<!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 upstream 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/fbd8c7112ffd8865e5f149001211e24270a4ac87">fbd8c711</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2025-10-16T13:07:10+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;'>New upstream version 9.1.0</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
72 changed files:
</h4>
<ul>
<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="#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="#734cb112ea615891b9ef15d07ae7bc1dee10abc3">
docker/Dockerfile.py
</a>
</li>
<li class="file-stats">
<a href="#4ec21f7a5e9be43613b40a694d2370760519a131">
docs/appendices/aws_min_permissions.rst
</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="#ba1737f2ce7d642bbfa3bdf256e038820d8cc5ca">
requirements-google.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="#19359a61ae2446b51b549167b014da2fcf265768">
requirements.txt
</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="#9859689e8bd3ddc443a4adadad9053893501bd72">
src/toil/batchSystems/kubernetes.py
</a>
</li>
<li class="file-stats">
<a href="#51c103b23323037f067bfea96a5cd293cbd8bfab">
src/toil/batchSystems/mesos/batchSystem.py
</a>
</li>
<li class="file-stats">
<a href="#a6f3af15c881ae20fc1a43acbbeb46501aac42d1">
src/toil/batchSystems/slurm.py
</a>
</li>
<li class="file-stats">
<a href="#0dbd18a5ef7b094b4ad2f95d5aa87ee2ed51212f">
src/toil/cwl/cwltoil.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="#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="#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="#8077e5b40b418b30c9294c0fc1311bf912a455d1">
<span class="new-file">
+
src/toil/lib/aws/config.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#84c3abe347344cd667c2bfdff9eea8ee645a7dca">
src/toil/lib/aws/s3.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">
<span class="new-file">
+
src/toil/lib/checksum.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#9056d8af23947aee1e915be6cd60e6b2ee4ecc18">
src/toil/lib/conversions.py
</a>
</li>
<li class="file-stats">
<a href="#d1ffcab97bd242b541753a6b0e700f31bf1f1bd6">
<span class="new-file">
+
src/toil/lib/directory.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#be8659e9cb9ae45387dc2fc94e58e1f395e2289e">
src/toil/lib/ec2.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="#817ec0b3e76cbfa8f89018c49dd5b1eb30013019">
src/toil/lib/generatedEC2Lists.py
</a>
</li>
<li class="file-stats">
<a href="#0d1324d0758acef9bc14db204a643f668ddf87ea">
src/toil/lib/io.py
</a>
</li>
<li class="file-stats">
<a href="#49d64eb057eb8dd38ac222ccae1a42910cd715cf">
<span class="deleted-file">
โˆ’
src/toil/lib/iterables.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#15b495fc2788a08f0f59f40e5f5268885cf20d87">
src/toil/lib/memoize.py
</a>
</li>
<li class="file-stats">
<a href="#4264087475e0f1f4a13c0d939f49907bc8ed7157">
<span class="new-file">
+
src/toil/lib/pipes.py
</span>
</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="#af2a19ec5c04229ee32c33f7b1df4f420b9542b1">
src/toil/lib/web.py
</a>
</li>
<li class="file-stats">
<a href="#aafbcbd682e5739a85dbe72712e7e41023cfa9c0">
src/toil/provisioners/__init__.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="#72ca00d19dfa2460df5b9f2612345bb7233d68cc">
src/toil/provisioners/node.py
</a>
</li>
<li class="file-stats">
<a href="#67b0e9a4c7ac917353df601be79a4d9c712d09f3">
src/toil/resource.py
</a>
</li>
<li class="file-stats">
<a href="#d0bde58f1db120631635b5f3fff16dd1cd6ad2a1">
src/toil/test/__init__.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="#52931d4bdd1a16dc0f492f0a0fe45f3ced13c5c7">
<span class="deleted-file">
โˆ’
src/toil/test/docs/scripts/stagingExampleFiles/in.txt
</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="#7b28935ee3039820ba3818dd9e6a950820feabc1">
src/toil/test/lib/aws/test_utils.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="#e7807804fcae32bf67c5a5470d9efe11b7aaf4a0">
src/toil/test/src/autoDeploymentTest.py
</a>
</li>
<li class="file-stats">
<a href="#93d686c757d84c5ca681669cd6a8d45fefdfe4ac">
src/toil/test/src/fileStoreTest.py
</a>
</li>
<li class="file-stats">
<a href="#17528bb33673010fbbdc48b72a271b2849ba0be6">
src/toil/test/utils/ABCWorkflowDebug/debugWorkflow.py
</a>
</li>
<li class="file-stats">
<a href="#4c42f44481d9d3db8f4b1616555ef0757393578b">
src/toil/test/utils/toilKillTest.py
</a>
</li>
<li class="file-stats">
<a href="#5aaf2f7543f865350b99a686fbf7f34c59ff2af4">
src/toil/test/wdl/md5sum/md5sum.json
</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="#79c8388962e19282aa7a55845958f1f619623895">
src/toil/utils/toilDebugFile.py
</a>
</li>
<li class="file-stats">
<a href="#fe8e9873b69059b703135f9f716477ef74f28609">
src/toil/utils/toilStats.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;">
โ€”
<br>
<a href="https://salsa.debian.org/med-team/toil/-/commit/fbd8c7112ffd8865e5f149001211e24270a4ac87">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> ยท <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/-/commit/fbd8c7112ffd8865e5f149001211e24270a4ac87 at 1760695035
</span>
<script type="application/ld+json">{"@context":"http://schema.org","@type":"EmailMessage","action":{"@type":"ViewAction","name":"View Commit","url":"https://salsa.debian.org/med-team/toil/-/commit/fbd8c7112ffd8865e5f149001211e24270a4ac87"}}</script>


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