<!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=US-ASCII" 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/5ac7c5356ec4c00de60c23e4db1836a4772aaf35">5ac7c535</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2025-02-13T08:43:57+01:00 </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; 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 8.0.0</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/toil/-/commit/b5fb9b0299074ef1ee0b207f450fb5ed37713dec">b5fb9b02</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2025-02-13T08:43:57+01:00 </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; 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/bb29127b6122f8de578309b0f50ca0631f934277">bb29127b</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2025-02-13T08:44:05+01:00 </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; 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/8.0.0'

Update to upstream version '8.0.0'
with Debian dir a551f7d4c542493a833e1bd903436c3d7e480e1d</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/toil/-/commit/66209bd8f99abff1df5b7551004978ece00f63fa">66209bd8</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2025-02-13T08:44:10+01:00 </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; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Remove duplicate line from changelog.

Changes-By: lintian-brush
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/toil/-/commit/2434e877c5a4192265ee7460750736706acd5eee">2434e877</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2025-02-13T09:28:14+01:00 </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; 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; removed "skip-mypy-boto3" and "python3.12- syntax.patch" as they are no longer needed.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/toil/-/commit/859f978463c04defb9f6128a5ebd52cea084fac4">859f9784</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2025-02-13T09:28:14+01:00 </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; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added patch to remove the restrictions on the psutil Python package version.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/toil/-/commit/b72d78c05530d33e7fa26be0ee02ae66aee62d2f">b72d78c0</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2025-02-13T12:35:58+01:00 </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; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Updated the fix-tests patch to fix more tests.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/toil/-/commit/e23862a418ca7eb978effe440a96c4e3f52b5056">e23862a4</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2025-02-13T12:35:58+01:00 </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; 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: cwl-utils is needed for the tests
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/toil/-/commit/7b43abe0268cd33adf5f6bb79899aa7d63cfcdcf">7b43abe0</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2025-02-13T17:22:40+01:00 </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; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Added patch with a minimal PEP-517 pyproject.toml, to improve how we run the tests.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/toil/-/commit/c85ec6e92a7df830aa9d77286968a5063ace1bdb">c85ec6e9</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2025-02-13T17:22:40+01:00 </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; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/rules: simplify
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/toil/-/commit/a7a58c3ee7cddd6c83ad6a14e2de09e81ca1cbc0">a7a58c3e</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2025-02-13T17:22:40+01:00 </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; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/rules: skip manual page building in when the "nodoc" build profile is active.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/toil/-/commit/25b25d8a2a529e0d67f3852e0e13ebb2cbc3174c">25b25d8a</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2025-02-13T17:22:40+01:00 </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; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Switch autopkgtest to autopkgtest-pkg-pybuild
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/toil/-/commit/2f492fc9082116051709bca9b59074cc5fd98124">2f492fc9</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2025-02-13T17:22:40+01:00 </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; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/TODO: removed several completed items.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/toil/-/commit/38cc9947973c4d84ab5a59883270161cb55aa77e">38cc9947</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2025-02-13T17:25:16+01:00 </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; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/toil.lintian-overrides: removed, no longer applicable
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/toil/-/commit/7ed375e7a5dd86bf7400dc5d4919255975475194">7ed375e7</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2025-02-13T17:26:10+01:00 </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; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>fixup Added patch with a minimal PEP-517 pyproject.toml, to improve how we run the tests
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/toil/-/commit/d01104ffbcb8907adfbf06986e8827f80c5bf83d">d01104ff</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2025-02-13T18:12:47+01:00 </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; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>WIP
</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
30 changed files:
</h4>
<ul>
<li class="file-stats">
<a href="#e59566cf4999e6050a54787f9582ad9e95ddf314">
<span class="new-file">
+
.git-blame-ignore-revs
</span>
</a>
</li>
<li class="file-stats">
<a href="#b8baf23d7ed7f2b79b86aeb041867428fb196428">
.github/PULL_REQUEST_TEMPLATE.md
</a>
</li>
<li class="file-stats">
<a href="#091aff741808a09242f252264b14f4a9adaa5305">
.github/dependabot.yml
</a>
</li>
<li class="file-stats">
<a href="#e73fe7e7ba5b9214b9d6b212c8dee832600dfcdc">
<span class="deleted-file">

.github/workflows/autoupdate.yaml
</span>
</a>
</li>
<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
</a>
</li>
<li class="file-stats">
<a href="#587d266bb27a4dc3022bbed44dfa19849df3044c">
.gitlab-ci.yml
</a>
</li>
<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
</a>
</li>
<li class="file-stats">
<a href="#1a86abc3ec747473c3837236573ac86517bdc99e">
contrib/admin/cleanup_aws_resources.py
</a>
</li>
<li class="file-stats">
<a href="#889c91308449c65c309146f6487ae74af64de5e9">
contrib/admin/mypy-with-ignore.py
</a>
</li>
<li class="file-stats">
<a href="#20c1179934225e6a98875d30142f626f1622d2ba">
contrib/mypy-stubs/configargparse/__init__.pyi
</a>
</li>
<li class="file-stats">
<a href="#ad935fbf2b16b0bdedb44db15dacbb096b52df34">
contrib/mypy-stubs/configargparse/configargparse.pyi
</a>
</li>
<li class="file-stats">
<a href="#0f1f5be0a2e0d9a959a8c508d8813319a535bc93">
contrib/mypy-stubs/dill/_dill.pyi
</a>
</li>
<li class="file-stats">
<a href="#f2cae28ff947280bf74c8b836b708eca4231c8a7">
contrib/mypy-stubs/pubsub/core/topictreetraverser.pyi
</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="#d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba">
debian/TODO
</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="#68e0b13744e158347bfd74ebaaca667435f07d14">
debian/manpages
</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="#9f2bb23950c3371d81e699162117b1d95f9bd8d9">
debian/patches/atomic_copy_as_alternative.patch
</a>
</li>
<li class="file-stats">
<a href="#7d50ce949dd83a42315e1f32258188ca8a9ffb91">
debian/patches/fix_tests
</a>
</li>
<li class="file-stats">
<a href="#a63209f1dc647c99f0d0169edd0d41b5666ae012">
debian/patches/needs_aws-proxyfix
</a>
</li>
<li class="file-stats">
<a href="#e94fbb8719c4a68a67df894f2683205bb9914852">
debian/patches/no_galaxy_lib
</a>
</li>
<li class="file-stats">
<a href="#ce045391277954711a5859e9f4dca408ff018343">
<span class="new-file">
+
debian/patches/pyproject.toml
</span>
</a>
</li>
<li class="file-stats">
<a href="#af6304ecbc9db54d9736ecc134ff2dbda48645a7">
<span class="deleted-file">

debian/patches/python3.12-syntax.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="#1f3d45a2a8a53be57549f9311f83710b580e512f">
<span class="deleted-file">

debian/patches/skip-mypy-boto3
</span>
</a>
</li>
<li class="file-stats">
<a href="#ee6ceca55dcb70e41409534cdce765fc29138603">
debian/patches/soften-configargparser-deps
</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: #737278;">

<br>
<a href="https://salsa.debian.org/med-team/toil/-/compare/274ed606059d0fa73e38c9dfca4ad1bb5f8d0ab1...d01104ffbcb8907adfbf06986e8827f80c5bf83d">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>



</p>
</div>
</body>
</html>