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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/hyphy">Debian Med / hyphy</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/5c6383e31c91c40fc9d84c2de595592ed1578c5a">5c6383e3</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-10-08T22:48:25+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/b29971ab425e52781ca8a3847888371755ed60a3">b29971ab</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-10-08T22:48:44+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.5.19+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/5cd95e6b31121963c0a51dbfbda5966e7b8ba30b">5cd95e6b</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-10-08T22:48:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.5.19+dfsg'
Update to upstream version '2.5.19+dfsg'
with Debian dir 746c33edb1643525463009ddcf5f8a7778ffd55f</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/0e906cc83d15cbd61aaffbaeccfbbd17ff16ae52">0e906cc8</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-10-08T22:55:25+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/0127e9edf210aad28333a980a9c221bd9140e403">0127e9ed</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-10-09T00:14:42+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix_brace_mismatch.patch applied upstream
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/d048142a02e9c41eeec7d7b1541c2d243c3e4e28">d048142a</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-10-09T00:33:47+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add manual for hyphy
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/948243b59c596eb50cf56485ffd8cb2542e292e3">948243b5</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-10-09T00:34:14+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add manual page for HYPHYMPI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/713f7e228279f2111b63bbe9d08f835c95255e10">713f7e22</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-10-09T00:35:28+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add changelog entry for manual pages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/b8f7982f804754b2dd098ee918e536001d0d4954">b8f7982f</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-10-10T15:25:24+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/m/hyphy.1: update page to 2.5.19
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/b8c39452abc501bfc5ef6bee39675102ef402004">b8c39452</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-10-10T15:29:41+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
</ul>
<h4>30 changed files:</h4>
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<li class="file-stats">
<a href="#0aece8b45b329e391d84f37ccc266e69151e46a3">
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+
.coveralls.condarc
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<li class="file-stats">
<a href="#32b3affef3f6fdd8a77e3890911abf3701cae832">
<span class="new-file">
+
.coveralls.env.yml
</span>
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<li class="file-stats">
<a href="#e5a6f1ed046081016d3663d7c080e9a742d096d0">
<span class="new-file">
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.github/workflows/coverage.yml
</span>
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<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#8fce03645a9333472ba052de989c3984a5d6176a">
<span class="new-file">
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debian/hyphy-mpi.manpages
</span>
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</li>
<li class="file-stats">
<a href="#a63b5435bb8d3f2b33e58650edac763363d7108c">
<span class="new-file">
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debian/hyphy-pt.manpages
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<li class="file-stats">
<a href="#767b396c66a70a2248e5b5439c1d9480d33aa247">
<span class="new-file">
+
debian/manuals/HYPHYMPI.1
</span>
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<li class="file-stats">
<a href="#c72fadc42d1caaada4fa7786d43a551db6e91b8b">
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<li class="file-stats">
<a href="#9ec1f3c883730f3a852a134f64f6d329a12cb33c">
<span class="deleted-file">
−
debian/patches/fix_brace_mismatch.patch
</span>
</a>
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<li class="file-stats">
<a href="#63c3307a25f0c1334b59e145f9fc809c05bbfa70">
debian/patches/rm_arch_specific_flags.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<a href="#d185b62d54557160e7ddc743405a9cec66dcaa96">
debian/patches/use_debian_sqlite.patch
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<a href="#c772592437fe6a7d4e11445521dd00b76827f448">
res/TemplateBatchFiles/CleanStopCodons.bf
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<a href="#595b42362bc80e51259da598ac8ff2dd32cd7358">
res/TemplateBatchFiles/GARD.bf
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<a href="#bc98d7300147ce39ef8ee0f9b35f3252bebd01d2">
res/TemplateBatchFiles/SelectionAnalyses/MEME.bf
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<a href="#43faaf1f56e02d91be5b281472029a32276f7b4c">
res/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf
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<a href="#6912998957054caec329b3714223c03f20dbbd3e">
res/TemplateBatchFiles/SelectionAnalyses/modules/selection_lib.ibf
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res/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.bf
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res/TemplateBatchFiles/libv3/models/codon.bf
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res/TemplateBatchFiles/libv3/models/codon/BS_REL.bf
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res/TemplateBatchFiles/libv3/models/model_functions.bf
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res/TemplateBatchFiles/libv3/models/parameters.bf
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res/TemplateBatchFiles/libv3/tasks/alignments.bf
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<a href="#e4533799d11373671179a1fba2e20b7dea98db29">
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res/TemplateBatchFiles/libv3/tasks/estimators.bf
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<a href="#3945e6db8feb0e4ed58719b69ff3d8485bc45e87">
res/TemplateBatchFiles/libv3/tasks/trees.bf
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<a href="#02cbcb76e8ce1aa3e72d55e6696cda20813d57b6">
src/core/batchlan.cpp
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<h5>The diff was not included because it is too large.</h5>
</div>
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—
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/a3361c89d3347c324dac6a7b3529f0ffab4510a5...b8c39452abc501bfc5ef6bee39675102ef402004">View it on GitLab</a>.
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