<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN" "http://www.w3.org/TR/REC-html40/loose.dtd">
<html lang="en">
<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: 0.875rem;
}
body {
-webkit-text-shadow: rgba(255,255,255,0.01) 0 0 1px;
}
body {
font-family: -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(255,255,255,0.01) 0 0 1px; font-family: -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 master at <a href="https://salsa.debian.org/med-team/pangolin">Debian Med / pangolin</a>
</h3>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
</h4>
<ul>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/pangolin/-/commit/d2a74681f3682029a846c1dcf39425a1f6ecedac">d2a74681</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2022-12-23T16:17:04+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "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: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>Fix watch file
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/pangolin/-/commit/032c4949807a3aee7cad8bfc5338fbdbb98890f7">032c4949</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2022-12-23T16:18:38+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "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: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>routine-update: New upstream version
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/pangolin/-/commit/2726a5f55cf63579be66d64c4e2650fe664bb560">2726a5f5</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2022-12-23T16:18:39+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "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: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>New upstream version 4.1.3</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/pangolin/-/commit/ba93f738522cc49c3ec01d5215ed904d9278b030">ba93f738</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2022-12-23T16:18:40+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "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: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>Update upstream source from tag 'upstream/4.1.3'

Update to upstream version '4.1.3'
with Debian dir 67597d006c3507f9a9f4d0a13a8124c8e9006afd</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/pangolin/-/commit/8f5c8361856aed04ea2923f9e66d88fa42975c23">8f5c8361</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2022-12-23T16:18:51+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "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: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>Set upstream metadata fields: Bug-Database, Bug-Submit, Repository-Browse.

Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/pangolin/-/commit/c6b46885270ac233f28ad375cc62865606540494">c6b46885</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2022-12-23T16:29:48+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "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: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>lineages was replaced by pango-designation (to be packaged)
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/pangolin/-/commit/a9c3195ea0286c0825d3b83bf927c599453afa0c">a9c3195e</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2022-12-24T16:07:33+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "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: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>Add new depends
</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
30 changed files:
</h4>
<ul>
<li class="file-stats">
<a href="#05a721ebe3ba0754116825ed1359ff1785f4bbac">
<span class="new-file">
+
.dockerignore
</span>
</a>
</li>
<li class="file-stats">
<a href="#f61bbc766fa65dfc6096bea80e8e3c618de239fe">
<span class="new-file">
+
.github/workflows/pangolin.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#e1bdfa007690616a07064b88a85fdf026711dc4f">
<span class="new-file">
+
.github/workflows/pangolin_macos.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#223fa2faca2ab668f5691f5d3d8960a909d6a199">
<span class="new-file">
+
.github/workflows/push_dockerhub.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
<span class="new-file">
+
.gitignore
</span>
</a>
</li>
<li class="file-stats">
<a href="#6651ddff6eb82c840ced7c1dddee15c6e1913dd4">
<span class="new-file">
+
Dockerfile
</span>
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#9b016839f597d6fbeae6366cc8bf0534482fb2ef">
<span class="new-file">
+
TESTING.md
</span>
</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="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
</a>
</li>
<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
<li class="file-stats">
<a href="#54c391de2500e0856c23737daf64f9d931569110">
environment.yml
</a>
</li>
<li class="file-stats">
<a href="#60689126e5715c7faafb13aac1a6b41458ff6610">
pangolin/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#2d7bbafc280c7e0a0c3a21278bba02fd2ad79b26">
pangolin/command.py
</a>
</li>
<li class="file-stats">
<a href="#3430c0a7471940bb79f4a8034807c2651d2e5658">
<span class="new-file">
+
pangolin/data/data_compatibility.csv
</span>
</a>
</li>
<li class="file-stats">
<a href="#f7c6419f603c601db06b9e9482cb864505430b2f">
<span class="new-file">
+
pangolin/pangolearn/__init__.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#e227b65fffda398b26727419d98106f6ffbd7036">
<span class="new-file">
+
pangolin/pangolearn/pangolearn.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#44cf6305859fe745235022d0d75b79ca2a8311cf">
<span class="deleted-file">

pangolin/scripts/Snakefile
</span>
</a>
</li>
<li class="file-stats">
<a href="#a48aeae9ec66517d89a9e3e2c68e01a15c3df17d">
<span class="deleted-file">

pangolin/scripts/assign_lineage.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#04f8bd5a813fe95adf98aeb8e58f50f4f791b1bf">
<span class="deleted-file">

pangolin/scripts/assign_query_file.smk
</span>
</a>
</li>
<li class="file-stats">
<a href="#cd14abdd6e98c3652a51b5671b97b22325127ef7">
<span class="deleted-file">

pangolin/scripts/assign_query_lineage.smk
</span>
</a>
</li>
<li class="file-stats">
<a href="#4ad702b49dffc8603ddf84110c87fe6952ae8512">
<span class="deleted-file">

pangolin/scripts/categorise_snps.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#fad4ca1af98c37e477c1d17973ea6d22558ad7f0">
<span class="deleted-file">

pangolin/scripts/defining_snps.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#fa434491f7961c39617fcc7a77dcc584029a7310">
<span class="deleted-file">

pangolin/scripts/lineage_classes.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#50e12fdec024ffceda45e560e0e360a979fe32da">
<span class="deleted-file">

pangolin/scripts/lineage_finder.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#da7eead64dc68fb4a867b9ccba9df358660936b8">
<span class="deleted-file">

pangolin/scripts/pangolearn.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#8b4392fd17abc8f2ac8d1fe9088a8f852e50bd92">
pangolin/scripts/pangolearn.smk
</a>
</li>
<li class="file-stats">
<a href="#a979550df3658180658ee871ddd5e3418feab13b">
<span class="new-file">
+
pangolin/scripts/preprocessing.smk
</span>
</a>
</li>
</ul>
<h5 style="margin-top: 10px; margin-bottom: 10px; font-size: 0.875rem;">
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: #666;">

<br>
<a href="https://salsa.debian.org/med-team/pangolin/-/compare/65914a4374a2c64f28783d07c7b551199dccf9d2...a9c3195ea0286c0825d3b83bf927c599453afa0c">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>