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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/toil">Debian Med / toil</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/-/commit/fc18dd269f963de1b6bf0f4d985be46288192803">fc18dd26</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-09-29T17:31:01+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/-/commit/033eb5257f0fb2759ac2567d5922617d53e804a3">033eb525</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-09-29T17:31:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 5.5.0</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/-/commit/9afc56028cf3fda2bc1e84d378a4c7b0e771bf03">9afc5602</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-09-29T17:31:08+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/5.5.0'
Update to upstream version '5.5.0'
with Debian dir d5581870d1015c9a38efacb08415df1a8140a189</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/-/commit/fe54480b5697c782a5ac228d0495577cb312472e">fe54480b</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-09-29T19:47:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/-/commit/bb28fd33df26c012bf81a0c4427c91d503b81eda">bb28fd33</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-09-29T19:47:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bump minimum version of cwltool needed to 3.1.20210922203925
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/-/commit/61c53f83153b279907698dd730621536bb8cb3e4">61c53f83</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-09-29T19:47:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Testing: ignore src/toil/test/lib/aws/test_s3.py
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/-/commit/fb41ee3619e4189798f25f4254f03fa1525ab9d7">fb41ee36</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-09-29T19:47:08+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add testing dependency on python3-yaml.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/-/commit/e27f61e28b5a850f1d2bd3ce3789fb6ad0c03ed0">e27f61e2</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-09-29T19:47:08+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/patches/spelling: fix some typos
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/-/commit/955cc96b9a281bfe60b34bee4e919ac056638771">955cc96b</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-09-29T19:47:08+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/toil.lintian-overrides: documented another false positive
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/-/commit/5f4599637a6819ce191fb6c437e2a75e2c9705c7">5f459963</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-09-29T20:36:37+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
</ul>
<h4>30 changed files:</h4>
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<a href="#b8baf23d7ed7f2b79b86aeb041867428fb196428">
.github/PULL_REQUEST_TEMPLATE.md
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<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
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<a href="#587d266bb27a4dc3022bbed44dfa19849df3044c">
.gitlab-ci.yml
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.travis.yml
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<a href="#889c91308449c65c309146f6487ae74af64de5e9">
contrib/admin/mypy-with-ignore.py
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#e94fbb8719c4a68a67df894f2683205bb9914852">
debian/patches/no_galaxy_lib
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<a href="#bbcb48e2be151813ceeaaec7eadcaf824b49c1c6">
debian/patches/setting_version.patch
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<a href="#8f10e7fbf208d7b374153f7fd9e71e1bb75ca9ca">
debian/patches/ship_tests
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<a href="#c1fb0e9c942747a583cd8adc2707dd0cb1d97505">
debian/patches/soften-mesos-deps
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<a href="#037df6725949b5d76b6bcc0423f4f7b7f07f1ffa">
debian/patches/soften-pydocker-dep
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<a href="#e4c19aed51618bf0c7ebd03189c67e422f84d4eb">
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debian/patches/spelling
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<a href="#6187ccefe18309cfee9995c8b0d7b481c9971218">
debian/patches/test_with_less_memory
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<a href="#cb805f74cef9b2dafa0758f976c0bcadda0b7dde">
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debian/patches/version.patch
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
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<li class="file-stats">
<a href="#76aed571fa1aedc45cdf5c839049852f3158917e">
debian/toil.lintian-overrides
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<li class="file-stats">
<a href="#f99c72d2aacbf31ded1872c66de3f988dced0301">
docs/appendices/environment_vars.rst
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<a href="#5e25feb6b25012c00d6a27af4470f92ec5ccb67b">
docs/developingWorkflows/developing.rst
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<a href="#32be2c2e3690a70b96e3263f2bb4aa0ce226602a">
docs/running/cliOptions.rst
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<a href="#9d336859ebc50ce12f946e32de94343f00be9ebb">
docs/running/cloud/clusterUtils.rst
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<a href="#54aa56c0c0e2cd49ea7a6083879baecb55a418b1">
docs/running/cwl.rst
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<a href="#f4fb69164b97e1b6f17984369c9c382573a3f919">
requirements-dev.txt
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<li class="file-stats">
<a href="#59062b9d0a92eb7800de569b9a6c8818efe8a415">
src/toil/batchSystems/abstractBatchSystem.py
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<h5>The diff was not included because it is too large.</h5>
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