<!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/macsyfinder">Debian Med / macsyfinder</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/macsyfinder/-/commit/bc360d51b2407cf323b3b18cfe679dd52b97aaed">bc360d51</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-01-31T13:34:17+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; 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 2.1.6</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
68 changed files:
</h4>
<ul>
<li class="file-stats">
<a href="#ce75854ec9a744f62faf4ef473f64a99029ae864">
.github/workflows/testing.yml
</a>
</li>
<li class="file-stats">
<a href="#419d52dcfa39c76bbf72833eb6f5f7152f6ec661">
CONTRIBUTORS.md
</a>
</li>
<li class="file-stats">
<a href="#8ca8894c9aed8564142f753fdc3d43b313a19e19">
codemeta.json
</a>
</li>
<li class="file-stats">
<a href="#68b718df468222fa978bd6704f137e3a9f7c15ba">
doc/source/modeler_guide/modeling.rst
</a>
</li>
<li class="file-stats">
<a href="#885a57142051ed7f5891824f47a5c8fa85c691f8">
doc/source/user_guide/input.rst
</a>
</li>
<li class="file-stats">
<a href="#49c54d1ce0f523461948decb7e1e5710dd0d92c7">
doc/source/user_guide/new_v2.rst
</a>
</li>
<li class="file-stats">
<a href="#183306ea9b8e66da1784ea513a70a541f0a41aff">
nextflow.config
</a>
</li>
<li class="file-stats">
<a href="#5d07e7d72637aa0d59c89d381fe6dc4cf46e2491">
pyproject.toml
</a>
</li>
<li class="file-stats">
<a href="#0711abb27931cdb86d962c06c7304ab683f1dbf5">
src/macsyfinder/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#a78f376ada87eff5de754bd4a915882102c4c40a">
src/macsyfinder/scripts/macsy_gembase_split.py
</a>
</li>
<li class="file-stats">
<a href="#9970b96750b7540df462ef37397f6d0245bee98d">
src/macsyfinder/scripts/macsy_merge_results.py
</a>
</li>
<li class="file-stats">
<a href="#e6c9e0403e489fbfeef2cc8b72e2a03090bff888">
src/macsyfinder/scripts/macsyconfig.py
</a>
</li>
<li class="file-stats">
<a href="#a167f50c460c68002e024f6de37ea90da664b0d3">
src/macsyfinder/scripts/macsyprofile.py
</a>
</li>
<li class="file-stats">
<a href="#cb4b46ccb2288e0064bc6ee0b67d56aaddf8a3d7">
src/macsyfinder/scripts/msf.py
</a>
</li>
<li class="file-stats">
<a href="#c1dabfc5448f555ecb66bf995599259a05cb0403">
<span class="new-file">
+
tests/data/base/test_16.faa
</span>
</a>
</li>
<li class="file-stats">
<a href="#8bf840ad24be848496915a498efd207d2dac06c5">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small/all_best_solutions.tsv
</span>
</a>
</li>
<li class="file-stats">
<a href="#57bb98576cdebd9087316986d512393aa6cd360f">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small/all_systems.tsv
</span>
</a>
</li>
<li class="file-stats">
<a href="#23629cddff703b5da83a632e4747b3a5b9de8904">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small/all_systems.txt
</span>
</a>
</li>
<li class="file-stats">
<a href="#67c1143869fca1380a107d428f02493c8bd00bae">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small/best_solution.tsv
</span>
</a>
</li>
<li class="file-stats">
<a href="#9cfb9cecd02a40be86cc099a10e43170d5d4b246">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small/best_solution_loners.tsv
</span>
</a>
</li>
<li class="file-stats">
<a href="#d45f4da59825399fb37e3edea2604a7b618cb90e">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small/best_solution_multisystems.tsv
</span>
</a>
</li>
<li class="file-stats">
<a href="#a8052b200415a1b6bc9c6120ba398f64e87bbd5f">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small/best_solution_summary.tsv
</span>
</a>
</li>
<li class="file-stats">
<a href="#6dfa0263db14dbb3b2d2b30963ff623d509fd705">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small/hmmer_results/T4SS_MOBB.res_hmm_extract
</span>
</a>
</li>
<li class="file-stats">
<a href="#e385e5e11631d59e9662fdf55537bc8ba6f57ffc">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small/hmmer_results/T4SS_MOBB.search_hmm.err
</span>
</a>
</li>
<li class="file-stats">
<a href="#c51d49814cd7114784b2f4b41997dda9aee19d3f">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small/hmmer_results/T4SS_MOBB.search_hmm.out
</span>
</a>
</li>
<li class="file-stats">
<a href="#e7bae771c7e680c74e6702d7f6a99329a220022c">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small/hmmer_results/T4SS_MOBQ.res_hmm_extract
</span>
</a>
</li>
<li class="file-stats">
<a href="#ad06368693e75c36c763af0c5f46c57693fb1e91">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small/hmmer_results/T4SS_MOBQ.search_hmm.err
</span>
</a>
</li>
<li class="file-stats">
<a href="#87b4b361326aa7914d4139724b1069c0ea93b858">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small/hmmer_results/T4SS_MOBQ.search_hmm.out
</span>
</a>
</li>
<li class="file-stats">
<a href="#a6098a371b30b7820c9324fd95fc6267b2267eaf">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small/hmmer_results/T4SS_t4cp1.res_hmm_extract
</span>
</a>
</li>
<li class="file-stats">
<a href="#48880ee29d3f0d8ae8b20ab175ce26a5ff420f19">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small/hmmer_results/T4SS_t4cp1.search_hmm.err
</span>
</a>
</li>
<li class="file-stats">
<a href="#879a374a7a6de9d8b743723044cc7a8a3563168f">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small/hmmer_results/T4SS_t4cp1.search_hmm.out
</span>
</a>
</li>
<li class="file-stats">
<a href="#e44d1d9fb2eaa586e59a538155ea29c9ea10232d">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small/hmmer_results/T4SS_virb4.res_hmm_extract
</span>
</a>
</li>
<li class="file-stats">
<a href="#eea84a35f0dab785dcc05188255777ccfd8fdcb7">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small/hmmer_results/T4SS_virb4.search_hmm.err
</span>
</a>
</li>
<li class="file-stats">
<a href="#80fb9e018a9e2e9028cb115778dcf34bd1c6405b">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small/hmmer_results/T4SS_virb4.search_hmm.out
</span>
</a>
</li>
<li class="file-stats">
<a href="#8cb58bab34a92e2878bed5dfa1545b61af3fa077">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small/macsyfinder.conf
</span>
</a>
</li>
<li class="file-stats">
<a href="#84305f3c9f08453449a10ea81bfdb5622c8f7e29">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small/rejected_candidates.tsv
</span>
</a>
</li>
<li class="file-stats">
<a href="#d904932afb381539a4e7055d0940c95826ca6441">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small/rejected_candidates.txt
</span>
</a>
</li>
<li class="file-stats">
<a href="#865af91b01cefd7ee0fd00393ebc716c2d14e838">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small_2/all_best_solutions.tsv
</span>
</a>
</li>
<li class="file-stats">
<a href="#647ffa706e214e937dfd40cd55cc5b87b1665593">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small_2/all_systems.tsv
</span>
</a>
</li>
<li class="file-stats">
<a href="#ec7b21665ccf1f3196a401318cc4979ed2efe481">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small_2/all_systems.txt
</span>
</a>
</li>
<li class="file-stats">
<a href="#7106c19cba5c4c15dc46b5abd0e0ef16435585e2">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small_2/best_solution.tsv
</span>
</a>
</li>
<li class="file-stats">
<a href="#359abb5047794fb2b37bbe312a6091f9b452b5fc">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small_2/best_solution_loners.tsv
</span>
</a>
</li>
<li class="file-stats">
<a href="#f7d02c60c44bd647a60ce39262732121b8394daf">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small_2/best_solution_multisystems.tsv
</span>
</a>
</li>
<li class="file-stats">
<a href="#6a8794f6bb891d9fb973733536272f0e9b244af9">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small_2/best_solution_summary.tsv
</span>
</a>
</li>
<li class="file-stats">
<a href="#e45b4b407251bb812de122f542e06ab6e3f45a02">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small_2/hmmer_results/T4SS_MOBB.res_hmm_extract
</span>
</a>
</li>
<li class="file-stats">
<a href="#e5454f33f2bba4ecff32ec889aaeccc02b92fc64">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small_2/hmmer_results/T4SS_MOBB.search_hmm.err
</span>
</a>
</li>
<li class="file-stats">
<a href="#bd9e0b0c29d4c5e5d3ba3224c27bc065c6948e0f">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small_2/hmmer_results/T4SS_MOBB.search_hmm.out
</span>
</a>
</li>
<li class="file-stats">
<a href="#664118a61f5700b7526951677a8a57e9b25639de">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small_2/hmmer_results/T4SS_MOBQ.res_hmm_extract
</span>
</a>
</li>
<li class="file-stats">
<a href="#0f91f7498daedba9dc087401a606ae0df237329d">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small_2/hmmer_results/T4SS_MOBQ.search_hmm.err
</span>
</a>
</li>
<li class="file-stats">
<a href="#85ee4c8a95f34e7ce4778b77e5372f37ba79946f">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small_2/hmmer_results/T4SS_MOBQ.search_hmm.out
</span>
</a>
</li>
<li class="file-stats">
<a href="#8c4e526e815352956935d706b6d3d0181fbccebe">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small_2/hmmer_results/T4SS_t4cp1.res_hmm_extract
</span>
</a>
</li>
<li class="file-stats">
<a href="#d17f4a3fd30da2bdc97784a23b3a7f570a24ac44">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small_2/hmmer_results/T4SS_t4cp1.search_hmm.err
</span>
</a>
</li>
<li class="file-stats">
<a href="#5e67c3bf11b78860f4256dba071ed696cd6c6e99">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small_2/hmmer_results/T4SS_t4cp1.search_hmm.out
</span>
</a>
</li>
<li class="file-stats">
<a href="#054bd9b0aefe2950749573fc852070267611c2e2">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small_2/hmmer_results/T4SS_virb4.res_hmm_extract
</span>
</a>
</li>
<li class="file-stats">
<a href="#7af68dc32a1945c661b0f480b398c603c4ff3f14">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small_2/hmmer_results/T4SS_virb4.search_hmm.err
</span>
</a>
</li>
<li class="file-stats">
<a href="#ecf9a863e43c66826374af9787163d1a50f0134f">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small_2/hmmer_results/T4SS_virb4.search_hmm.out
</span>
</a>
</li>
<li class="file-stats">
<a href="#8cb29a3652e537ccfb93ea6e0d89a6c2e996835b">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small_2/macsyfinder.conf
</span>
</a>
</li>
<li class="file-stats">
<a href="#c799f3f4896943bc7adb1ed71c47d03b9e97a1b3">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small_2/rejected_candidates.tsv
</span>
</a>
</li>
<li class="file-stats">
<a href="#760bb040f8fe02d792842237c816e4470335290c">
<span class="new-file">
+
tests/data/functional_test_ordered_circular_small_2/rejected_candidates.txt
</span>
</a>
</li>
<li class="file-stats">
<a href="#9f166078da0edef9a1b5551979c642a72ffee437">
<span class="new-file">
+
tests/data/models/functional/definitions/MOB_light.xml
</span>
</a>
</li>
<li class="file-stats">
<a href="#d209d9c4b9790a858afc030ae4b7ebf48f1736f9">
<span class="new-file">
+
tests/data/models/functional/definitions/MOB_light_no_loner.xml
</span>
</a>
</li>
<li class="file-stats">
<a href="#a7f3f7414b7a674fd04b33435608a8800c69fe89">
<span class="new-file">
+
tests/data/models/functional/profiles/T4SS_MOBB.hmm
</span>
</a>
</li>
<li class="file-stats">
<a href="#6636866a2d8b55aeb5bd07e9e090d4fc65ac7398">
<span class="new-file">
+
tests/data/models/functional/profiles/T4SS_MOBQ.hmm
</span>
</a>
</li>
<li class="file-stats">
<a href="#d076c07b82bbe03fcad0f550efb6e8396c95d1c4">
<span class="new-file">
+
tests/data/models/functional/profiles/T4SS_t4cp1.hmm
</span>
</a>
</li>
<li class="file-stats">
<a href="#4f652f54e999af5a33c3568bb312b2fa9a6e3f87">
<span class="new-file">
+
tests/data/models/functional/profiles/T4SS_virb4.hmm
</span>
</a>
</li>
<li class="file-stats">
<a href="#8b2170032364fa713b3fda5b8d59f380baca4f25">
tests/test_functional_test.py
</a>
</li>
<li class="file-stats">
<a href="#97345dd9f8c3895dbefe0ead8d432a199c727f04">
tests/test_macsyconfig.py
</a>
</li>
<li class="file-stats">
<a href="#974d8e21b6f3368d487f14e219ce372f6bebdb7b">
tests/test_scripts.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/macsyfinder/-/commit/bc360d51b2407cf323b3b18cfe679dd52b97aaed">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/macsyfinder/-/commit/bc360d51b2407cf323b3b18cfe679dd52b97aaed at 1769865025
</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/macsyfinder/-/commit/bc360d51b2407cf323b3b18cfe679dd52b97aaed"}}</script>


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