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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/kleborate">Debian Med / kleborate</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kleborate/-/commit/533bbc421096110b31fb5ee4ad9958029eccb0e3">533bbc42</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-09-19T16:14:12+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added myself to uploaders.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kleborate/-/commit/b32aa1672229b7c26859ae9db9d90fedcfc9171d">b32aa167</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-09-19T17:51:57+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">improved build reproducibility
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kleborate/-/commit/7cf27a2a8d39441c4f41606fbae8cc1b607da47e">7cf27a2a</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-09-19T17:54:09+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added fix-ftbfs-biopython-1.78.patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kleborate/-/commit/59eeca346c2f9722d99a4a8c437ff51ac1f23d1e">59eeca34</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-09-19T18:06:02+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/kleborate/-/commit/66cdc707d94c1fbb63f92488c247ba19b73ee49d">66cdc707</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-09-19T18:06:05+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Add salsa-ci file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kleborate/-/commit/0b8c329f34f8040c5b1b1b5db4adf1b756e3ff06">0b8c329f</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-09-19T18:06:05+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/kleborate/-/commit/30da58f476cf8b54301c7878615e2b64fa4e4828">30da58f4</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-09-19T18:08:11+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>6 changed files:</h4>
<ul>
<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="#ce09002463acc33f527deeea60548ba4c53a739e">
<span class="new-file">
+
debian/patches/fix-ftbfs-biopython-1.78.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#b1dbf22e88351ec0d5d1d1a7f53295504b480e61">
<span class="new-file">
+
debian/salsa-ci.yml
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/kleborate/-/compare/15f181816c2f1bff70b161c033a5166901d748cc...30da58f476cf8b54301c7878615e2b64fa4e4828#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">kleborate (1.0.0-4) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">kleborate (1.0.0-4) <span class="idiff left right">unstable</span>; urgency=medium</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"> [ Andreas Tille ]</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Comment debugging code in postinst</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="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 29 Jan 2020 13:56:28 +0100</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> [ Étienne Mollier ]</span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="plaintext"> * Added myself to uploaders.</span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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="LC8" class="line" lang="plaintext"> * Improved build reproducibility.</span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> * Fixed FTBFS with python-biopython 1.78.</span>
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<td class="diff-line-num new new_line" data-linenumber="10" 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="LC10" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</span>
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<td class="diff-line-num new new_line" data-linenumber="11" 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="LC11" class="line" lang="plaintext"> * Add salsa-ci file (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Rules-Requires-Root: no (routine-update)</span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> -- Étienne Mollier <etienne.mollier@mailoo.org> Sat, 19 Sep 2020 18:06:07 +0200</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">kleborate (1.0.0-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/kleborate/-/compare/15f181816c2f1bff70b161c033a5166901d748cc...30da58f476cf8b54301c7878615e2b64fa4e4828#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: kleborate</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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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="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"> Étienne Mollier <etienne.mollier@mailoo.org></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC6" 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="LC7" 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="LC8" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python3,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> python3-setuptools,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" 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="15" 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">@@ -14,6 +15,7 @@ Standards-Version: 4.5.0</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/kleborate</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/kleborate.git</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Homepage: https://github.com/katholt/Kleborate</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Package: kleborate</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Architecture: any</span>
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<li id="ce09002463acc33f527deeea60548ba4c53a739e">
<a href="https://salsa.debian.org/med-team/kleborate/-/compare/15f181816c2f1bff70b161c033a5166901d748cc...30da58f476cf8b54301c7878615e2b64fa4e4828#ce09002463acc33f527deeea60548ba4c53a739e"><strong>debian/patches/fix-ftbfs-biopython-1.78.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: fix FTBFS with python-biopython 1.78</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> The module Bio.Alphabet has been removed in version 1.78.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> More details are available at:</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> https://biopython.org/wiki/Alphabet</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Author: Étienne Mollier <etienne.mollier@mailoo.org></span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">Last-Update: 2020-09-19</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- kleborate.orig/kleborate/truncation.py</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ kleborate/kleborate/truncation.py</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="p">@@ -13,7 +13,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> from Bio.Seq import Seq</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from Bio.Alphabet import IUPAC</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> from .misc import reverse_complement</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="p">@@ -51,7 +50,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> # denominator for coverage.</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> ref_aa_length = (hit.ref_length - 3) // 3</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- coding_dna = Seq(nucl_seq, IUPAC.unambiguous_dna)</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ coding_dna = Seq(nucl_seq)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> translation = str(coding_dna.translate(table='Bacterial', to_stop=True))</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> coverage = 100.0 * len(translation) / ref_aa_length</span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">python3.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">use_debian_installed_kaptive.patch</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">fix-ftbfs-biopython-1.78.patch</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/kleborate/-/compare/15f181816c2f1bff70b161c033a5166901d748cc...30da58f476cf8b54301c7878615e2b64fa4e4828#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</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="plaintext"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">export LC_ALL=C</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">%:</span>
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4
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<td class="diff-line-num new_line" data-linenumber="6" 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">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> dh $@ --with python3 --buildsystem=pybuild</span>
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5
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<td class="diff-line-num new_line" data-linenumber="7" 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">
7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/kleborate/-/compare/15f181816c2f1bff70b161c033a5166901d748cc...30da58f476cf8b54301c7878615e2b64fa4e4828#b1dbf22e88351ec0d5d1d1a7f53295504b480e61"><strong>debian/salsa-ci.yml</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="nn" style="color: #555;">---</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">include</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;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml</span></span></pre>
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