<!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: hsla(0,0%,100%,.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: hsla(0,0%,100%,.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;">
Andreas Tille pushed to branch upstream at <a href="https://salsa.debian.org/med-team/python-cobra">Debian Med / python-cobra</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/python-cobra/-/commit/3bd1dd72d8fe07f4baf91e94cbd760678874391b">3bd1dd72</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2026-06-02T16:53:09+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 0.31.1</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
49 changed files:
</h4>
<ul>
<li class="file-stats">
<a href="#626a747c8694eaae66f2afb3d1a745b045782c70">
.editorconfig
</a>
</li>
<li class="file-stats">
<a href="#d12a654f2dea6dc04ae8a20c71803086befd45b0">
.github/CONTRIBUTING.rst
</a>
</li>
<li class="file-stats">
<a href="#d0c1e77a16bd94cf0323d146780779dd42fcf13c">
.github/workflows/cron.yml
</a>
</li>
<li class="file-stats">
<a href="#c778226b6c4c0fb51cf7942c8ee1f3d9fc1249d0">
.github/workflows/main.yml
</a>
</li>
<li class="file-stats">
<a href="#16911b9809e0d05b7b124ba8453fa5303d74924c">
.github/workflows/release.yml
</a>
</li>
<li class="file-stats">
<a href="#c35bc83d626f67e197849c9795030a02efe21488">
<span class="new-file">
+
.github/workflows/safety.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#7ceee5d954a74b8640cc2bfd6c27b8fdf07d7045">
.github/workflows/test.yml
</a>
</li>
<li class="file-stats">
<a href="#e7d14d429f898757a423156de0e8c49d75240694">
<span class="new-file">
+
.pre-commit-config.yaml
</span>
</a>
</li>
<li class="file-stats">
<a href="#8b28ba38a2c1b980c9846458130ebd674aea62fa">
.readthedocs.yaml
</a>
</li>
<li class="file-stats">
<a href="#561b88e19de321ca62c7590bbb350765fb110905">
README.rst
</a>
</li>
<li class="file-stats">
<a href="#0f0892525b132e72892c1b9ed74e358194bd4672">
documentation_builder/conf.py
</a>
</li>
<li class="file-stats">
<a href="#8caf48fe09170eb6771b443c3ebd3a886799143d">
documentation_builder/requirements.txt
</a>
</li>
<li class="file-stats">
<a href="#ba404afeea797243439f5224dcefb483ab25dab2">
<span class="new-file">
+
release-notes/0.30.0.md
</span>
</a>
</li>
<li class="file-stats">
<a href="#56e7e8232c8126a9d31fe6ca9efafe588b5109c6">
<span class="new-file">
+
release-notes/0.31.0.md
</span>
</a>
</li>
<li class="file-stats">
<a href="#8d9c2dece85169a8c8a5bb0e328990f743b93b8d">
<span class="new-file">
+
release-notes/0.31.1.md
</span>
</a>
</li>
<li class="file-stats">
<a href="#327ebaa25ec0630b95cfd4d7e339b8e2f40f6d2e">
release-notes/next-release.md
</a>
</li>
<li class="file-stats">
<a href="#8c91c0296909b5ea3c496fde69e9dc44a6c6ae5f">
setup.cfg
</a>
</li>
<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
</a>
</li>
<li class="file-stats">
<a href="#1de6b4f3a254357ed4adcffc483949c14961379d">
src/cobra/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#1a83bb5fa417ddb7e799b7504ecdf5d363382fd1">
src/cobra/core/dictlist.py
</a>
</li>
<li class="file-stats">
<a href="#f0e79d24023abfd5dcafb0b13978ae10f44f1f8d">
src/cobra/core/gene.py
</a>
</li>
<li class="file-stats">
<a href="#d7e1aee9380ea447e4ffdfa59bb2fef1043e0908">
src/cobra/core/model.py
</a>
</li>
<li class="file-stats">
<a href="#47fe15ff8f4f2a4270d636a18428ed512655c8ae">
src/cobra/core/reaction.py
</a>
</li>
<li class="file-stats">
<a href="#e2f334d3eb4a5aa4a93e160e38024b3b8e413181">
src/cobra/flux_analysis/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#b579a30f1eb45288a41742c77351157d0cb6a12b">
<span class="new-file">
+
src/cobra/flux_analysis/fast_snp.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#4889e7c0b5e27a6986d471038e0d27f57ff675e5">
src/cobra/flux_analysis/fastcc.py
</a>
</li>
<li class="file-stats">
<a href="#afe1f487761ba4731f93f34f9d9d633a77a05259">
<span class="new-file">
+
src/cobra/flux_analysis/find_cyclic_reactions.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#9ee780a2f5e06ddd02c2f05c4a5adc95f34e6f50">
src/cobra/flux_analysis/loopless.py
</a>
</li>
<li class="file-stats">
<a href="#f4897730b8bf8b48da1f599da1f9f283a0bd7d41">
src/cobra/flux_analysis/variability.py
</a>
</li>
<li class="file-stats">
<a href="#e38fad9d079b0e7ed4a28fb0718a76bab7967cdc">
src/cobra/io/dict.py
</a>
</li>
<li class="file-stats">
<a href="#16a818ae5b42b5bfd1c41bfe3c93719c98b2c083">
src/cobra/io/web/biomodels_repository.py
</a>
</li>
<li class="file-stats">
<a href="#0141a05dd61c45851074eeaca1c385823d31d9a5">
src/cobra/io/web/cobrapy_repository.py
</a>
</li>
<li class="file-stats">
<a href="#f5de29d9aaf2e4a433b795ce5cc796b94434395d">
src/cobra/io/web/load.py
</a>
</li>
<li class="file-stats">
<a href="#0f5b03cc5687fa2a8288e16140b6c49bc849e303">
src/cobra/sampling/hr_sampler.py
</a>
</li>
<li class="file-stats">
<a href="#4abf3b6326bc03e90e8ba8f506b24164aeb0048b">
src/cobra/util/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#626af34e8204774ea46e20955936146dedc828eb">
tests/conftest.py
</a>
</li>
<li class="file-stats">
<a href="#2eec0845238f5856f0bea08cd1fd6305c2fea51a">
tests/data/update_pickles.py
</a>
</li>
<li class="file-stats">
<a href="#63dd3ae6d9014c82234e1987f7c52343dd6a14d2">
tests/test_core/test_core_reaction.py
</a>
</li>
<li class="file-stats">
<a href="#4ae1df68a4ac71ec82edca32a171a6a5334db7bf">
tests/test_core/test_gpr.py
</a>
</li>
<li class="file-stats">
<a href="#188ab55a0acecffd683ad213292b8fcbbe66087e">
tests/test_core/test_solution.py
</a>
</li>
<li class="file-stats">
<a href="#c5bec4ad5adfeab8f1f5aee0cfecff8eeaeb48cf">
<span class="new-file">
+
tests/test_flux_analysis/test_fast_snp.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#4ec3096f30da8ce6c1c778e088e6fc1cb3b01ad3">
tests/test_flux_analysis/test_fastcc.py
</a>
</li>
<li class="file-stats">
<a href="#f13ae666c16e4adaae2a34166104dc623b08f7a7">
<span class="new-file">
+
tests/test_flux_analysis/test_find_cyclic_reactions.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#7bd24d60cbc205c82cadc8bba0bd46e1f8b94474">
tests/test_flux_analysis/test_loopless.py
</a>
</li>
<li class="file-stats">
<a href="#842d585b147242919fb6c71bde6c28c0815cfce7">
tests/test_flux_analysis/test_variability.py
</a>
</li>
<li class="file-stats">
<a href="#565a04ecf535df910917cc91845937d68f89ee39">
tests/test_io/test_json.py
</a>
</li>
<li class="file-stats">
<a href="#e2b0b590491a5636188c3c64a51184100af25bad">
tests/test_io/test_web/test_load.py
</a>
</li>
<li class="file-stats">
<a href="#22a64b67b642d0a49a1145d368149111631aa021">
tests/test_util/test_solver.py
</a>
</li>
<li class="file-stats">
<a href="#61be067c7cf3bdbf8a6b021a2b5167eb30612d0c">
tox.ini
</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/python-cobra/-/commit/3bd1dd72d8fe07f4baf91e94cbd760678874391b">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/python-cobra/-/commit/3bd1dd72d8fe07f4baf91e94cbd760678874391b at 1780416314
</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/python-cobra/-/commit/3bd1dd72d8fe07f4baf91e94cbd760678874391b"}}</script>


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