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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/kaptive">Debian Med / kaptive</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kaptive/-/commit/bc5edcba6e1909ec24e69837302a31012e5b5d89">bc5edcba</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-09-22T17:21:39+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add fix-which-error-output.patch; fix `which` parsing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kaptive/-/commit/10868232d4167cc03062d747b1684bc90bb0494a">10868232</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-09-22T17:22:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Fix watchfile to detect new versions on github
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kaptive/-/commit/8664b4b08e149a65f5024f5e93b066a950b71d30">8664b4b0</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-09-22T17:23:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.6.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kaptive/-/commit/4f2432d7e57e0e57e100af370cebc3d72fc57657">4f2432d7</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-09-22T17:23:57+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Apply multi-arch hints.
+ kaptive-data, kaptive-example: Add Multi-Arch: foreign.
Changes-By: apply-multiarch-hints
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kaptive/-/commit/2d9d650cf509355dd2af0822907cf9347deab38d">2d9d650c</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-09-22T17:37:19+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/t/run-unit-test: run kaptive.py multi threaded
This restores the autopkgtest to its initial condition, since the
bug #970344 is resolved.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kaptive/-/commit/7d83b1410ebc16f1b69cc77f09faf41f3e3de5f0">7d83b141</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-09-22T17:43:15+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ready for team upload to unstable
</pre>
</li>
</ul>
<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#798654c34bc2d9091cde827f942a4d9f5db6b524">
<span class="new-file">
+
debian/patches/fix-which-error-output.patch
</span>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/kaptive/-/compare/61bc03e075a93af23653f5d3aabec210444f91a7...7d83b1410ebc16f1b69cc77f09faf41f3e3de5f0#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">kaptive (0.7.3-4) unstable; 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"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Add fix-which-error-output.patch to fix the way kaptive.py parses `which`</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> output; this is necessary since `which` in Debian issues a deprecation</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> warning.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Fix watchfile to detect new versions on github (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Standards-Version: 4.6.0 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Apply multi-arch hints.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> + kaptive-data, kaptive-example: Add Multi-Arch: foreign.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * d/t/run-unit-test: run kaptive.py in multiple threads again, since the bug</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> #970344, affecting tblastn, is now solved.</span>
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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 <emollier@debian.org> Wed, 22 Sep 2021 17:38:14 +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">kaptive (0.7.3-3) unstable; urgency=high</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/kaptive/-/compare/61bc03e075a93af23653f5d3aabec210444f91a7...7d83b1410ebc16f1b69cc77f09faf41f3e3de5f0#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">@@ -8,7 +8,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> python3-all,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python3-setuptools,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> python3-biopython <!nocheck></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5</span>.0</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">6</span>.0</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/kaptive</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/kaptive.git</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Homepage: https://github.com/katholt/Kaptive</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="54" 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="54" 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">@@ -54,6 +54,7 @@ Package: kaptive-data</td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext">Depends: ${misc:Depends}</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext">Enhances: kaptive</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">Multi-Arch: foreign</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext">Description: reference data for kaptive for Klebsiella genome assemblies</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext"> Kaptive reports information about K and O types for Klebsiella genome</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext"> assemblies.</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="89" 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="90" 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">@@ -89,6 +90,7 @@ Package: kaptive-example</td>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext">Depends: ${misc:Depends}</span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="plaintext">Enhances: kaptive</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">Multi-Arch: foreign</span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext">Description: example data for kaptive for Klebsiella genome assemblies</span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext"> Kaptive reports information about K and O types for Klebsiella genome</span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="plaintext"> assemblies.</span>
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<li id="798654c34bc2d9091cde827f942a4d9f5db6b524">
<a href="https://salsa.debian.org/med-team/kaptive/-/compare/61bc03e075a93af23653f5d3aabec210444f91a7...7d83b1410ebc16f1b69cc77f09faf41f3e3de5f0#798654c34bc2d9091cde827f942a4d9f5db6b524"><strong>debian/patches/fix-which-error-output.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: address handling of `which` command</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> kaptive.py is unable to run any meaningful computation, due to the way it</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> handles the output of the command `which makeblastdb` in a context of `which`</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> outputing deprecation messages in the standard error. The patch is a way to</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> approximate the behavior of the regular shell use of the command `which` which</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> consists in checking the error code of the command, and discarding the</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> standard output. Standard error is left around in case the command `which`</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> were to have interesting diagnostic messages to the user.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">Author: Étienne Mollier <emollier@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">Last-Update: 2021-09-22</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC13" 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="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- kaptive.orig/kaptive.py</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ kaptive/kaptive.py</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -171,9 +171,11 @@</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"> def find_program(name):</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> """Checks to see if a program exists."""</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- process = subprocess.Popen(['which', name], stdout=subprocess.PIPE, stderr=subprocess.PIPE)</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- out, err = process.communicate()</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return bool(out) and not bool(err)</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ try:</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ subprocess.check_call(['which', name], stdout=subprocess.DEVNULL)</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;">+ except subprocess.CalledProcessError:</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return False</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return True</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> def fix_paths(args):</span></pre>
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<a href="https://salsa.debian.org/med-team/kaptive/-/compare/61bc03e075a93af23653f5d3aabec210444f91a7...7d83b1410ebc16f1b69cc77f09faf41f3e3de5f0#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">blastdb_4</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">extend_bad_versions</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">fix-which-error-output.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/kaptive/-/compare/61bc03e075a93af23653f5d3aabec210444f91a7...7d83b1410ebc16f1b69cc77f09faf41f3e3de5f0#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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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>
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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">@@ -14,6 +14,4 @@ cd "${AUTOPKGTEST_TMP}"</td>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"FIXME: Due to bug #970344 we are using single threaded mode (-t 1) here."</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell">kaptive.py <span class="nt" style="color: #000080;">-t</span> 1 <span class="nt" style="color: #000080;">-a</span> exact_match.fasta <span class="nt" style="color: #000080;">-k</span> /usr/share/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/reference_database/Klebsiella_k_locus_primary_reference.gbk <span class="nt" style="color: #000080;">-o</span> output/test</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"FIXME: Make sure to remove '-t 1' from the kaptive call once bug #970344 is fixed."</span></span></pre>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">kaptive.py <span class="nt" style="color: #000080;">-a</span> exact_match.fasta <span class="nt" style="color: #000080;">-k</span> /usr/share/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/reference_database/Klebsiella_k_locus_primary_reference.gbk <span class="nt" style="color: #000080;">-o</span> output/test</span></pre>
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<a href="https://salsa.debian.org/med-team/kaptive/-/compare/61bc03e075a93af23653f5d3aabec210444f91a7...7d83b1410ebc16f1b69cc77f09faf41f3e3de5f0#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">https://github.com/katholt/Kaptive/releases .*/<span class="idiff left right">archive/</span>v?@ANY_VERSION@@ARCHIVE_EXT@</span></pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">https://github.com/katholt/Kaptive/releases .*/v?@ANY_VERSION@@ARCHIVE_EXT@</span></pre>
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