<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN" "http://www.w3.org/TR/REC-html40/loose.dtd">
<html lang="en" style='--code-editor-font: var(--default-mono-font, "GitLab Mono"), JetBrains Mono, Menlo, DejaVu Sans Mono, Liberation Mono, Consolas, Ubuntu Mono, Courier New, andale mono, lucida console, monospace;'>
<head>
<meta content="text/html; charset=utf-8" http-equiv="Content-Type">
<title>
GitLab
</title>
<style data-premailer="ignore" type="text/css">
a { color: #1068bf; }
</style>
<style>img {
max-width: 100%; height: auto;
}
body {
font-size: .875rem;
}
body {
-webkit-text-shadow: rgba(255,255,255,.01) 0 0 1px;
}
body {
font-family: "GitLab Sans",-apple-system,BlinkMacSystemFont,"Segoe UI",Roboto,"Noto Sans",Ubuntu,Cantarell,"Helvetica Neue",sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol","Noto Color Emoji"; font-size: inherit;
}
</style>
</head>
<body style='font-size: inherit; -webkit-text-shadow: rgba(255,255,255,.01) 0 0 1px; font-family: "GitLab Sans",-apple-system,BlinkMacSystemFont,"Segoe UI",Roboto,"Noto Sans",Ubuntu,Cantarell,"Helvetica Neue",sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol","Noto Color Emoji";'>
<div class="content">
<h3 style="margin-top: 20px; margin-bottom: 10px;">
Michael R. Crusoe pushed to branch master at <a href="https://salsa.debian.org/med-team/toil">Debian Med / toil</a>
</h3>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
</h4>
<ul>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/toil/-/commit/a78392a7f682f380b34be3a4b4a88ce06a2a011f">a78392a7</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-04-16T10:12:37+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 9.2.0</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/toil/-/commit/139ff3de0451968a07f021b81e860ca097ef5d89">139ff3de</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-04-16T10:13:05+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update upstream source from tag 'upstream/9.2.0'
Update to upstream version '9.2.0'
with Debian dir ad3d89414d917a2834cc722d51c26fe068da882d</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/toil/-/commit/62191bbb81c493d3262341cb6b93259b49c1e600">62191bbb</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-04-16T10:22:17+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/toil/-/commit/80d05d911c2167c6f44d967045b49cca1b12e14c">80d05d91</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-04-16T10:22:42+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Refreshed patches, removing 3 not-needed or applied upstream.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/toil/-/commit/6ac2888b1bf2d7da2a3e6cf68cc33e5ce5c955c4">6ac2888b</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-04-16T10:22:43+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/control: build-dep & recommend python3-galaxy-tool-util.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/toil/-/commit/80ff8d890835eecbed8833e8ff5823dc4d174f46">80ff8d89</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-04-16T10:40:41+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/toil/-/commit/f81ad2cc09ff41969aeaeddd79f4e7e7f8bb3718">f81ad2cc</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-04-16T10:40:43+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 9.3.0</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/toil/-/commit/5fd7ea9796b3c998d5af8f72a2d5307ad1533cad">5fd7ea97</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-04-16T10:41:10+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update upstream source from tag 'upstream/9.3.0'
Update to upstream version '9.3.0'
with Debian dir 25e0b7d9dddc832ddd029957d04a900f8bc17ac7</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/toil/-/commit/1b7c634ecf5a53f5b5d4e33d2049df49bfdc611a">1b7c634e</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-04-16T10:41:11+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Standards-Version: 4.7.4 (routine-update)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/toil/-/commit/f56d95de1238b417a6d11dbda56a92af5cd8134e">f56d95de</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-04-16T10:44:22+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Refreshed patches
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/toil/-/commit/a39d32acc4d7dbecc5b4208deea1658d87a26385">a39d32ac</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-04-16T14:55:49+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Cherry-picked patch from upstream for newer cwltool & cwl-utils.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/toil/-/commit/0d4c478d1b7863008f7609c1684a71c3f44102f1">0d4c478d</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-04-16T15:14:15+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>release to unstable
</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
191 changed files:
</h4>
<ul>
<li class="file-stats">
<a href="#e59566cf4999e6050a54787f9582ad9e95ddf314">
.git-blame-ignore-revs
</a>
</li>
<li class="file-stats">
<a href="#c3aa8b7f1c613e43d3bb9d5ac52ac6603d945e89">
.github/workflows/codeql-analysis.yml
</a>
</li>
<li class="file-stats">
<a href="#587d266bb27a4dc3022bbed44dfa19849df3044c">
.gitlab-ci.yml
</a>
</li>
<li class="file-stats">
<a href="#8b28ba38a2c1b980c9846458130ebd674aea62fa">
.readthedocs.yaml
</a>
</li>
<li class="file-stats">
<a href="#a88e2a926426071529e2985b4ee35848bb987e65">
<span class="new-file">
+
BOTS.md
</span>
</a>
</li>
<li class="file-stats">
<a href="#2d5d10cfc503b52b745a2f437966ee1b895371af">
<span class="new-file">
+
CLAUDE.md
</span>
</a>
</li>
<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
</a>
</li>
<li class="file-stats">
<a href="#561b88e19de321ca62c7590bbb350765fb110905">
README.rst
</a>
</li>
<li class="file-stats">
<a href="#889c91308449c65c309146f6487ae74af64de5e9">
contrib/admin/mypy-with-ignore.py
</a>
</li>
<li class="file-stats">
<a href="#f2cae28ff947280bf74c8b836b708eca4231c8a7">
contrib/mypy-stubs/pubsub/core/topictreetraverser.pyi
</a>
</li>
<li class="file-stats">
<a href="#1bb7dd9b86c17fdc59275faf0c2e42101a532ad8">
contrib/slurm-test/docker-compose.yml
</a>
</li>
<li class="file-stats">
<a href="#8524728fbf28cb298eaacbb804b0625bedc4bdb4">
contrib/slurm-test/slurm.conf
</a>
</li>
<li class="file-stats">
<a href="#0aedc60470678ece7ebbdf7ca05da313d67367a0">
contrib/slurm-test/slurm_test.sh
</a>
</li>
<li class="file-stats">
<a href="#d807c24a76d4ce4f9a5fb9b51a34ba348080e3df">
contrib/toil-ci-prebake/Dockerfile
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#1ed36e80e111aab3ca3ff493855a17b0a45f6a3d">
<span class="new-file">
+
debian/patches/0001-upgrade-typing.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#7ba7e16fece655aac534679ade36127282441e6b">
debian/patches/accept_debian_packaged_docker_version.patch
</a>
</li>
<li class="file-stats">
<a href="#fbbe74fc36641fc70c11103ff1c8487c826b5a03">
debian/patches/allow_newer_requests
</a>
</li>
<li class="file-stats">
<a href="#7d50ce949dd83a42315e1f32258188ca8a9ffb91">
debian/patches/fix_tests
</a>
</li>
<li class="file-stats">
<a href="#e94fbb8719c4a68a67df894f2683205bb9914852">
<span class="deleted-file">
−
debian/patches/no_galaxy_lib
</span>
</a>
</li>
<li class="file-stats">
<a href="#af8447cfc8c60567c37ef54187e57893b7f5e568">
<span class="deleted-file">
−
debian/patches/remove_pytest-subtests.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#bbcb48e2be151813ceeaaec7eadcaf824b49c1c6">
debian/patches/setting_version.patch
</a>
</li>
<li class="file-stats">
<a href="#9016d006f9077fa6a613bd573e3a818a30fa0896">
debian/patches/soften-cwltool-dep.patch
</a>
</li>
<li class="file-stats">
<a href="#c1fb0e9c942747a583cd8adc2707dd0cb1d97505">
debian/patches/soften-mesos-deps
</a>
</li>
<li class="file-stats">
<a href="#e4c19aed51618bf0c7ebd03189c67e422f84d4eb">
<span class="deleted-file">
−
debian/patches/spelling
</span>
</a>
</li>
<li class="file-stats">
<a href="#734cb112ea615891b9ef15d07ae7bc1dee10abc3">
docker/Dockerfile.py
</a>
</li>
<li class="file-stats">
<a href="#862135262c5ca67586f30b468ef8270441e3c69b">
docs/appendices/deploy.rst
</a>
</li>
<li class="file-stats">
<a href="#d0b9e2e85a8d665bb1dc6e7086aa57bf41909d31">
docs/cwl/conformance.rst
</a>
</li>
<li class="file-stats">
<a href="#32be2c2e3690a70b96e3263f2bb4aa0ce226602a">
docs/running/cliOptions.rst
</a>
</li>
<li class="file-stats">
<a href="#23df65cbc06731222c916cd45cb6b24f00c5460e">
docs/running/hpcEnvironments.rst
</a>
</li>
<li class="file-stats">
<a href="#94ef85ac03a9b3926d1726c51aaf7e720200965d">
requirements-aws.txt
</a>
</li>
<li class="file-stats">
<a href="#b1f2507748c66f157346e017893778f0bef7bab0">
requirements-cwl.txt
</a>
</li>
<li class="file-stats">
<a href="#f4fb69164b97e1b6f17984369c9c382573a3f919">
requirements-dev.txt
</a>
</li>
<li class="file-stats">
<a href="#0bae7071779d2e7f48d89f07e811af4b111c6484">
requirements-kubernetes.txt
</a>
</li>
<li class="file-stats">
<a href="#8f82779feb90c0fb03a473c5e041127d75b7becd">
requirements-server.txt
</a>
</li>
<li class="file-stats">
<a href="#fc2ca49802c35d519775bde7394d6a8c4024b678">
requirements-wdl.txt
</a>
</li>
<li class="file-stats">
<a href="#19359a61ae2446b51b549167b014da2fcf265768">
requirements.txt
</a>
</li>
<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
</a>
</li>
<li class="file-stats">
<a href="#17984cec5ed84120fcb74b591a95036dae2f4400">
setup_gitlab_docker.py
</a>
</li>
<li class="file-stats">
<a href="#42e82db8dfc40fc9f2df468cc92584cb0441719f">
src/toil/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#59062b9d0a92eb7800de569b9a6c8818efe8a415">
src/toil/batchSystems/abstractBatchSystem.py
</a>
</li>
<li class="file-stats">
<a href="#e80ba9107fbe8c247c4a06d919de60d903b13b57">
src/toil/batchSystems/abstractGridEngineBatchSystem.py
</a>
</li>
<li class="file-stats">
<a href="#ba9874937eb6ae181d36bbf4200e0990b9a14568">
src/toil/batchSystems/awsBatch.py
</a>
</li>
<li class="file-stats">
<a href="#ad7d2d18aa5357175a5b826d596fe75eddf5624b">
src/toil/batchSystems/cleanup_support.py
</a>
</li>
<li class="file-stats">
<a href="#d6f551010d930851e552b6da33f34ae7615e38fd">
src/toil/batchSystems/contained_executor.py
</a>
</li>
<li class="file-stats">
<a href="#8665892a623b484a6317e6aef58200c3f489951b">
src/toil/batchSystems/gridengine.py
</a>
</li>
<li class="file-stats">
<a href="#8354e49ab5525eaccab005722337809789a2b4c8">
src/toil/batchSystems/htcondor.py
</a>
</li>
<li class="file-stats">
<a href="#9859689e8bd3ddc443a4adadad9053893501bd72">
src/toil/batchSystems/kubernetes.py
</a>
</li>
<li class="file-stats">
<a href="#6b4c7a814f910ffc8b4f065b91de99d5e1996217">
src/toil/batchSystems/local_support.py
</a>
</li>
<li class="file-stats">
<a href="#184892bb0e21972b1bc724ffc0b62a4c3616a44c">
src/toil/batchSystems/lsf.py
</a>
</li>
<li class="file-stats">
<a href="#51c103b23323037f067bfea96a5cd293cbd8bfab">
src/toil/batchSystems/mesos/batchSystem.py
</a>
</li>
<li class="file-stats">
<a href="#f186059ee2f5bb74d12be47bf27a34af0aa4daac">
src/toil/batchSystems/mesos/test/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#99c24d1b30534d665746feee900c46f6e8459b39">
src/toil/batchSystems/options.py
</a>
</li>
<li class="file-stats">
<a href="#e5d02c7b50182649b621d35c687c50730f0655de">
src/toil/batchSystems/registry.py
</a>
</li>
<li class="file-stats">
<a href="#40d7e534600c41f2ac23866cd2edfb31bccd3afe">
src/toil/batchSystems/singleMachine.py
</a>
</li>
<li class="file-stats">
<a href="#a6f3af15c881ae20fc1a43acbbeb46501aac42d1">
src/toil/batchSystems/slurm.py
</a>
</li>
<li class="file-stats">
<a href="#613fd687d50c98ed88dd86e84d2d6b01865013f3">
src/toil/batchSystems/torque.py
</a>
</li>
<li class="file-stats">
<a href="#b5ab9a61b11b6e94229af5e4ca02bbd23c142a9d">
src/toil/bus.py
</a>
</li>
<li class="file-stats">
<a href="#e4fd847d42e121b772337a96bada018b0e6ad45c">
src/toil/common.py
</a>
</li>
<li class="file-stats">
<a href="#a6644c2fafa6ddade32ff78abd9bb07dccfe49c6">
<span class="new-file">
+
src/toil/conftest.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#0dbd18a5ef7b094b4ad2f95d5aa87ee2ed51212f">
src/toil/cwl/cwltoil.py
</a>
</li>
<li class="file-stats">
<a href="#89fb9fd3f9c0ed49d506a50d1fde61bdea550984">
src/toil/cwl/utils.py
</a>
</li>
<li class="file-stats">
<a href="#cba2923ab2fdd1898642e543e045ee91ec857871">
src/toil/deferred.py
</a>
</li>
<li class="file-stats">
<a href="#b6f67b1641126abae4f36960038d066540471dfc">
src/toil/fileStores/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#a4add364610812caa42a9215ebab384cc263e063">
src/toil/fileStores/abstractFileStore.py
</a>
</li>
<li class="file-stats">
<a href="#7bacd2a077f0dc4dd68b8f4bb4edb4cb762f9823">
src/toil/fileStores/cachingFileStore.py
</a>
</li>
<li class="file-stats">
<a href="#2e740f2c14c1744d1a97bb6dc673ff7864e2d9b1">
src/toil/fileStores/nonCachingFileStore.py
</a>
</li>
<li class="file-stats">
<a href="#25bb698efc92d8425e6ea48ef986d72d2cf62017">
src/toil/job.py
</a>
</li>
<li class="file-stats">
<a href="#596e3e7c16c66f62cd45824e69b58880ea4b9027">
src/toil/jobStores/abstractJobStore.py
</a>
</li>
<li class="file-stats">
<a href="#a13607e119e7ea420a0824a7cdbd58157a4965f0">
src/toil/jobStores/aws/jobStore.py
</a>
</li>
<li class="file-stats">
<a href="#4235e02b3af6b47301e96b7bfe9967d850ff1a72">
src/toil/jobStores/aws/utils.py
</a>
</li>
<li class="file-stats">
<a href="#f8698b8c91b4525c2e8a2cc4fe1f8b489291216f">
src/toil/jobStores/fileJobStore.py
</a>
</li>
<li class="file-stats">
<a href="#dd045e3729cc148b776666a18ef81c339828c1ff">
src/toil/jobStores/googleJobStore.py
</a>
</li>
<li class="file-stats">
<a href="#ea5270bc3abd520281f872efd33d52f850400455">
src/toil/jobStores/utils.py
</a>
</li>
<li class="file-stats">
<a href="#b423c2afb0f414beab2120da703bd01ca2a7bb55">
src/toil/leader.py
</a>
</li>
<li class="file-stats">
<a href="#00bfc0233160e805130f8bc41d9a30b3f3fb8391">
src/toil/lib/accelerators.py
</a>
</li>
<li class="file-stats">
<a href="#4a3591374d94bc6fbbb43b521255db31528dce0d">
src/toil/lib/aws/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#d2a4d1d054bb6dc634380e8cfbc9edc686908ca0">
src/toil/lib/aws/ami.py
</a>
</li>
<li class="file-stats">
<a href="#b84b0a847482072950f543a99b06ea99e6ec9b85">
src/toil/lib/aws/iam.py
</a>
</li>
<li class="file-stats">
<a href="#84c3abe347344cd667c2bfdff9eea8ee645a7dca">
src/toil/lib/aws/s3.py
</a>
</li>
<li class="file-stats">
<a href="#e261735446c0c623daacadf1d3f4234a772381b7">
src/toil/lib/aws/session.py
</a>
</li>
<li class="file-stats">
<a href="#065cfdfc8307da59883dcdd3a1b1dfa50e5efc60">
src/toil/lib/aws/utils.py
</a>
</li>
<li class="file-stats">
<a href="#ab760b1d9cac832da8cd8bd4ee62b94d1f48165b">
src/toil/lib/checksum.py
</a>
</li>
<li class="file-stats">
<a href="#28e9b1aede74a9eaad2cfa54c2c2f4d3bfe1cb2d">
src/toil/lib/compatibility.py
</a>
</li>
<li class="file-stats">
<a href="#9056d8af23947aee1e915be6cd60e6b2ee4ecc18">
src/toil/lib/conversions.py
</a>
</li>
<li class="file-stats">
<a href="#d1ffcab97bd242b541753a6b0e700f31bf1f1bd6">
src/toil/lib/directory.py
</a>
</li>
<li class="file-stats">
<a href="#b9e12697d92644b5c5066ea90567c44a73829875">
src/toil/lib/docker.py
</a>
</li>
<li class="file-stats">
<a href="#460f3d5c776a826343975b0da552913dbfb62d1e">
src/toil/lib/dockstore.py
</a>
</li>
<li class="file-stats">
<a href="#be8659e9cb9ae45387dc2fc94e58e1f395e2289e">
src/toil/lib/ec2.py
</a>
</li>
<li class="file-stats">
<a href="#2b82c47683e450f3df99701fa77fa3f90f67ca39">
src/toil/lib/ec2nodes.py
</a>
</li>
<li class="file-stats">
<a href="#81dab898147fcf4beeb989e2a7f220c8b48d3657">
src/toil/lib/exceptions.py
</a>
</li>
<li class="file-stats">
<a href="#57ba65e1c674dd0bd22676e1c16c415ffd927607">
src/toil/lib/expando.py
</a>
</li>
<li class="file-stats">
<a href="#f57b42b11d2438911946c4a577e4ffb0a6bdbf71">
src/toil/lib/ftp_utils.py
</a>
</li>
<li class="file-stats">
<a href="#817ec0b3e76cbfa8f89018c49dd5b1eb30013019">
src/toil/lib/generatedEC2Lists.py
</a>
</li>
<li class="file-stats">
<a href="#ab57733d763c0577cb29ea55288ee91f853f76cc">
src/toil/lib/history.py
</a>
</li>
<li class="file-stats">
<a href="#88bb609be2d4204220abbd8b51882cdce6f7d31c">
src/toil/lib/history_submission.py
</a>
</li>
<li class="file-stats">
<a href="#0d1324d0758acef9bc14db204a643f668ddf87ea">
src/toil/lib/io.py
</a>
</li>
<li class="file-stats">
<a href="#15b495fc2788a08f0f59f40e5f5268885cf20d87">
src/toil/lib/memoize.py
</a>
</li>
<li class="file-stats">
<a href="#f79f42b6f106c28017c38d5755a5a6b851c8cae2">
src/toil/lib/misc.py
</a>
</li>
<li class="file-stats">
<a href="#4264087475e0f1f4a13c0d939f49907bc8ed7157">
src/toil/lib/pipes.py
</a>
</li>
<li class="file-stats">
<a href="#e9838e680fefe7abcab72c4473d44e787bca4631">
src/toil/lib/plugins.py
</a>
</li>
<li class="file-stats">
<a href="#a4f71f95dfa7fa57c3ccd3f758f6df359040f91c">
src/toil/lib/resources.py
</a>
</li>
<li class="file-stats">
<a href="#7d9bb5e112f44c84aaece70564a669a79d886816">
src/toil/lib/retry.py
</a>
</li>
<li class="file-stats">
<a href="#7e71432f91b03a2d090d368d005146e20d34f040">
src/toil/lib/threading.py
</a>
</li>
<li class="file-stats">
<a href="#6b3406470b6f57a03ca70e29e020c473edbd4040">
src/toil/lib/throttle.py
</a>
</li>
<li class="file-stats">
<a href="#a24d888fc0c63a8ac00968c572a985b9a7acecaf">
src/toil/lib/trs.py
</a>
</li>
<li class="file-stats">
<a href="#83a9ae17596a7983ba967ab88b49b14f2490c565">
src/toil/lib/url.py
</a>
</li>
<li class="file-stats">
<a href="#af2a19ec5c04229ee32c33f7b1df4f420b9542b1">
src/toil/lib/web.py
</a>
</li>
<li class="file-stats">
<a href="#1f6fe96dc4e51d95c4498587a35e85202aecce21">
src/toil/options/common.py
</a>
</li>
<li class="file-stats">
<a href="#0432790a6b154f9d7a9e459bd928de67a3f9f45b">
src/toil/options/cwl.py
</a>
</li>
<li class="file-stats">
<a href="#0dce75647659fbd2a59bbb208060707ad95d736b">
src/toil/options/runner.py
</a>
</li>
<li class="file-stats">
<a href="#5c4d830cd5e957b201b1d6279433b1b879f38ca4">
src/toil/options/wdl.py
</a>
</li>
<li class="file-stats">
<a href="#aafbcbd682e5739a85dbe72712e7e41023cfa9c0">
src/toil/provisioners/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#ebacd73950dc03a7e19229812bb91650181fb787">
src/toil/provisioners/abstractProvisioner.py
</a>
</li>
<li class="file-stats">
<a href="#43292feaa91573b749f502eef7628a410cd62709">
src/toil/provisioners/aws/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#0ee38d0ed1e526aa2564ef01d7d5c989aa73153a">
src/toil/provisioners/aws/awsProvisioner.py
</a>
</li>
<li class="file-stats">
<a href="#4fdd980a9183fab0c434ee4d0a6b3ca38c006cf6">
src/toil/provisioners/clusterScaler.py
</a>
</li>
<li class="file-stats">
<a href="#320f6a22bb8ff032012f70b0f94f0b66b25ff06d">
src/toil/provisioners/gceProvisioner.py
</a>
</li>
<li class="file-stats">
<a href="#72ca00d19dfa2460df5b9f2612345bb7233d68cc">
src/toil/provisioners/node.py
</a>
</li>
<li class="file-stats">
<a href="#55b4831a87dfdae83ee6bf12de389a338b6a9606">
src/toil/realtimeLogger.py
</a>
</li>
<li class="file-stats">
<a href="#67b0e9a4c7ac917353df601be79a4d9c712d09f3">
src/toil/resource.py
</a>
</li>
<li class="file-stats">
<a href="#c7a23edbc9a1596ced12d48514de54fc469c0175">
src/toil/server/app.py
</a>
</li>
<li class="file-stats">
<a href="#e8ec7ad1a31a7f9f3b92a6bd2c15046a16b68138">
src/toil/server/cli/wes_cwl_runner.py
</a>
</li>
<li class="file-stats">
<a href="#82dde4d87a0b34aa10700980edf89ce21c963d35">
src/toil/server/utils.py
</a>
</li>
<li class="file-stats">
<a href="#8b7ba8e799c2fcf4cf264cddc9ac3b84484cc4ce">
src/toil/server/wes/abstract_backend.py
</a>
</li>
<li class="file-stats">
<a href="#e51f6883bd213f09bff85070db72346e279bd886">
src/toil/server/wes/amazon_wes_utils.py
</a>
</li>
<li class="file-stats">
<a href="#b2ca73ff51071002707030835126638fb0cd22cf">
src/toil/server/wes/tasks.py
</a>
</li>
<li class="file-stats">
<a href="#623995010dbeadf4844d4a0764bda6aba746ba62">
src/toil/server/wes/toil_backend.py
</a>
</li>
<li class="file-stats">
<a href="#daa94b7532f7f167763ab71046b4f7585b0b351d">
src/toil/server/wsgi_app.py
</a>
</li>
<li class="file-stats">
<a href="#2e037cccc6d585d98ea1a7f2fe303016d335720c">
src/toil/serviceManager.py
</a>
</li>
<li class="file-stats">
<a href="#5912984dc30bcff0ad0e03fd9bf2d9edd91e579c">
src/toil/statsAndLogging.py
</a>
</li>
<li class="file-stats">
<a href="#d0bde58f1db120631635b5f3fff16dd1cd6ad2a1">
src/toil/test/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#5b8a5dc6da7348cb5ead39c3598b7cc403e5d23c">
src/toil/test/batchSystems/batchSystemTest.py
</a>
</li>
<li class="file-stats">
<a href="#f38c3cd9b0bcb2378f50a8ea83b90f191b026ac8">
src/toil/test/batchSystems/batch_system_plugin_test.py
</a>
</li>
<li class="file-stats">
<a href="#96459f5054e9121215b86d0ba6dacef97a87d08e">
src/toil/test/batchSystems/test_slurm.py
</a>
</li>
<li class="file-stats">
<a href="#59c0ce8642bfcd9622049d2865f4a3ea4989f0fa">
src/toil/test/cwl/conftest.py
</a>
</li>
<li class="file-stats">
<a href="#6e8ee3e619de891a48dbafa4f9851650bf598f6a">
src/toil/test/cwl/cwlTest.py
</a>
</li>
<li class="file-stats">
<a href="#c919bcbfa38026a7ececfb70f137d6fd56e9542b">
<span class="new-file">
+
src/toil/test/cwl/download_file_uri.json
</span>
</a>
</li>
<li class="file-stats">
<a href="#54997237b9dfd9d62e84b91bc6f303629db1ef85">
<span class="new-file">
+
src/toil/test/cwl/download_file_uri_no_hostname.json
</span>
</a>
</li>
<li class="file-stats">
<a href="#239eb2b3cdb5c0ecd1002c18249bce812f901f73">
<span class="new-file">
+
src/toil/test/cwl/echo_string_and_fail.cwl
</span>
</a>
</li>
<li class="file-stats">
<a href="#ecf69d6f6c68f31ca192fa6798efcca367cb6845">
src/toil/test/docs/scripts/tutorial_staging.py
</a>
</li>
<li class="file-stats">
<a href="#6cc2a02da82aa69708f1a6aa58ba449f1e9efca4">
src/toil/test/jobStores/jobStoreTest.py
</a>
</li>
<li class="file-stats">
<a href="#1fdc3b91ae6fa1991d407d895bd4521e68fd6ff5">
src/toil/test/lib/aws/test_iam.py
</a>
</li>
<li class="file-stats">
<a href="#876450e6b3c52e697610ada827e7a5de6bebb2ad">
src/toil/test/lib/aws/test_s3.py
</a>
</li>
<li class="file-stats">
<a href="#7a4c60e14a2c71acc0930cfd7829ad0afa470f86">
src/toil/test/lib/dockerTest.py
</a>
</li>
<li class="file-stats">
<a href="#ef25cfb593a2f0783873d2998e712509ab96fbe8">
src/toil/test/lib/test_ec2.py
</a>
</li>
<li class="file-stats">
<a href="#105b34fca7da6d4335c966897dc228a6c6276cc3">
src/toil/test/lib/test_history.py
</a>
</li>
<li class="file-stats">
<a href="#3335920a2a53f0e13399113d3de145be00fa9d18">
src/toil/test/lib/test_trs.py
</a>
</li>
<li class="file-stats">
<a href="#462e2170297843d8d3d032cb7a8134b2845dc6d3">
src/toil/test/lib/test_url.py
</a>
</li>
<li class="file-stats">
<a href="#e4ca37ba2e5652637382e8d52deca7284e03a7c8">
src/toil/test/lib/url_plugin_test.py
</a>
</li>
<li class="file-stats">
<a href="#84879046ea081f5042e579a005700b0e11e7fc16">
src/toil/test/provisioners/aws/awsProvisionerTest.py
</a>
</li>
<li class="file-stats">
<a href="#d575e966bc4084df86249416273b73122836bad2">
src/toil/test/provisioners/clusterScalerTest.py
</a>
</li>
<li class="file-stats">
<a href="#5df835d4a638ac31ef351f1901fa863905f7ed5c">
src/toil/test/provisioners/clusterTest.py
</a>
</li>
<li class="file-stats">
<a href="#609501b782d03445ce7741ac239762f4e79127d7">
<span class="new-file">
+
src/toil/test/server/safeFileTest.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#e8cf4884fd997f632402cd0ba6a820be65eb0393">
src/toil/test/server/serverTest.py
</a>
</li>
<li class="file-stats">
<a href="#2349589b98e5cd1590a06bb99877100f8d42dd01">
src/toil/test/sort/restart_sort.py
</a>
</li>
<li class="file-stats">
<a href="#0077f8aafb74fc2a8ac8c1a35436f322bc387271">
src/toil/test/sort/sort.py
</a>
</li>
<li class="file-stats">
<a href="#b08e97a3544710fa5315e150a7cbbe2b2961f6b4">
src/toil/test/src/deferredFunctionTest.py
</a>
</li>
<li class="file-stats">
<a href="#df77822fe9dc55e19afffcf4572c69bf0184dd5a">
src/toil/test/src/environmentTest.py
</a>
</li>
<li class="file-stats">
<a href="#93d686c757d84c5ca681669cd6a8d45fefdfe4ac">
src/toil/test/src/fileStoreTest.py
</a>
</li>
<li class="file-stats">
<a href="#1d5fe112ef9322dceab89da22d844a8cd6bd3c3f">
src/toil/test/src/importExportFileTest.py
</a>
</li>
<li class="file-stats">
<a href="#01d228cf121ceae7de71a180ebacd021160f1ce8">
src/toil/test/src/jobServiceTest.py
</a>
</li>
<li class="file-stats">
<a href="#79348eba06f26e52854cd55548d2b6883dabc5ea">
src/toil/test/src/jobTest.py
</a>
</li>
<li class="file-stats">
<a href="#5524a929f7a637498fc018f78d497e74e64ee63f">
src/toil/test/src/miscTests.py
</a>
</li>
<li class="file-stats">
<a href="#0b256ea61d382ba95b8ff4c260dc2249fb6a0c02">
src/toil/test/src/promisedRequirementTest.py
</a>
</li>
<li class="file-stats">
<a href="#d9ad70520b1af5ee57128b68dbfc04680c66dfb4">
src/toil/test/src/regularLogTest.py
</a>
</li>
<li class="file-stats">
<a href="#97929ef0202b3abaeee3855c898868f4920ca0dc">
src/toil/test/src/resourceTest.py
</a>
</li>
<li class="file-stats">
<a href="#f54ade111e4a81ec7a63f7094ed5a19910262c33">
src/toil/test/src/restartDAGTest.py
</a>
</li>
<li class="file-stats">
<a href="#58a890cd89b58577aa6f512186d523da351d6ebe">
src/toil/test/src/resumabilityTest.py
</a>
</li>
<li class="file-stats">
<a href="#dbf620bf4ee45982928be23b7f4d143d12b05105">
src/toil/test/src/retainTempDirTest.py
</a>
</li>
<li class="file-stats">
<a href="#ed7559bec478ee94bdb22edf0f22f34993b6b6d5">
src/toil/test/src/systemTest.py
</a>
</li>
<li class="file-stats">
<a href="#aa778e586c5ff04b65bbd49d47553924fbc420be">
src/toil/test/src/threadingTest.py
</a>
</li>
<li class="file-stats">
<a href="#d47436d6fa233213a0a4bb9d112c965b0f481f9c">
src/toil/test/src/workerTest.py
</a>
</li>
<li class="file-stats">
<a href="#104e3d36618063f76831cd47f740a73e677f2734">
src/toil/test/utils/toilDebugTest.py
</a>
</li>
<li class="file-stats">
<a href="#4c42f44481d9d3db8f4b1616555ef0757393578b">
src/toil/test/utils/toilKillTest.py
</a>
</li>
<li class="file-stats">
<a href="#6b418636a667f91d454914499d033fd505219722">
src/toil/test/utils/utilsTest.py
</a>
</li>
<li class="file-stats">
<a href="#27552fb9014a40588b6749318b1c883ea55e25d6">
<span class="new-file">
+
src/toil/test/wdl/singularity/singularity.wdl
</span>
</a>
</li>
<li class="file-stats">
<a href="#a043d4531bf930211a0105c42e5be6d94c36dcd8">
src/toil/test/wdl/wdltoil_test.py
</a>
</li>
<li class="file-stats">
<a href="#0a524bf31e44a6896a62c07d950d2e5d4ae7f728">
src/toil/test/wdl/wdltoil_test_kubernetes.py
</a>
</li>
<li class="file-stats">
<a href="#f2c899d8ec8d70ffe652a840e2a33468ea249db2">
src/toil/toilState.py
</a>
</li>
<li class="file-stats">
<a href="#79c8388962e19282aa7a55845958f1f619623895">
src/toil/utils/toilDebugFile.py
</a>
</li>
<li class="file-stats">
<a href="#3c342ba42f902e88b498e281970bbf70fb87183d">
src/toil/utils/toilDebugJob.py
</a>
</li>
<li class="file-stats">
<a href="#3dee82c92d6fe9e05c0636ad5b00785d59f2c7cc">
src/toil/utils/toilLaunchCluster.py
</a>
</li>
<li class="file-stats">
<a href="#bcfb7168fd08eeb1c1faeab5ab64e9525be74d90">
src/toil/utils/toilSshCluster.py
</a>
</li>
<li class="file-stats">
<a href="#fe8e9873b69059b703135f9f716477ef74f28609">
src/toil/utils/toilStats.py
</a>
</li>
<li class="file-stats">
<a href="#159ddcd64cbe692a4d2638f987db003cc024425c">
src/toil/utils/toilStatus.py
</a>
</li>
<li class="file-stats">
<a href="#4ba8173bb10fceebcd6ca502fa6cf48a28ebdf02">
src/toil/wdl/wdltoil.py
</a>
</li>
<li class="file-stats">
<a href="#18f9b5de2f811d48c647453af8626fed83792536">
src/toil/worker.py
</a>
</li>
<li class="file-stats">
<a href="#5924b9c92b6ea461ef4ffca6c6e00a0d1d183452">
version_template.py
</a>
</li>
</ul>
<h5 style="margin-top: 10px; margin-bottom: 10px; font-size: .875rem;">
The diff was not included because it is too large.
</h5>
</div>
<div class="footer" style="margin-top: 10px;">
<p style="font-size: small; color: #626168;">
—
<br>
<a href="https://salsa.debian.org/med-team/toil/-/compare/96b778d5aa37093e7d6e2c1e4dcae5bf968d8107...0d4c478d1b7863008f7609c1684a71c3f44102f1">View it on GitLab</a>.
<br>
You're receiving this email because of your account on <a target="_blank" rel="noopener noreferrer" href="https://salsa.debian.org">salsa.debian.org</a>. <a href="https://salsa.debian.org/-/profile/notifications" target="_blank" rel="noopener noreferrer" class="mng-notif-link">Manage all notifications</a> · <a href="https://salsa.debian.org/help" target="_blank" rel="noopener noreferrer" class="help-link">Help</a>
<span style="color: transparent; font-size: 0; display: none; overflow: hidden; opacity: 0; width: 0; height: 0; max-width: 0; max-height: 0;">
Notification message regarding https://salsa.debian.org/med-team/toil/-/compare/96b778d5aa37093e7d6e2c1e4dcae5bf968d8107...0d4c478d1b7863008f7609c1684a71c3f44102f1 at 1776345314
</span>
</p>
</div>
</body>
</html>