<!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, "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: 0.875rem;
}
body {
-webkit-text-shadow: rgba(255,255,255,0.01) 0 0 1px;
}
body {
font-family: var(--default-regular-font, -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: var(--default-regular-font, -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;">
Étienne Mollier pushed to branch master at <a href="https://salsa.debian.org/med-team/hyphy">Debian Med / hyphy</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/hyphy/-/commit/897900f694604127dcdd7ce17bb444caf1a4c994">897900f6</a></strong>
<div>
<span> by Nilesh Patra </span> <i> at 2023-05-09T22:19:19+05:30 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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 2.5.50+dfsg</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/hyphy/-/commit/1982811a1610e7878720646381402bb94356cf4e">1982811a</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-07-09T13:15:29+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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;'>routine-update: New upstream version
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/hyphy/-/commit/36f9a9c3a57c5f916df2f86d21c804f863593952">36f9a9c3</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-07-09T13:15:47+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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 2.5.51+dfsg</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/hyphy/-/commit/920f55d396037bee71966c1b45b82592956bf85d">920f55d3</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-07-09T13:15:55+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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/2.5.51+dfsg'

Update to upstream version '2.5.51+dfsg'
with Debian dir d2ac2ffb41008671ef3e51a26c074d25ac0d8d47</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/hyphy/-/commit/b9efc15691c25dbe7c0704fac75fa6a1a98bce98">b9efc156</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-07-09T13:16:19+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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 constraints unnecessary since bullseye (oldstable)

* Remove 3 maintscript entries from 3 files.

Changes-By: deb-scrub-obsolete</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/hyphy/-/commit/4d6a6bfe551eab077c37037fe8b6b358cc47c62c">4d6a6bfe</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-07-09T13:23:45+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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;'>rm_arch_specific_flags.patch: refresh.
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/hyphy/-/commit/68cc3c7623679a99932f82adb9cb910d398621f4">68cc3c76</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-07-09T13:23:54+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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: build now depends on swig.
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/hyphy/-/commit/7a939b2f17ed10f5e4e31941920e15714fea5e97">7a939b2f</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-07-09T13:40:32+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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: build now depends on python3 sdk.
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/hyphy/-/commit/0445805f87fd22ea8aa29b40308cdc395a745e61">0445805f</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-07-09T14:28:55+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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;'>fix-configure-failure.patch: add: fix a cmake error.
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/hyphy/-/commit/e3ed17ca64527d4d123568c9dc66156507e26adf">e3ed17ca</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-07-09T14:34:51+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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;'>ready to upload to unstable.
</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
30 changed files:
</h4>
<ul>
<li class="file-stats">
<a href="#2988cbe972fe24aeb6ee4536af0d0adb14495729">
<span class="new-file">
+
.github/workflows/benchmark.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#37c182e857c9d9bb0eb6218a00392ab9f8e4d264">
<span class="new-file">
+
.github/workflows/codeql.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#e5a6f1ed046081016d3663d7c080e9a742d096d0">
<span class="new-file">
+
.github/workflows/coverage.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#1d19aad7b7b27d190877325ddc2bf187f2ea4808">
<span class="new-file">
+
.github/workflows/stale.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
<span class="new-file">
+
.travis.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</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="#210cd648f16968303ed89acb049b5f431b866c4c">
<span class="deleted-file">

debian/hyphy-common.maintscript
</span>
</a>
</li>
<li class="file-stats">
<a href="#b19de2bd0579666d65ac105320286c4954a14966">
<span class="deleted-file">

debian/hyphy-mpi.maintscript
</span>
</a>
</li>
<li class="file-stats">
<a href="#f5fb0be5349d7e1ba3b55f8aa386c2ef27cbcdf1">
<span class="deleted-file">

debian/hyphy-pt.maintscript
</span>
</a>
</li>
<li class="file-stats">
<a href="#7a753745e0a1908635aacec0f3a06118f6126802">
<span class="new-file">
+
debian/patches/fix-configure-failure.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#63c3307a25f0c1334b59e145f9fc809c05bbfa70">
debian/patches/rm_arch_specific_flags.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#4ed0809c2483f5150cdfd2c3bf07d212387406d0">
res/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf
</a>
</li>
<li class="file-stats">
<a href="#80cb7c212661a2afbd05c16dce9f84f45709578e">
res/TemplateBatchFiles/SelectionAnalyses/PRIME.bf
</a>
</li>
<li class="file-stats">
<a href="#cf5243a3058ebeab74574f8cd2c771cd63a43208">
res/TemplateBatchFiles/SelectionAnalyses/RELAX.bf
</a>
</li>
<li class="file-stats">
<a href="#c259485f7f96dc2ad350d5448508de915c6a9885">
res/TemplateBatchFiles/SelectionAnalyses/modules/io_functions.ibf
</a>
</li>
<li class="file-stats">
<a href="#9cebc147cfbaaa726aceb79b45e393912c2e38ca">
res/TemplateBatchFiles/TemplateModels/defineGamma.mdl
</a>
</li>
<li class="file-stats">
<a href="#9f6d2efd39d3afa147f430ca6d771b8d64f20a55">
res/TemplateBatchFiles/libv3/models/codon/MG_REV_PROPERTIES.bf
</a>
</li>
<li class="file-stats">
<a href="#c7933e171033f4eac9d83419583cca5474f9266c">
res/TemplateBatchFiles/libv3/tasks/estimators.bf
</a>
</li>
<li class="file-stats">
<a href="#02cbcb76e8ce1aa3e72d55e6696cda20813d57b6">
src/core/batchlan.cpp
</a>
</li>
<li class="file-stats">
<a href="#984635b15ce26c0824ba85946c002feb3137c030">
src/core/batchlan2.cpp
</a>
</li>
<li class="file-stats">
<a href="#cbedcf5fec686e5f563504b995c5d7d07fd8c6b2">
src/core/batchlanruntime.cpp
</a>
</li>
<li class="file-stats">
<a href="#7474aa77ff4fbb7ca8b12091ad6d5e459fdc18c6">
src/core/dataset.cpp
</a>
</li>
<li class="file-stats">
<a href="#e5a5cb83991ca482b4f0a3424fd55eea54f6d652">
src/core/fisher_exact.cpp
</a>
</li>
<li class="file-stats">
<a href="#d09b45303442d6299978fa8d0c8f3338d6a17886">
src/core/formula.cpp
</a>
</li>
<li class="file-stats">
<a href="#59d202cc6599be3167fc3bd731039997dcaf9c72">
src/core/fstring.cpp
</a>
</li>
<li class="file-stats">
<a href="#07aceb8d215a75908cea626d9c80bc2a7c06639c">
src/core/global_things.cpp
</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: #737278;">

<br>
<a href="https://salsa.debian.org/med-team/hyphy/-/compare/e188fe37a66ce1e931acb7a788da11bbade65570...e3ed17ca64527d4d123568c9dc66156507e26adf">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>