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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/e5b407fe8698550efa31df9ddcd510c3b249f1cb">e5b407fe</a></strong>
<div>
<span>by Rebecca N. Palmer</span>
<i>at 2020-04-09T18:12:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Reproducibility: don't ship (timestamped) test logs.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snakemake/-/commit/a767af98c0dc2e75ed4559e08d39d974ca9b6141">a767af98</a></strong>
<div>
<span>by Rebecca N. Palmer</span>
<i>at 2020-04-09T18:14:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add self to Uploaders.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snakemake/-/commit/f156c10e5d0a4e3bdef12ac635f7a66cac50efad">f156c10e</a></strong>
<div>
<span>by Rebecca N. Palmer</span>
<i>at 2020-04-09T22:13:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update d/copyright.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snakemake/-/commit/e5cc7980fc0ee227c5e7fcb907ec558de2474671">e5cc7980</a></strong>
<div>
<span>by Rebecca N. Palmer</span>
<i>at 2020-04-09T22:15:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove Files-Excluded: the excluded directory no longer exists upstream.
</pre>
</li>
</ul>
<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/1cf3a516468339a8a3489b681efa689a876cab46...e5cc7980fc0ee227c5e7fcb907ec558de2474671#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,6 +13,9 @@ snakemake (5.14.0-1) UNRELEASED; urgency=medium</td>
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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> * Disable buggy test (upstream 322) and tests needing conda or docker.</span>
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<td class="diff-line-num old_line" data-linenumber="14" 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="14" 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="LC14" class="line" lang="plaintext"> * Delete unused patches.</span>
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<td class="diff-line-num old_line" data-linenumber="15" 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="15" 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="LC15" class="line" lang="plaintext"> * Use boto3 (like upstream) not boto.</span>
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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> * Reproducibility: don't ship (timestamped) test logs.</span>
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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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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="LC17" class="line" lang="plaintext"> * Add self to Uploaders.</span>
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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="18" 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="LC18" class="line" lang="plaintext"> * Update d/copyright, remove no longer needed Files-Excluded.</span>
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<td class="diff-line-num new_line" data-linenumber="19" 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="LC19" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="17" 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="LC20" class="line" lang="plaintext"> -- Rebecca N. Palmer <rebecca_palmer@zoho.com> Thu, 09 Apr 2020 14:57:00 +0100</span>
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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
</pre>
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</li>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/1cf3a516468339a8a3489b681efa689a876cab46...e5cc7980fc0ee227c5e7fcb907ec558de2474671#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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1
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1
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: snakemake</span>
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<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
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<td class="diff-line-num old old_line" data-linenumber="3" 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="LC3" class="line" lang="plaintext">Uploaders: Kevin Murray <kdmfoss@gmail.com></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Kevin Murray <kdmfoss@gmail.com><span class="idiff left right">, Rebecca N. Palmer <rebecca_palmer@zoho.com></span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: ca-certificates,</span>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/1cf3a516468339a8a3489b681efa689a876cab46...e5cc7980fc0ee227c5e7fcb907ec558de2474671#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,14 +2,24 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Upstream-Name: snakemake</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Upstream-Contact: Johannes Köster <johannes.koester@tu-dortmund.de></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Source: https://github.com/snakemake/snakemake</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">Files-Excluded: docker</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Files: *</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">Copyright: 2015<span class="idiff left right"> Johannes Köster <johannes.koester@tu-dortmund.de></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Copyright: 2015<span class="idiff left right">-2020 Johannes Köster <johannes.koester@tu-dortmund.de>, Manuel Holtgrewe, Christopher Tomkins-Tinch, Sven Nahnsen, Sebastian Kurscheid and contributors</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">License: Expat</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Files: tests/test_script/expected-results/test.html</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Copyright: 2005, 2015 jQuery Foundation, Inc. (jquery)</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> 2011-2015 Twitter, Inc. (bootstrap)</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> 2014 Alexander Farkas (@afarkas), @jdalton, @jon_neal, @rem (html5shiv)</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> 2013 Scott Jehl (Respond.js)</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> 2008-2016 jQuery Foundation and other contributors (jquery-ui)</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> 2013 Greg Franko (jquery Tocify)</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> 2014 Aidan Lister and Ruben Arslan (jQuery Plugin: Sticky Tabs)</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">License: Expat</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Comment: This is a test reference, we don't actually run this code. For source code of these modules, see r-cran-rmarkdown (0.8 for this version) and dependencies.</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Files: debian/*</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">Copyright: 2015<span class="idiff left right"> Kevin Murray <spam@kdmurray.id.au></span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Copyright: 2015<span class="idiff left right">-2020 Kevin Murray <spam@kdmurray.id.au> and Debian Med Team</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">License: Expat</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">License: Expat</span>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/1cf3a516468339a8a3489b681efa689a876cab46...e5cc7980fc0ee227c5e7fcb907ec558de2474671#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,7 +23,7 @@ export PYBUILD_TEST_ARGS=python{version} -m pytest tests/test*.py -n auto -k 'no</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"># test_container uses docker://bash</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"># test_cluster_sync is broken (https://github.com/snakemake/snakemake/issues/322)</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">export PYBUILD_AFTER_TEST_python3=rm -fr {build_dir}/bin {build_dir}/tests {dir}/tests/test_filegraph/.snakemake/</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">export PYBUILD_AFTER_TEST_python3=rm -fr {build_dir}/bin {build_dir}/tests {dir}/tests/test_filegraph/.snakemake/<span class="idiff left right"> {dir}/tests/linting/*/.snakemake/</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">export PATH:=$(shell pybuild --print build_dir --interpreter python3 --name $(PYBUILD_NAME))/bin:$(PATH)</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"></span>
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