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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/cat-bat">Debian Med / cat-bat</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/cat-bat/-/commit/c4dd24add4b76ad6038a8619d82f7f49f76e66dd">c4dd24ad</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-27T13:26:43+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 5.0.5</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cat-bat/-/commit/6254575d5e9fb06d3ec07d043f2d68df929115f9">6254575d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-27T13:26:43+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/cat-bat/-/commit/75de3c8a146c1556ef8b0241f9823e68ac5ad9d3">75de3c8a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-27T13:26:43+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/5.0.5'
Update to upstream version '5.0.5'
with Debian dir fdbff0efba49ce98c46a67c38ceb0266a834d44e</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cat-bat/-/commit/55921d6344c009364ec28d7d855a0aea33078527">55921d63</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-27T13:26:44+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cat-bat/-/commit/4a5ec638b5cf02181484b86dca5b2b0e6c35a8df">4a5ec638</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-27T13:26:47+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Rules-Requires-Root: no
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cat-bat/-/commit/6046a68a7ffed4122868851e21e4d3f74e547050">6046a68a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-27T13:26:53+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cat-bat/-/commit/3ce2bea04d1f50bbc999b6fb6cf5e2493ca68954">3ce2bea0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-27T13:27:49+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>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#6fd8d419abb30b8ad718bd6afa3bf33bf27bae47">
CAT_pack/about.py
</a>
</li>
<li class="file-stats">
<a href="#e8222836be7fdb29f66b8b4d17f23b4258132af6">
CAT_pack/bins.py
</a>
</li>
<li class="file-stats">
<a href="#3bde2f4ee51ad9ed542735d302116cb0044e0701">
CAT_pack/check.py
</a>
</li>
<li class="file-stats">
<a href="#ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
CHANGELOG.md
</a>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
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<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="6fd8d419abb30b8ad718bd6afa3bf33bf27bae47">
<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/d88bd6803ccabda697f75d0ab33e2cc2b4fb510c...3ce2bea04d1f50bbc999b6fb6cf5e2493ca68954#6fd8d419abb30b8ad718bd6afa3bf33bf27bae47"><strong>CAT_pack/about.py</strong></a>
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1
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1
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python3</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>
</pre>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="n" style="color: #333;">__author__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'F. A. Bastiaan von Meijenfeldt'</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4
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<pre style="margin: 0;">-<span id="LC4" 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;">'5.0.<span class="idiff left right">4</span>'</span></span>
</pre>
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5
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<td class="diff-line-num new_line old" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__date__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Ma<span class="idiff left right">rch 18</span>, 2020'</span></span></pre>
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4
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<pre style="margin: 0;">+<span id="LC4" 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;">'5.0.<span class="idiff left right">5</span>'</span></span>
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5
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__date__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Ma<span class="idiff left right">y 26</span>, 2020'</span></span></pre>
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<li id="e8222836be7fdb29f66b8b4d17f23b4258132af6">
<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/d88bd6803ccabda697f75d0ab33e2cc2b4fb510c...3ce2bea04d1f50bbc999b6fb6cf5e2493ca68954#e8222836be7fdb29f66b8b4d17f23b4258132af6"><strong>CAT_pack/bins.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -236,6 +236,10 @@ def import_bins(bin_folder,</td>
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236
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236
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="python"> <span class="n" style="color: #333;">contig_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">file_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">listdir</span><span class="p">(</span><span class="n" style="color: #333;">bin_folder</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">file_</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Skip hidden files.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="diff-line-num new new_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC243" 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;">file_</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="n" style="color: #333;">bin_suffix</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="python"> </span>
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<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/d88bd6803ccabda697f75d0ab33e2cc2b4fb510c...3ce2bea04d1f50bbc999b6fb6cf5e2493ca68954#3bde2f4ee51ad9ed542735d302116cb0044e0701"><strong>CAT_pack/check.py</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">@@ -232,6 +232,10 @@ def check_bin_folder(bin_folder, bin_suffix, log_file, quiet):</td>
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232
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python"> </span>
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233
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233
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="python"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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234
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234
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">file_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">listdir</span><span class="p">(</span><span class="n" style="color: #333;">bin_folder</span><span class="p">):</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">file_</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Skip hidden files.</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC239" 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;">file_</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="n" style="color: #333;">bin_suffix</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/d88bd6803ccabda697f75d0ab33e2cc2b4fb510c...3ce2bea04d1f50bbc999b6fb6cf5e2493ca68954#ab09011fa121d0a2bb9fa4ca76094f2482b902b7"><strong>CHANGELOG.md</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Changelog</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 5.0.5.</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown">Skip hidden files in bin folder.</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"></span>
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3
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 5.0.4.</span></span>
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4
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown">We have added the <span class="sb" style="color: #d14;">`--no_stars`</span> flag alongside a minor bug fix.</span>
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5
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"></span>
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<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/d88bd6803ccabda697f75d0ab33e2cc2b4fb510c...3ce2bea04d1f50bbc999b6fb6cf5e2493ca68954#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">cat-bat (5.0.5-1) unstable; urgency=medium</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Rules-Requires-Root: no (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> Repository-Browse.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 27 May 2020 13:26:54 +0200</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">cat-bat (5.0.4-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> * Initial release (Closes: #960937)</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/d88bd6803ccabda697f75d0ab33e2cc2b4fb510c...3ce2bea04d1f50bbc999b6fb6cf5e2493ca68954#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -3,13 +3,14 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> python3</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/cat-bat</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/cat-bat.git</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Homepage: https://github.com/dutilh/CAT</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Package: cat-bat</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Architecture: any</span>
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<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/d88bd6803ccabda697f75d0ab33e2cc2b4fb510c...3ce2bea04d1f50bbc999b6fb6cf5e2493ca68954#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Bug-Database: https://github.com/dutilh/CAT/issues</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Bug-Submit: https://github.com/dutilh/CAT/issues/new</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Reference:</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Author: ></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> F. A. Bastiaan von Meijenfeldt and Ksenia Arkhipova and Diego D. Cambuy</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,3 +20,5 @@ Reference:</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Registry:</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> - Name: conda:bioconda</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> Entry: cat</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Repository: https://github.com/dutilh/CAT.git</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Repository-Browse: https://github.com/dutilh/CAT</span></pre>
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