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<h3>

Rebecca N. Palmer pushed to branch debian_for_upstream_5.14.0_which_requires_conda

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/ae057049ab68ec6742eb78605dfa9d823d335f65">ae057049</a></strong>

<div>

<span>by Rebecca N. Palmer</span>

<i>at 2020-04-25T15:53:53+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix link_security.patch (needs both upstream commits,

and overlaps with local_javascript.patch)

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/snakemake/-/commit/d5c191a18c323a7df976012e72014ead257ac2ad">d5c191a1</a></strong>

<div>

<span>by Rebecca N. Palmer</span>

<i>at 2020-04-25T17:35:43+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove inconveniently licensed (CC-BY-SA) snippets.

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/snakemake/-/commit/ff24eb24855ae1cf2e52bd66f4a0d41d66858d01">ff24eb24</a></strong>

<div>

<span>by Rebecca N. Palmer</span>

<i>at 2020-04-25T19:01:32+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install examples.

</pre>

</li>

</ul>

<h4>7 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">

debian/copyright

</a>

</li>

<li class="file-stats">

<a href="#7af1b47e7c28e029594f4457cc27d4671dc7fd42">

debian/patches/link_security.patch

</a>

</li>

<li class="file-stats">

<a href="#3a60a3d8ad77c5d7b9f50f6d9e07887ec385a803">

debian/patches/local_javascript.patch

</a>

</li>

<li class="file-stats">

<a href="#aef4fc475d9c2698d0de9e80b3256895c791f41e">

<span class="new-file">

+

debian/patches/remove_ccbysa_snippets.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

debian/patches/series

</a>

</li>

<li class="file-stats">

<a href="#f60d76f1358e5eff9d34bd211f2a52c51b3228ba">

<span class="new-file">

+

debian/snakemake.examples

</span>

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/snakemake/-/compare/7d50f8d318478b6bb767b008c540da954f4fc92a...ff24eb24855ae1cf2e52bd66f4a0d41d66858d01#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="22" 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="22" 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">@@ -22,6 +22,8 @@ snakemake (5.14.0-1) UNRELEASED; urgency=medium</td>

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<td class="diff-line-num old_line" data-linenumber="22" 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">

22

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<td class="diff-line-num new_line" data-linenumber="22" 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">

22

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">  * Privacy: use local dagre-d3, add missing Javascript dependencies,</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="23" 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">

23

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">    don't appear to show live status when we don't.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="24" 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">

24

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<td class="diff-line-num new_line" data-linenumber="24" 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">

24

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">  * Use https for links where available.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="25" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="25" 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">

25

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">  * Remove inconveniently licensed (CC-BY-SA) snippets.</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="25" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

26

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">  * Install examples.</span>

</pre>

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25

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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"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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">

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> -- Rebecca N. Palmer <rebecca_palmer@zoho.com>  Thu, 09 Apr 2020 14:57:00 +0100</span>

</pre>

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27

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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">

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">

<a href="https://salsa.debian.org/med-team/snakemake/-/compare/7d50f8d318478b6bb767b008c540da954f4fc92a...ff24eb24855ae1cf2e52bd66f4a0d41d66858d01#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_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="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">@@ -6,6 +6,7 @@ Source: https://github.com/snakemake/snakemake</td>

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<td class="diff-line-num old_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">

6

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Files: *</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Copyright: 2015-2020 Johannes Köster <johannes.koester@tu-dortmund.de>, Manuel Holtgrewe, Christopher Tomkins-Tinch, Sven Nahnsen, Sebastian Kurscheid and contributors</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">License: Expat</span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Comment: The original source contains some CC-BY-SA snippets by Stack Overflow users (https://stackoverflow.com/users/2012682/brice-m-dempsey, https://stackoverflow.com/users/650222/coldfix, https://stackoverflow.com/users/14343/ned-batchelder, https://stackoverflow.com/users/5299236/kevin-guan, https://stackoverflow.com/users/20713/ephemient, https://stackoverflow.com/users/34910/nate-parsons, https://stackoverflow.com/users/4785947/christian-zielinski, https://stackoverflow.com/users/3743213/seth127, https://stackoverflow.com/users/2838606/amir, https://stackoverflow.com/users/4159907/schoyen, https://stackoverflow.com/users/95810/alex-martelli, https://stackoverflow.com/users/1723886/alex-telon, https://stackoverflow.com/users/1417016/wpoely86, https://stackoverflow.com/users/97828/nadia-alramli, https://stackoverflow.com/users/35070/phihag), but these may be too small to be copyrightable, and the less trivial ones are patched out in this package</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>

</pre>

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10

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Files: tests/test_script/expected-results/test.html</span>

</pre>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">       tests/test_issue635/expected-results/report.html</span>

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</li>

<li id="7af1b47e7c28e029594f4457cc27d4671dc7fd42">

<a href="https://salsa.debian.org/med-team/snakemake/-/compare/7d50f8d318478b6bb767b008c540da954f4fc92a...ff24eb24855ae1cf2e52bd66f4a0d41d66858d01#7af1b47e7c28e029594f4457cc27d4671dc7fd42"><strong>debian/patches/link_security.patch</strong></a>

<hr>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* Park et al. 2015. `Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone <https://doi.org/10.1016/j.cell.2015.06.007>`_. Cell.</span></span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* Břinda et al. 2015. `RNF: a general framework to evaluate NGS read mappers <https://bioinformatics.oxfordjournals.org/content/early/2015/09/30/bioinformatics.btv524>`_. Bioinformatics.</span></span>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* Břinda et al. 2015. `Spaced seeds improve k-mer-based metagenomic classification <https://bioinformatics.oxfordjournals.org/content/early/2015/08/10/bioinformatics.btv419>`_. Bioinformatics.</span></span>

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="diff"> * Spjuth et al. 2015. `Experiences with workflows for automating data-intensive bioinformatics <https://biologydirect.biomedcentral.com/articles/10.1186/s13062-015-0071-8>`_. Biology Direct.</span>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* Spjuth et al. 2015. `Experiences with workflows for automating data-intensive bioinformatics <http://www.biologydirect.com/content/10/1/43>`_. Biology Direct.</span></span>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* Spjuth et al. 2015. `Experiences with workflows for automating data-intensive bioinformatics <https://biologydirect.biomedcentral.com/articles/10.1186/s13062-015-0071-8>`_. Biology Direct.</span></span>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* Schramm et al. 2015. `Mutational dynamics between primary and relapse neuroblastomas <http://www.nature.com/ng/journal/v47/n8/full/ng.3349.html>`_. Nature Genetics.</span></span>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* Berulava et al. 2015. `N6-Adenosine Methylation in MiRNAs <http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118438>`_. PLOS ONE.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* The Genome of the Netherlands Consortium 2014. `Whole-genome sequence variation, population structure and demographic history of the Dutch population <http://www.nature.com/ng/journal/v46/n8/full/ng.3021.html>`_. Nature Genetics.</span></span>

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="diff"> .. _Atom: https://atom.io</span>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="diff"> .. _Anaconda: https://anaconda.org</span>

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<pre style="margin: 0;"> <span id="LC349" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Graphviz: http://www.graphviz.org</span></span>

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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _RestructuredText: http://docutils.sourceforge.net/rst.html</span></span>

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<pre style="margin: 0;"> <span id="LC351" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Graphviz: https://www.graphviz.org</span></span>

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<pre style="margin: 0;">-<span id="LC350" class="line" lang="diff"><span class="idiff left right"> </span>.. _RestructuredText: https://docutils.sourceforge.io/docs/user/rst/quickstart.html</span>

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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;"><span class="idiff left right">+</span>.. _RestructuredText: https://docutils.sourceforge.io/docs/user/rst/quickstart.html</span></span>

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<pre style="margin: 0;"> <span id="LC353" class="line" lang="diff"> .. _data URI: https://developer.mozilla.org/en-US/docs/Web/HTTP/data_URIs</span>

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<pre style="margin: 0;"> <span id="LC354" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _JSON: http://json.org</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC355" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _YAML: http://yaml.org</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC356" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _DRMAA: http://www.drmaa.org</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="357" 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="LC357" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _rpy2: http://rpy.sourceforge.net</span></span>

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<pre style="margin: 0;"> <span id="LC358" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _JSON: https://json.org</span></span>

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<pre style="margin: 0;"> <span id="LC359" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _YAML: https://yaml.org</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC360" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _DRMAA: https://www.drmaa.org</span></span>

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<pre style="margin: 0;">-<span id="LC358" class="line" lang="diff"><span class="idiff left right"> </span>.. _rpy2: https://rpy2.github.io</span>

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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;"><span class="idiff left right">+</span>.. _rpy2: https://rpy2.github.io</span></span>

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<pre style="margin: 0;"> <span id="LC362" class="line" lang="diff"> .. _R: https://www.r-project.org</span>

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<pre style="margin: 0;"> <span id="LC363" class="line" lang="diff"> .. _Rscript: https://stat.ethz.ch/R-manual/R-devel/library/utils/html/Rscript.html</span>

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<pre style="margin: 0;"> <span id="LC364" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _PyYAML: http://pyyaml.org</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Docutils: http://docutils.sourceforge.net</span></span>

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<pre style="margin: 0;"> <span id="LC366" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _PyYAML: https://pyyaml.org</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC363" class="line" lang="diff"><span class="idiff left right"> </span>.. _Docutils: https://docutils.sourceforge.io</span>

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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;"><span class="idiff left right">+</span>.. _Docutils: https://docutils.sourceforge.io</span></span>

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<pre style="margin: 0;"> <span id="LC368" class="line" lang="diff"> .. _Bioconda: https://bioconda.github.io</span>

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<pre style="margin: 0;"> <span id="LC369" class="line" lang="diff"> .. _Vagrant: https://www.vagrantup.com</span>

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<pre style="margin: 0;"> <span id="LC370" class="line" lang="diff"> .. _Vagrant Documentation: https://docs.vagrantup.com</span>

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<pre style="margin: 0;"> <span id="LC410" class="line" lang="diff"> .. _Atom: https://atom.io</span>

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<pre style="margin: 0;"> <span id="LC411" class="line" lang="diff"> .. _Anaconda: https://anaconda.org</span>

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<pre style="margin: 0;"> <span id="LC412" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Graphviz: http://www.graphviz.org</span></span>

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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _RestructuredText: http://docutils.sourceforge.net/rst.html</span></span>

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<pre style="margin: 0;"> <span id="LC414" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Graphviz: https://www.graphviz.org</span></span>

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<pre style="margin: 0;">-<span id="LC410" class="line" lang="diff"><span class="idiff left right"> </span>.. _RestructuredText: https://docutils.sourceforge.io/docs/user/rst/quickstart.html</span>

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<pre style="margin: 0;">+<span id="LC415" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;"><span class="idiff left right">+</span>.. _RestructuredText: https://docutils.sourceforge.io/docs/user/rst/quickstart.html</span></span>

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<pre style="margin: 0;"> <span id="LC416" class="line" lang="diff"> .. _data URI: https://developer.mozilla.org/en-US/docs/Web/HTTP/data_URIs</span>

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<pre style="margin: 0;"> <span id="LC417" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _JSON: http://json.org</span></span>

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<pre style="margin: 0;"> <span id="LC418" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _YAML: http://yaml.org</span></span>

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<pre style="margin: 0;"> <span id="LC419" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _DRMAA: http://www.drmaa.org</span></span>

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<pre style="margin: 0;">+<span id="LC420" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _rpy2: http://rpy.sourceforge.net</span></span>

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<pre style="margin: 0;"> <span id="LC421" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _JSON: https://json.org</span></span>

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<pre style="margin: 0;"> <span id="LC422" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _YAML: https://yaml.org</span></span>

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<pre style="margin: 0;"> <span id="LC423" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _DRMAA: https://www.drmaa.org</span></span>

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<pre style="margin: 0;">-<span id="LC418" class="line" lang="diff"><span class="idiff left right"> </span>.. _rpy2: https://rpy2.github.io</span>

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<pre style="margin: 0;">+<span id="LC424" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;"><span class="idiff left right">+</span>.. _rpy2: https://rpy2.github.io</span></span>

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<pre style="margin: 0;"> <span id="LC425" class="line" lang="diff"> .. _R: https://www.r-project.org</span>

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<pre style="margin: 0;"> <span id="LC426" class="line" lang="diff"> .. _Rscript: https://stat.ethz.ch/R-manual/R-devel/library/utils/html/Rscript.html</span>

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<pre style="margin: 0;"> <span id="LC427" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _PyYAML: http://pyyaml.org</span></span>

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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Docutils: http://docutils.sourceforge.net</span></span>

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<pre style="margin: 0;"> <span id="LC429" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _PyYAML: https://pyyaml.org</span></span>

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<pre style="margin: 0;">-<span id="LC423" class="line" lang="diff"><span class="idiff left right"> </span>.. _Docutils: https://docutils.sourceforge.io</span>

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<pre style="margin: 0;">+<span id="LC430" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;"><span class="idiff left right">+</span>.. _Docutils: https://docutils.sourceforge.io</span></span>

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<pre style="margin: 0;"> <span id="LC431" class="line" lang="diff"> .. _Bioconda: https://bioconda.github.io</span>

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<pre style="margin: 0;"> <span id="LC432" class="line" lang="diff"> .. _Vagrant: https://www.vagrantup.com</span>

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<pre style="margin: 0;"> <span id="LC433" class="line" lang="diff"> .. _Vagrant Documentation: https://docs.vagrantup.com</span>

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<pre style="margin: 0;"> <span id="LC464" class="line" lang="diff"> .. _Atom: https://atom.io</span>

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<pre style="margin: 0;"> <span id="LC465" class="line" lang="diff"> .. _Anaconda: https://anaconda.org</span>

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<pre style="margin: 0;"> <span id="LC466" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Graphviz: http://www.graphviz.org</span></span>

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<pre style="margin: 0;">+<span id="LC467" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _RestructuredText: http://docutils.sourceforge.net/rst.html</span></span>

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<pre style="margin: 0;"> <span id="LC468" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Graphviz: https://www.graphviz.org</span></span>

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<pre style="margin: 0;">-<span id="LC461" class="line" lang="diff"><span class="idiff left right"> </span>.. _RestructuredText: https://docutils.sourceforge.io/docs/user/rst/quickstart.html</span>

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<pre style="margin: 0;">+<span id="LC469" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;"><span class="idiff left right">+</span>.. _RestructuredText: https://docutils.sourceforge.io/docs/user/rst/quickstart.html</span></span>

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<td class="diff-line-num new_line" data-linenumber="470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC470" class="line" lang="diff"> .. _data URI: https://developer.mozilla.org/en-US/docs/Web/HTTP/data_URIs</span>

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<td class="diff-line-num new_line" data-linenumber="471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC471" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _JSON: http://json.org</span></span>

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<pre style="margin: 0;"> <span id="LC472" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _YAML: http://yaml.org</span></span>

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<pre style="margin: 0;"> <span id="LC473" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _DRMAA: http://www.drmaa.org</span></span>

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<pre style="margin: 0;">+<span id="LC474" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _rpy2: http://rpy.sourceforge.net</span></span>

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<pre style="margin: 0;"> <span id="LC475" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _JSON: https://json.org</span></span>

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<pre style="margin: 0;"> <span id="LC476" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _YAML: https://yaml.org</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC477" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _DRMAA: https://www.drmaa.org</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC469" class="line" lang="diff"><span class="idiff left right"> </span>.. _rpy2: https://rpy2.github.io</span>

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<td class="diff-line-num new new_line" data-linenumber="478" 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="LC478" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;"><span class="idiff left right">+</span>.. _rpy2: https://rpy2.github.io</span></span>

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<pre style="margin: 0;"> <span id="LC479" class="line" lang="diff"> .. _R: https://www.r-project.org</span>

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<pre style="margin: 0;"> <span id="LC480" class="line" lang="diff"> .. _Rscript: https://stat.ethz.ch/R-manual/R-devel/library/utils/html/Rscript.html</span>

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<pre style="margin: 0;"> <span id="LC481" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _PyYAML: http://pyyaml.org</span></span>

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<pre style="margin: 0;">+<span id="LC482" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Docutils: http://docutils.sourceforge.net</span></span>

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<pre style="margin: 0;"> <span id="LC483" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _PyYAML: https://pyyaml.org</span></span>

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<pre style="margin: 0;">-<span id="LC474" class="line" lang="diff"><span class="idiff left right"> </span>.. _Docutils: https://docutils.sourceforge.io</span>

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<pre style="margin: 0;">+<span id="LC484" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;"><span class="idiff left right">+</span>.. _Docutils: https://docutils.sourceforge.io</span></span>

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<pre style="margin: 0;"> <span id="LC485" class="line" lang="diff"> .. _Bioconda: https://bioconda.github.io</span>

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<pre style="margin: 0;"> <span id="LC486" class="line" lang="diff"> .. _Vagrant: https://www.vagrantup.com</span>

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<pre style="margin: 0;"> <span id="LC487" class="line" lang="diff"> .. _Vagrant Documentation: https://docs.vagrantup.com</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">@@ -486,7 +496,7 @@ diff --git a/docs/tutorial/setup.rst b/docs/tutorial/setup.rst</td>

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<pre style="margin: 0;"> <span id="LC496" class="line" lang="diff"><span class="gh" style="color: #999;">index 32ff8ca3..a098bc28 100644</span></span>

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<pre style="margin: 0;"> <span id="LC497" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/docs/tutorial/setup.rst</span></span>

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<pre style="margin: 0;"> <span id="LC498" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/docs/tutorial/setup.rst</span></span>

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<pre style="margin: 0;">-<span id="LC489" class="line" lang="diff"><span class="p">@@ -4,2<span class="idiff left right">0 +4,20</span> @@</span></span>

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<pre style="margin: 0;">+<span id="LC499" class="line" lang="diff"><span class="p">@@ -4,2<span class="idiff left right">9 +4,29</span> @@</span></span>

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<pre style="margin: 0;"> <span id="LC500" class="line" lang="diff"> Setup</span>

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<pre style="margin: 0;"> <span id="LC501" class="line" lang="diff"> -----</span>

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<pre style="margin: 0;"> <span id="LC502" class="line" lang="diff"> </span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="513" 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">@@ -513,12 +523,15 @@ index 32ff8ca3..a098bc28 100644</td>

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<pre style="margin: 0;"> <span id="LC523" class="line" lang="diff"> .. _Atom: https://atom.io</span>

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<pre style="margin: 0;"> <span id="LC524" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Graphviz: http://www.graphviz.org</span></span>

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<td class="diff-line-num old_line" data-linenumber="515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC525" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _PyYAML: http://pyyaml.org</span></span>

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<td class="diff-line-num new old_line" data-linenumber="516" 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="526" 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="LC526" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Docutils: http://docutils.sourceforge.net</span></span>

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<td class="diff-line-num new old_line" data-linenumber="516" 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="LC527" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Jinja2: http://jinja.pocoo.org</span></span>

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<td class="diff-line-num new_line" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC528" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Graphviz: https://www.graphviz.org</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC529" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _PyYAML: https://pyyaml.org</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC518" class="line" lang="diff"><span class="idiff left right"> </span>.. _Docutils: https://docutils.sourceforge.io</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC519" class="line" lang="diff"><span class="idiff left right"> </span>.. _Jinja2: https://jinja.palletsprojects.com</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="530" 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="LC530" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;"><span class="idiff left right">+</span>.. _Docutils: https://docutils.sourceforge.io</span></span>

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<td class="diff-line-num new new_line" data-linenumber="531" 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="LC531" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;"><span class="idiff left right">+</span>.. _Jinja2: https://jinja.palletsprojects.com</span></span>

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<td class="diff-line-num new_line" data-linenumber="532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC532" class="line" lang="diff"> .. _NetworkX: https://networkx.github.io</span>

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<td class="diff-line-num old old_line" data-linenumber="521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC521" class="line" lang="diff"><span class="p">@@ -26,7 +26,7 @@</span> Setup</span>

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<td class="diff-line-num new old_line" data-linenumber="522" 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="533" 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="LC533" class="line" lang="diff"> .. _Matplotlib: https://matplotlib.org</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="522" 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="534" 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="LC534" class="line" lang="diff"> .. _Pysam: https://pysam.readthedocs.io</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="535" 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">

535

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<pre style="margin: 0;"> <span id="LC535" class="line" lang="diff"> .. _Bioconda: https://bioconda.github.io</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="536" 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">

536

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<pre style="margin: 0;"> <span id="LC536" class="line" lang="diff"> .. _Vagrant: https://www.vagrantup.com</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="524" 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">

524

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<td class="diff-line-num new_line" data-linenumber="537" 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">

537

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<pre style="margin: 0;"> <span id="LC537" class="line" lang="diff"> .. _Vagrant Documentation: https://docs.vagrantup.com</span>

</pre>

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<li id="3a60a3d8ad77c5d7b9f50f6d9e07887ec385a803">

<a href="https://salsa.debian.org/med-team/snakemake/-/compare/7d50f8d318478b6bb767b008c540da954f4fc92a...ff24eb24855ae1cf2e52bd66f4a0d41d66858d01#3a60a3d8ad77c5d7b9f50f6d9e07887ec385a803"><strong>debian/patches/local_javascript.patch</strong></a>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        <link rel="stylesheet" type="text/css" href="http<span class="idiff left right">s</span>://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.1.1/css/bootstrap.min.css"/></span></span>

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39

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        <link rel="stylesheet" type="text/css" href="file:///usr/share/javascript/bootstrap/css/bootstrap.min.css"/></span></span>

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40

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff">         <link rel="stylesheet" type="text/css" href="http://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.5.4/bootstrap-select.min.css"/></span>

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40

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff">         <link rel="stylesheet" type="text/css" href="http<span class="idiff left right">s</span>://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.5.4/bootstrap-select.min.css"/></span>

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41

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41

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="diff">         <style></span>

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42

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42

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="diff">         body {</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="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/docs/index.rst</span></span>

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<br>

</li>

<li id="aef4fc475d9c2698d0de9e80b3256895c791f41e">

<a href="https://salsa.debian.org/med-team/snakemake/-/compare/7d50f8d318478b6bb767b008c540da954f4fc92a...ff24eb24855ae1cf2e52bd66f4a0d41d66858d01#aef4fc475d9c2698d0de9e80b3256895c791f41e"><strong>debian/patches/remove_ccbysa_snippets.patch</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">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Remove code from Stack Overflow</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Stack Overflow content is CC-BY-SA licensed,</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">which this package is not supposed to be.  These snippets may be</span></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">too small to be copyrightable, but removing them to be safe.</span></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"></span>

</pre>

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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="diff">Author: Rebecca N. Palmer <rebecca_palmer@zoho.com></span>

</pre>

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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="diff"><span class="p">Forwarded: no - one part needs Python 3.6+</span></span>

</pre>

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9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff">diff --git a/snakemake/io.py b/snakemake/io.py</span>

</pre>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gh" style="color: #999;">index ff149c3..8fd767b 100755</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/snakemake/io.py</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/snakemake/io.py</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">@@ -1355,18 +1355,7 @@</span> def _load_configfile(configpath, filetype="Config"):</span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff">             except ValueError:</span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff">                 f.seek(0)  # try again</span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff">             try:</span>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                # From https://stackoverflow.com/a/21912744/84349</span></span>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                class OrderedLoader(yaml.Loader):</span></span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                    pass</span></span>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                def construct_mapping(loader, node):</span></span>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                    loader.flatten_mapping(node)</span></span>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                    return collections.OrderedDict(loader.construct_pairs(node))</span></span>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                OrderedLoader.add_constructor(</span></span>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                    yaml.resolver.BaseResolver.DEFAULT_MAPPING_TAG, construct_mapping</span></span>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                )</span></span>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                return yaml.load(f, Loader=OrderedLoader)</span></span>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                return yaml.full_load(f)</span></span>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff">             except yaml.YAMLError:</span>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff">                 raise WorkflowError(</span>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff">                     "Config file is not valid JSON or YAML. "</span>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/snakemake/remote/S3Mocked.py b/snakemake/remote/S3Mocked.py</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gh" style="color: #999;">index 81391ea..1b7646e 100644</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/snakemake/remote/S3Mocked.py</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/snakemake/remote/S3Mocked.py</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="p">@@ -10,6 +10,7 @@</span> import pickle</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> import time</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="40" 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="LC40" class="line" lang="diff"> import threading</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="41" 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="LC41" class="line" lang="diff"> import functools</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="42" 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="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import pathlib</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="44" 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="LC44" class="line" lang="diff"> # intra-module</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="45" 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="LC45" class="line" lang="diff"> from snakemake.remote.S3 import (</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="46" 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="LC46" class="line" lang="diff"><span class="p">@@ -122,26 +123,19 @@</span> class RemoteObject(S3RemoteObject):</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="47" 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="LC47" class="line" lang="diff"> # ====== Helpers =====</span>

</pre>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="49" 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="LC49" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="50" 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="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-def touch(fname, mode=0o666, dir_fd=None, **kwargs):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="51" 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="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    # create lock file faster</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="52" 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="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    # https://stackoverflow.com/a/1160227</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="53" 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="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    flags = os.O_CREAT | os.O_APPEND</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="54" 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="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    with os.fdopen(os.open(fname, flags=flags, mode=mode, dir_fd=dir_fd)) as f:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        os.utime(</span></span>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            f.fileno() if os.utime in os.supports_fd else fname,</span></span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            dir_fd=None if os.supports_fd else dir_fd,</span></span>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            **kwargs</span></span>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        )</span></span>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+def touch(fname, mode=0o666):</span></span>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    pathlib.Path(fname).touch(mode=mode, exist_ok=True)</span></span>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> @contextmanager</span>

</pre>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> def file_lock(filepath):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff">     lock_file = filepath + ".lock"</span>

</pre>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    while os.path.isfile(lock_file):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        time.sleep(2)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    touch(lock_file)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    while True:</span></span>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        try:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            pathlib.Path(lock_file).touch(exist_ok=False)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            break</span></span>

</pre>

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76

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        except FileExistsError:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="77" 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">

77

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            time.sleep(2)</span></span>

</pre>

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78

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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="LC78" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="79" 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">

79

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff">     try:</span>

</pre>

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80

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff">         yield</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="81" 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">

81

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/snakemake/utils.py b/snakemake/utils.py</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="82" 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">

82

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gh" style="color: #999;">index 451c25c..5750a7a 100644</span></span>

</pre>

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83

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/snakemake/utils.py</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="84" 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">

84

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/snakemake/utils.py</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="85" 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">

85

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="p">@@ -449,25 +449,23 @@</span> def min_version(version):</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="86" 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="LC86" class="line" lang="diff"> def update_config(config, overwrite_config):</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="87" 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">

87

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff">     """Recursively update dictionary config with overwrite_config.</span>

</pre>

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88

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="89" 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="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    See</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="90" 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">

90

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    https://stackoverflow.com/questions/3232943/update-value-of-a-nested-dictionary-of-varying-depth</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="91" 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="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    for details.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="92" 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="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff">     Args:</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="94" 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="LC94" class="line" lang="diff">       config (dict): dictionary to update</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="95" 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="LC95" class="line" lang="diff">       overwrite_config (dict): dictionary whose items will overwrite those in config</span>

</pre>

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> </span>

</pre>

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97

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff">     """</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="98" 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">

98

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="99" 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">

99

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    def _update(d, u):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="100" 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">

100

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        for (key, value) in u.items():</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="101" 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">

101

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            if isinstance(value, collections.abc.Mapping):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="102" 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">

102

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                d[key] = _update(d.get(key, {}), value)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="103" 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">

103

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    def nestedupdate(old_d, new_d):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="104" 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="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        for k, v in new_d.items():</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="105" 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">

105

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            if isinstance(v, collections.abc.Mapping):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="106" 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">

106

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                if k not in old_d:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="107" 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="LC107" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                    old_d[k] = {}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="108" 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">

108

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                nestedupdate(old_d[k], v)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="109" 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="LC109" class="line" lang="diff">             else:</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="110" 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="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                d[key] = value</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="111" 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="LC111" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        return d</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="112" 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="LC112" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                old_d[k] = v</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="113" 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="LC113" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="114" 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">

114

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="115" 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="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    _update(config, overwrite_config)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="116" 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="LC116" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    nestedupdate(config, overwrite_config)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> def available_cpu_count():</span>

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="p">@@ -476,22 +472,16 @@</span> def available_cpu_count():</span>

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff">     The number of available CPUs can be smaller than the total number of CPUs</span>

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff">     when the cpuset(7) mechanism is in use, as is the case on some cluster</span>

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff">     systems.</span>

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    Adapted from https://stackoverflow.com/a/1006301/715090</span></span>

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff">     """</span>

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff">     try:</span>

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        with open("/proc/self/status") as f:</span></span>

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            status = f.read()</span></span>

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        m = re.search(r"(?m)^Cpus_allowed:\s*(.*)$", status)</span></span>

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        if m:</span></span>

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            res = bin(int(m.group(1).replace(",", ""), 16)).count("1")</span></span>

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            if res > 0:</span></span>

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                return min(res, multiprocessing.cpu_count())</span></span>

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    except IOError:</span></span>

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        pass</span></span>

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="138" 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="LC138" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    return multiprocessing.cpu_count()</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="139" 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="LC139" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="140" 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="LC140" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        cpu_count = len(os.sched_getaffinity(0))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    except Exception:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="142" 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="LC142" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        cpu_count = 0</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="143" 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="LC143" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    if cpu_count == 0:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        cpu_count = os.cpu_count()</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="145" 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="LC145" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        if not cpu_count:  # None if unknown</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="146" 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="LC146" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            cpu_count = 1</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="147" 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="LC147" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    return cpu_count</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="149" 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="LC149" class="line" lang="diff"> def argvquote(arg, force=True):</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="150" 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="LC150" class="line" lang="diff">     """ Returns an argument quoted in such a way that that CommandLineToArgvW</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="151" 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="LC151" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/tests/test_static_remote/S3MockedForStaticTest.py b/tests/test_static_remote/S3MockedForStaticTest.py</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="152" 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="LC152" class="line" lang="diff"><span class="gh" style="color: #999;">index 4f6c343..42403f4 100644</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/test_static_remote/S3MockedForStaticTest.py</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="154" 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="LC154" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/test_static_remote/S3MockedForStaticTest.py</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="155" 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="LC155" class="line" lang="diff"><span class="p">@@ -10,6 +10,7 @@</span> import pickle</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="156" 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="LC156" class="line" lang="diff"> import time</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="157" 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="LC157" class="line" lang="diff"> import threading</span>

</pre>

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> import functools</span>

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import pathlib</span></span>

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> # intra-module</span>

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> from snakemake.remote.S3 import RemoteObject as S3RemoteObject, RemoteProvider as S3RemoteProvider</span>

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="p">@@ -116,22 +117,19 @@</span> class RemoteObject(S3RemoteObject):</span>

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> # ====== Helpers =====</span>

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-def touch(fname, mode=0o666, dir_fd=None, **kwargs):</span></span>

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    # create lock file faster</span></span>

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    # https://stackoverflow.com/a/1160227</span></span>

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    flags = os.O_CREAT | os.O_APPEND</span></span>

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    with os.fdopen(os.open(fname, flags=flags, mode=mode, dir_fd=dir_fd)) as f:</span></span>

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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        os.utime(f.fileno() if os.utime in os.supports_fd else fname,</span></span>

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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            dir_fd=None if os.supports_fd else dir_fd, **kwargs)</span></span>

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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+def touch(fname, mode=0o666):</span></span>

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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    pathlib.Path(fname).touch(mode=mode, exist_ok=True)</span></span>

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> @contextmanager</span>

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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> def file_lock(filepath):</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="179" 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">

179

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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff">     lock_file = filepath + ".lock"</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="180" 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">

180

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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="181" 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">

181

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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    while os.path.isfile(lock_file):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="182" 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">

182

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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="LC182" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        time.sleep(2)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="184" 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">

184

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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="LC184" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    touch(lock_file)</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="185" 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">

185

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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="LC185" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    while True:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="186" 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">

186

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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        try:</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="187" 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">

187

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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            pathlib.Path(lock_file).touch(exist_ok=False)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="188" 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">

188

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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="LC188" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            break</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="189" 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">

189

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        except FileExistsError:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="190" 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">

190

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            time.sleep(2)</span></span>

</pre>

</td>

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<td class="diff-line-num new new_line" data-linenumber="191" 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">

191

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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="LC191" class="line" lang="diff"> </span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="192" 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">

192

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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff">     try:</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="193" 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">

193

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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="LC193" class="line" lang="diff">         yield</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<a href="https://salsa.debian.org/med-team/snakemake/-/compare/7d50f8d318478b6bb767b008c540da954f4fc92a...ff24eb24855ae1cf2e52bd66f4a0d41d66858d01#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1" 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">

1

</td>

<td class="diff-line-num new_line" data-linenumber="1" 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">

1

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">0001-Use-the-inbuild-sphinx.ext.napoleon.patch</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_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">

</td>

<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">

2

</td>

<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">link_security.patch</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2" 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">

2

</td>

<td class="diff-line-num new_line" data-linenumber="3" 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">

3

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">local_javascript.patch</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="3" 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">

3

</td>

<td class="diff-line-num new_line" data-linenumber="4" 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">

4

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">0003-Compat-fix.patch</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4" 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">

4

</td>

<td class="diff-line-num new_line" data-linenumber="5" 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">

5

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">0006-restore-bin.patch</span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_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="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,5 +7,5 @@ local_javascript.patch</td>

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<td class="diff-line-num old_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">

6

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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">0009-skip-test-without-google-cloud-sdk.patch</span>

</pre>

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<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">python3.patch</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">workaround_sphinx_issue.patch</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

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<td class="diff-line-num new_line old" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">link_security.patch</span>

</pre>

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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="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">bug322_cluster_sync.patch</span>

</pre>

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<td class="diff-line-num new old_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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<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">

11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">remove_ccbysa_snippets.patch</span></pre>

</td>

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</table>

<br>

</li>

<li id="f60d76f1358e5eff9d34bd211f2a52c51b3228ba">

<a href="https://salsa.debian.org/med-team/snakemake/-/compare/7d50f8d318478b6bb767b008c540da954f4fc92a...ff24eb24855ae1cf2e52bd66f4a0d41d66858d01#f60d76f1358e5eff9d34bd211f2a52c51b3228ba"><strong>debian/snakemake.examples</strong></a>

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1

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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="LC1" class="line" lang="plaintext">examples/* </span></pre>

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