_files</span></span>
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="python"> <span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Constraints:</span></span>
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</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;">workflow</span><span class="p">.</span><span class="n" style="color: #333;">global_resources</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="python"> <span class="n" style="color: #333;">prob</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="python"> <span class="n" style="color: #333;">lpSum</span><span class="p">(</span></span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="python"> <span class="p">[</span><span class="n" style="color: #333;">scheduled_jobs</span><span class="p">[</span><span class="n" style="color: #333;">job</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">job</span><span class="p">.</span><span class="n" style="color: #333;">resources</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">job</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">jobs</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="python"> <span class="o" style="font-weight: 600;"><=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">resources</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="LC596" class="line" lang="python"> <span class="s" style="color: #d14;">f"Limitation of resource: </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">name</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Choose jobs that lead to "fastest" (minimum steps) removal of existing temp file</span></span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">temp_file</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">temp_files</span><span class="p">:</span></span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="python"> <span class="n" style="color: #333;">prob</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">temp_job_improvement</span><span class="p">[</span><span class="n" style="color: #333;">temp_file</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">lpSum</span><span class="p">(</span></span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="python"> <span class="p">[</span></span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="python"> <span class="n" style="color: #333;">scheduled_jobs</span><span class="p">[</span><span class="n" style="color: #333;">job</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">required_by_job</span><span class="p">(</span><span class="n" style="color: #333;">temp_file</span><span class="p">,</span> <span class="n" style="color: #333;">job</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">job</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">jobs</span></span>
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="python"> <span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="python"> <span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">lpSum</span><span class="p">([</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">required_by_job</span><span class="p">(</span><span class="n" style="color: #333;">temp_file</span><span class="p">,</span> <span class="n" style="color: #333;">job</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">job</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">jobs</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="python"> <span class="n" style="color: #333;">prob</span><span class="p">.</span><span class="n" style="color: #333;">solve</span><span class="p">()</span></span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="python"> <span class="n" style="color: #333;">selected_jobs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="python"> <span class="n" style="color: #333;">job</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">job</span><span class="p">,</span> <span class="n" style="color: #333;">variable</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">scheduled_jobs</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">()</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">variable</span><span class="p">.</span><span class="n" style="color: #333;">value</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mf" style="color: #099;">1.0</span></span>
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611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="python"> <span class="p">]</span></span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</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;">workflow</span><span class="p">.</span><span class="n" style="color: #333;">global_resources</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">resources</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="python"> <span class="p">[</span><span class="n" style="color: #333;">job</span><span class="p">.</span><span class="n" style="color: #333;">resources</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">job</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">selected_jobs</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">selected_jobs</span></span>
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="python"></span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">required_by_job</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">temp_file</span><span class="p">,</span> <span class="n" style="color: #333;">job</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">temp_file</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;">dag</span><span class="p">.</span><span class="n" style="color: #333;">temp_input</span><span class="p">(</span><span class="n" style="color: #333;">job</span><span class="p">)</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">job_selector_greedy</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">jobs</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC622" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC623" class="line" lang="python"><span class="s" style="color: #d14;"> Using the greedy heuristic from</span></span>
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624
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<pre style="margin: 0;"> <span id="LC624" class="line" lang="python"><span class="s" style="color: #d14;"> "A Greedy Algorithm for the General Multidimensional Knapsack</span></span>
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<pre style="margin: 0;">-<span id="LC529" class="line" lang="python"><span class="s" style="color: #d14;">Problem", Akcay, Li, Xu, Annals of Operations Research, 2012</span></span>
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right"> </span>Problem", Akcay, Li, Xu, Annals of Operations Research, 2012</span></span>
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<pre style="margin: 0;"> <span id="LC626" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC627" class="line" lang="python"><span class="s" style="color: #d14;"> Args:</span></span>
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<pre style="margin: 0;"> <span id="LC628" class="line" lang="python"><span class="s" style="color: #d14;"> jobs (list): list of jobs</span></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/4b95c63220e2d1360913804c11116ddd7a1a7fa6...a056d4757cee7ceeb9fa894d04268a56381678a2#cb9e107597e441fb1c0d61663359d9cf1dbfe04d"><strong>snakemake/workflow.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">@@ -91,6 +91,7 @@ class Workflow:</td>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">singularity_prefix</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">singularity_args</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">shadow_prefix</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">scheduler_type</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Mode</span><span class="p">.</span><span class="n" style="color: #333;">default</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">wrapper_prefix</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">printshellcmds</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -155,6 +156,7 @@ class Workflow:</td>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">singularity_prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">singularity_prefix</span></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">singularity_args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">singularity_args</span></span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">shadow_prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">shadow_prefix</span></span>
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">scheduler_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scheduler_type</span></span>
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158
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">global_container_img</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mode</span></span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">wrapper_prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">wrapper_prefix</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="456" 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">@@ -454,6 +456,7 @@ class Workflow:</td>
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="python"> <span class="n" style="color: #333;">targets</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="python"> <span class="n" style="color: #333;">dryrun</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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458
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="python"> <span class="n" style="color: #333;">touch</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="python"> <span class="n" style="color: #333;">scheduler_type</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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460
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="python"> <span class="n" style="color: #333;">local_cores</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="n" style="color: #333;">forcetargets</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="python"> <span class="n" style="color: #333;">forceall</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -891,6 +894,7 @@ class Workflow:</td>
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<pre style="margin: 0;"> <span id="LC894" class="line" lang="python"> <span class="n" style="color: #333;">force_use_threads</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">force_use_threads</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC895" class="line" lang="python"> <span class="n" style="color: #333;">assume_shared_fs</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">assume_shared_fs</span><span class="p">,</span></span>
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896
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<pre style="margin: 0;"> <span id="LC896" class="line" lang="python"> <span class="n" style="color: #333;">keepincomplete</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">keepincomplete</span><span class="p">,</span></span>
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897
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="python"> <span class="n" style="color: #333;">scheduler_type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">scheduler_type</span><span class="p">,</span></span>
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898
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<pre style="margin: 0;"> <span id="LC898" class="line" lang="python"> <span class="p">)</span></span>
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899
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<pre style="margin: 0;"> <span id="LC899" class="line" lang="python"></span>
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900
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<pre style="margin: 0;"> <span id="LC900" 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;">dryrun</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">@@ -1085,6 +1089,32 @@ class Workflow:</td>
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<pre style="margin: 0;"> <span id="LC1089" class="line" lang="python"> <span class="n" style="color: #333;">update_config</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">)</span></span>
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1090
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<pre style="margin: 0;"> <span id="LC1090" class="line" lang="python"> <span class="n" style="color: #333;">update_config</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">overwrite_config</span><span class="p">)</span></span>
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1091
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<pre style="margin: 0;"> <span id="LC1091" class="line" lang="python"></span>
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1092
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<pre style="margin: 0;">+<span id="LC1092" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">pepfile</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">):</span></span>
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1093
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<pre style="margin: 0;">+<span id="LC1093" class="line" lang="python"> <span class="k" style="font-weight: 600;">global</span> <span class="n" style="color: #333;">pep</span></span>
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1094
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<pre style="margin: 0;">+<span id="LC1094" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC1095" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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1096
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<pre style="margin: 0;">+<span id="LC1096" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">peppy</span></span>
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1097
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<pre style="margin: 0;">+<span id="LC1097" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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1098
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<pre style="margin: 0;">+<span id="LC1098" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">WorkflowError</span><span class="p">(</span><span class="s" style="color: #d14;">"For PEP support, please install peppy."</span><span class="p">)</span></span>
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1099
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<pre style="margin: 0;">+<span id="LC1099" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="1100" 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">
1100
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<pre style="margin: 0;">+<span id="LC1100" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pepfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span></span>
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1101
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<pre style="margin: 0;">+<span id="LC1101" class="line" lang="python"> <span class="n" style="color: #333;">pep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">peppy</span><span class="p">.</span><span class="n" style="color: #333;">Project</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pepfile</span><span class="p">)</span></span>
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1102
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<pre style="margin: 0;">+<span id="LC1102" class="line" lang="python"></span>
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1103
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<pre style="margin: 0;">+<span id="LC1103" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">pepschema</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">schema</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1104" 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">
1104
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<pre style="margin: 0;">+<span id="LC1104" class="line" lang="python"> <span class="k" style="font-weight: 600;">global</span> <span class="n" style="color: #333;">pep</span></span>
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1105
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<pre style="margin: 0;">+<span id="LC1105" class="line" lang="python"></span>
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1106
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<pre style="margin: 0;">+<span id="LC1106" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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1107
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<pre style="margin: 0;">+<span id="LC1107" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">eido</span></span>
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1108
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<pre style="margin: 0;">+<span id="LC1108" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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1109
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<pre style="margin: 0;">+<span id="LC1109" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">WorkflowError</span><span class="p">(</span><span class="s" style="color: #d14;">"For PEP schema support, please install eido."</span><span class="p">)</span></span>
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1110
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<pre style="margin: 0;">+<span id="LC1110" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="1111" 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">
1111
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<pre style="margin: 0;">+<span id="LC1111" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">urlparse</span><span class="p">(</span><span class="n" style="color: #333;">schema</span><span class="p">).</span><span class="n" style="color: #333;">scheme</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">""</span> <span class="ow" style="font-weight: 600;">and</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;">isabs</span><span class="p">(</span><span class="n" style="color: #333;">schema</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1112" 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">
1112
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<pre style="margin: 0;">+<span id="LC1112" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># schema is relative to current Snakefile</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1113" 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">
1113
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<pre style="margin: 0;">+<span id="LC1113" class="line" lang="python"> <span class="n" style="color: #333;">schema</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;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">current_basedir</span><span class="p">,</span> <span class="n" style="color: #333;">schema</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1114" 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">
1114
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<pre style="margin: 0;">+<span id="LC1114" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pepfile</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1115" 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">
1115
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<pre style="margin: 0;">+<span id="LC1115" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">WorkflowError</span><span class="p">(</span><span class="s" style="color: #d14;">"Please specify a PEP with the pepfile directive."</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1116" 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">
1116
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<pre style="margin: 0;">+<span id="LC1116" class="line" lang="python"> <span class="n" style="color: #333;">eido</span><span class="p">.</span><span class="n" style="color: #333;">validate_project</span><span class="p">(</span><span class="n" style="color: #333;">project</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">pep</span><span class="p">,</span> <span class="n" style="color: #333;">schema</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">schema</span><span class="p">,</span> <span class="n" style="color: #333;">exclude_case</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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1117
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<pre style="margin: 0;">+<span id="LC1117" class="line" lang="python"></span>
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1088
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1118
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<pre style="margin: 0;"> <span id="LC1118" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">report</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">):</span></span>
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1089
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1119
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<pre style="margin: 0;"> <span id="LC1119" class="line" lang="python"> <span class="s" style="color: #d14;">""" Define a global report description in .rst format."""</span></span>
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1090
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1120
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<pre style="margin: 0;"> <span id="LC1120" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">report_text</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;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">current_basedir</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/4b95c63220e2d1360913804c11116ddd7a1a7fa6...a056d4757cee7ceeb9fa894d04268a56381678a2#d1deee71de70305809d43086b13f7eb407aff6f2"><strong>test-environment.yml</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">@@ -42,9 +42,12 @@ dependencies:</td>
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42
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pygraphviz</span></span>
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43
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python-kubernetes</span></span>
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44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">gitpython</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pulp</span></span>
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">tibanna</span></span>
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46
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">environment-modules</span></span>
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">nbformat</span></span>
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">toposort</span></span>
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">mamba</span></span>
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">crc32c</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">peppy</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">eido</span></span></pre>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/4b95c63220e2d1360913804c11116ddd7a1a7fa6...a056d4757cee7ceeb9fa894d04268a56381678a2#8170eb84634a720714408bf5991cf0fe862aedc8"><strong>tests/test_peppy/pep/config.yaml</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">pep_version</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">2.0.0"</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">sample_table</span><span class="pi">:</span> <span class="s" style="color: #d14;">sample_table.csv</span></span></pre>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/4b95c63220e2d1360913804c11116ddd7a1a7fa6...a056d4757cee7ceeb9fa894d04268a56381678a2#30236538d99508b82b584f45580c3c0df56c0e7c"><strong>tests/test_peppy/pep/sample_table.csv</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">sample_name,protocol</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">a,test</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">b,test2</span></pre>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/4b95c63220e2d1360913804c11116ddd7a1a7fa6...a056d4757cee7ceeb9fa894d04268a56381678a2#bcab5d626d6045306643ffe54e563626806802d8"><strong>tests/test_peppy/workflow/Snakefile</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">pepfile: "pep/config.yaml"</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">pepschema: "schemas/pep.yaml"</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">rule all:</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> input:</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> expand("{sample}.txt", sample=pep.sample_table["sample_name"])</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">rule a:</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> output:</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> "{sample}.txt"</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> shell:</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> "touch {output}"</span></pre>
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<li id="e76fdd319bd72c5dffe8ebaa1ce6374f9188f2b7">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/4b95c63220e2d1360913804c11116ddd7a1a7fa6...a056d4757cee7ceeb9fa894d04268a56381678a2#e76fdd319bd72c5dffe8ebaa1ce6374f9188f2b7"><strong>tests/test_peppy/workflow/schemas/pep.yaml</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">description</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">Schema</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">for</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">a</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">minimal</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">PEP"</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">2.0.0"</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">properties</span><span class="pi">:</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> </span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"> <span class="na" style="color: #008080;">type</span><span class="pi">:</span> <span class="s" style="color: #d14;">string</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">pattern</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">^</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">S*$"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="na" style="color: #008080;">description</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">Project</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">name</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">with</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">no</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">whitespace"</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">config</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">pep_version</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="10" 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">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">description</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">Version</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">of</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">the</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">PEP</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">Schema</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">this</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">PEP</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">follows"</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"> <span class="na" style="color: #008080;">type</span><span class="pi">:</span> <span class="s" style="color: #d14;">string</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"> <span class="na" style="color: #008080;">sample_table</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"> <span class="na" style="color: #008080;">type</span><span class="pi">:</span> <span class="s" style="color: #d14;">string</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"> <span class="na" style="color: #008080;">description</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">Path</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">to</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">the</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">sample</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">annotation</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">table</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">with</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">one</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">row</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">per</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">sample"</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"> <span class="na" style="color: #008080;">subsample_table</span><span class="pi">:</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">type</span><span class="pi">:</span> <span class="s" style="color: #d14;">string</span></span>
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<td class="diff-line-num new new_line" data-linenumber="17" 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">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="na" style="color: #008080;">description</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">Path</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">to</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">the</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">subsample</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">annotation</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">table</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">with</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">one</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">row</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">per</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">subsample</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">and</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">sample_name</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">attribute</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">matching</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">an</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">entry</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">in</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">the</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">sample</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">table"</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="na" style="color: #008080;">sample_modifiers</span><span class="pi">:</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="na" style="color: #008080;">type</span><span class="pi">:</span> <span class="s" style="color: #d14;">object</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="na" style="color: #008080;">properties</span><span class="pi">:</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="na" style="color: #008080;">append</span><span class="pi">:</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="na" style="color: #008080;">type</span><span class="pi">:</span> <span class="s" style="color: #d14;">object</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> <span class="na" style="color: #008080;">duplicate</span><span class="pi">:</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"> <span class="na" style="color: #008080;">type</span><span class="pi">:</span> <span class="s" style="color: #d14;">object</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="na" style="color: #008080;">imply</span><span class="pi">:</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"> <span class="na" style="color: #008080;">type</span><span class="pi">:</span> <span class="s" style="color: #d14;">array</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"> <span class="na" style="color: #008080;">items</span><span class="pi">:</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="na" style="color: #008080;">type</span><span class="pi">:</span> <span class="s" style="color: #d14;">object</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="na" style="color: #008080;">properties</span><span class="pi">:</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"> <span class="na" style="color: #008080;">if</span><span class="pi">:</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="na" style="color: #008080;">type</span><span class="pi">:</span> <span class="s" style="color: #d14;">object</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <span class="na" style="color: #008080;">then</span><span class="pi">:</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"> <span class="na" style="color: #008080;">type</span><span class="pi">:</span> <span class="s" style="color: #d14;">object</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"> <span class="na" style="color: #008080;">derive</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="yaml"> <span class="na" style="color: #008080;">type</span><span class="pi">:</span> <span class="s" style="color: #d14;">object</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="yaml"> <span class="na" style="color: #008080;">properties</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="yaml"> <span class="na" style="color: #008080;">attributes</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="yaml"> <span class="na" style="color: #008080;">type</span><span class="pi">:</span> <span class="s" style="color: #d14;">array</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="yaml"> <span class="na" style="color: #008080;">items</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="yaml"> <span class="na" style="color: #008080;">type</span><span class="pi">:</span> <span class="s" style="color: #d14;">string</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="yaml"> <span class="na" style="color: #008080;">sources</span><span class="pi">:</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="yaml"> <span class="na" style="color: #008080;">type</span><span class="pi">:</span> <span class="s" style="color: #d14;">object</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="yaml"> <span class="na" style="color: #008080;">project_modifiers</span><span class="pi">:</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="yaml"> <span class="na" style="color: #008080;">type</span><span class="pi">:</span> <span class="s" style="color: #d14;">object</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="yaml"> <span class="na" style="color: #008080;">properties</span><span class="pi">:</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="yaml"> <span class="na" style="color: #008080;">amend</span><span class="pi">:</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="yaml"> <span class="na" style="color: #008080;">description</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">Object</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">overwriting</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">original</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">project</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">attributes"</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="yaml"> <span class="na" style="color: #008080;">type</span><span class="pi">:</span> <span class="s" style="color: #d14;">object</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="yaml"> <span class="na" style="color: #008080;">import</span><span class="pi">:</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="yaml"> <span class="na" style="color: #008080;">description</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">List</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">of</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">external</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">PEP</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">project</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">config</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">files</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">to</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">import"</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="yaml"> <span class="na" style="color: #008080;">type</span><span class="pi">:</span> <span class="s" style="color: #d14;">array</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="yaml"> <span class="na" style="color: #008080;">items</span><span class="pi">:</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="yaml"> <span class="na" style="color: #008080;">type</span><span class="pi">:</span> <span class="s" style="color: #d14;">string</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="yaml"> <span class="na" style="color: #008080;">required</span><span class="pi">:</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pep_version</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="yaml"> <span class="na" style="color: #008080;">samples</span><span class="pi">:</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="yaml"> <span class="na" style="color: #008080;">type</span><span class="pi">:</span> <span class="s" style="color: #d14;">array</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="yaml"> <span class="na" style="color: #008080;">items</span><span class="pi">:</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="yaml"> <span class="na" style="color: #008080;">type</span><span class="pi">:</span> <span class="s" style="color: #d14;">object</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="yaml"> <span class="na" style="color: #008080;">properties</span><span class="pi">:</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="yaml"> <span class="na" style="color: #008080;">sample_name</span><span class="pi">:</span> </span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="yaml"> <span class="na" style="color: #008080;">type</span><span class="pi">:</span> <span class="s" style="color: #d14;">string</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="yaml"> <span class="na" style="color: #008080;">pattern</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">^</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">S*$"</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="yaml"> <span class="na" style="color: #008080;">description</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">Unique</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">name</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">of</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">the</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">sample</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">with</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">no</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">whitespace"</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="yaml"> <span class="na" style="color: #008080;">required</span><span class="pi">:</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">sample_name</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="yaml"><span class="na" style="color: #008080;">required</span><span class="pi">:</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">samples</span></span></pre>
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