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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/parsnp">Debian Med / parsnp</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/-/commit/3c65618e847d2b59a3f28399a6df48b65137b8ec">3c65618e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-17T15:13:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix watchfile to detect new versions on github
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/-/commit/032c9a745b587b2b465fa1d1789d12d80c5ea518">032c9a74</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-17T15:13:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.6.2+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/-/commit/82e1055ab587fec1564a113e3ea598a23ee80c8e">82e1055a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-17T15:13:23+01:00</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/parsnp/-/commit/594679d6ecad00783b35936f4b413bb355fa073d">594679d6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-17T15:13:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.6.2+dfsg'
Update to upstream version '1.6.2+dfsg'
with Debian dir 9f342d18a4a7a3ce4dac87c58c00f9566f598e1c</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/-/commit/438fe8f7e6a08fbfbde951f3fa71281d90ddd78f">438fe8f7</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-17T15:14:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
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<h4>4 changed files:</h4>
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<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
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+
.travis.yml
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
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<li class="file-stats">
<a href="#3849e3531855982fc7f5e63b3b17488714940ae3">
parsnp
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<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/parsnp/-/compare/41828f6e417da5b1df7db81cd87b2970f547914c...438fe8f7e6a08fbfbde951f3fa71281d90ddd78f#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">cpp</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">compiler</span><span class="pi">:</span> </span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">gcc</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span> </span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">if [ $TRAVIS_OS_NAME == linux ]; then ./build_parsnp_linux.sh; fi</span> </span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"><span class="na" style="color: #008080;">notifications</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="na" style="color: #008080;">email</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">recipients</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">treangent@nbacc.net</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">on_success</span><span class="pi">:</span> <span class="s" style="color: #d14;">change</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"> <span class="na" style="color: #008080;">on_failure</span><span class="pi">:</span> <span class="s" style="color: #d14;">change</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"><span class="na" style="color: #008080;">os</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">linux</span></span></pre>
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<a href="https://salsa.debian.org/med-team/parsnp/-/compare/41828f6e417da5b1df7db81cd87b2970f547914c...438fe8f7e6a08fbfbde951f3fa71281d90ddd78f#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">parsnp (1.6.2+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Fix watchfile to detect new versions on github</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 17 Feb 2022 15:13:38 +0100</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">parsnp (1.6.1+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Team Upload.</span>
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<a href="https://salsa.debian.org/med-team/parsnp/-/compare/41828f6e417da5b1df7db81cd87b2970f547914c...438fe8f7e6a08fbfbde951f3fa71281d90ddd78f#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=4</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> https://github.com/marbl/parsnp/releases .*/<span class="idiff left right">archive/</span>.*/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)</span></pre>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> https://github.com/marbl/parsnp/releases .*/.*/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)</span></pre>
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<a href="https://salsa.debian.org/med-team/parsnp/-/compare/41828f6e417da5b1df7db81cd87b2970f547914c...438fe8f7e6a08fbfbde951f3fa71281d90ddd78f#3849e3531855982fc7f5e63b3b17488714940ae3"><strong>parsnp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,7 +14,7 @@ import signal</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">inspect</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">multiprocessing</span> <span class="kn" style="font-weight: 600;">import</span> <span class="o" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1.6.<span class="idiff left right">1</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1.6.<span class="idiff left right">2</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="n" style="color: #333;">reroot_tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span> <span class="c1" style="color: #998; font-style: italic;">#use --midpoint-reroot</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1508,8 +1508,8 @@ Please verify recruited genomes are all strain of interest""")</td>
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<pre style="margin: 0;"> <span id="LC1508" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">VERBOSE</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="s" style="color: #d14;">"%s/tmp"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="p">)):</span></span>
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<pre style="margin: 0;"> <span id="LC1509" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">rmtree</span><span class="p">(</span><span class="s" style="color: #d14;">"%s/tmp"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC1510" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC1511" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="s" style="color: #d14;">"%s/parsnp.snps.mblocks"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="p">)):</span></span>
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1512
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<pre style="margin: 0;">-<span id="LC1512" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">"%s/parsnp.snps.mblocks"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC1511" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># </span>if os.path.exists("%s/parsnp.snps.mblocks"%(outputDir)):</span></span>
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<pre style="margin: 0;">+<span id="LC1512" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># </span>os.remove("%s/parsnp.snps.mblocks"%(outputDir))</span></span>
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<pre style="margin: 0;"> <span id="LC1513" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="s" style="color: #d14;">"%s/parsnp.snps.mblocks.reduced"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="p">)):</span></span>
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<pre style="margin: 0;"> <span id="LC1514" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">"%s/parsnp.snps.mblocks.reduced"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC1515" class="line" lang="python"></span>
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