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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/bcalm">Debian Med / bcalm</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcalm/commit/66449a07e3d8083e27267c1536dd652ba3082729">66449a07</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-09-23T12:17:07Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Modify tests so they execute
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/bcalm/commit/287997278e2d7a8caab3a8e0bf67a519b8ff953a">28799727</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-09-23T12:22:19Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Write autopkgtest
Currently passes
</pre>
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#4e7bef039d1be849bcdebf9c5fa57692726875ec">
debian/bcalm.install
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<li class="file-stats">
<a href="#f5828d1c4782867effd59adbe71462118cbc2b2a">
debian/missing-sources/simple_test.sh
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="4e7bef039d1be849bcdebf9c5fa57692726875ec">
<a href="https://salsa.debian.org/med-team/bcalm/compare/700890df208d1f947781fbf17c1fde24262ebc09...287997278e2d7a8caab3a8e0bf67a519b8ff953a#4e7bef039d1be849bcdebf9c5fa57692726875ec"><strong>debian/bcalm.install</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">@@ -2,3 +2,6 @@ debian/missing-sources/compare_fasta.py usr/share/doc/bcalm/test</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">missing</span><span class="o" style="font-weight: 600;">-</span><span class="nx">sources</span><span class="o" style="font-weight: 600;">/</span><span class="nx">reference</span><span class="o" style="font-weight: 600;">.</span><span class="nx">fasta</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bcalm</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">missing</span><span class="o" style="font-weight: 600;">-</span><span class="nx">sources</span><span class="o" style="font-weight: 600;">/</span><span class="nx">simple_test</span><span class="o" style="font-weight: 600;">.</span><span class="nx">sh</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bcalm</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="php"><span class="nx">example</span><span class="o" style="font-weight: 600;">/*</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bcalm</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/*</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bcalm</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">missing</span><span class="o" style="font-weight: 600;">-</span><span class="nx">sources</span><span class="o" style="font-weight: 600;">/</span><span class="nx">compare_fasta</span><span class="o" style="font-weight: 600;">.</span><span class="nx">py</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bcalm</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"></span></pre>
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<li id="f5828d1c4782867effd59adbe71462118cbc2b2a">
<a href="https://salsa.debian.org/med-team/bcalm/compare/700890df208d1f947781fbf17c1fde24262ebc09...287997278e2d7a8caab3a8e0bf67a519b8ff953a#f5828d1c4782867effd59adbe71462118cbc2b2a"><strong>debian/missing-sources/simple_test.sh</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"> </span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> reference.fasta</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>rm -f reference.fasta</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#wget https://raw.githubusercontent.com/GATB/MindTheGap/f5cb0fec816686c7393772787d736565c4f056a4/test/full_test/reference.fasta >& /dev/null</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"><span class="idiff left right">../build/</span>bcalm <span class="nt" style="color: #000080;">-in</span> reference.fasta <span class="nt" style="color: #000080;">-abundance-min</span> 1 <span class="o" style="font-weight: 600;">></span> /dev/null <span class="o" style="font-weight: 600;">></span>& /dev/null</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> reference.unitigs.fa.glue<span class="k" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> compare_fasta.py</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell">bcalm <span class="nt" style="color: #000080;">-in</span> reference.fasta <span class="nt" style="color: #000080;">-abundance-min</span> 1 <span class="o" style="font-weight: 600;">></span> /dev/null <span class="o" style="font-weight: 600;">></span>& /dev/null</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>rm -rf reference.unitigs.fa.glue*</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>rm -f compare_fasta.py</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#wget https://raw.githubusercontent.com/GATB/minia/master/test/compare_fasta.py >& /dev/null</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell">python3 compare_fasta.py reference.fasta reference.unitigs.fa</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"><span class="nv" style="color: #008080;">res</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$?</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> reference.fasta reference.h5 reference.unitigs.fa compare_fasta.py </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>rm -f reference.fasta reference.h5 reference.unitigs.fa compare_fasta.py </span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$res</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"0"</span> <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"test OK"</span></span>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/bcalm/compare/700890df208d1f947781fbf17c1fde24262ebc09...287997278e2d7a8caab3a8e0bf67a519b8ff953a#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#PACKAGENAME#</span></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="idiff left right">bcalm</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Double quote below to expand the temporary directory variable now versus</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/<span class="idiff left right">examples</span>/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/<span class="idiff left right">test</span>/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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15
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"></span>
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<td class="diff-line-num old_line" data-linenumber="16" 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">
16
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<td class="diff-line-num new_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">
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num old_line" data-linenumber="17" 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">
17
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"></span>
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<td class="diff-line-num old old_line" data-linenumber="18" 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">
18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#do_stuff_to_test_package#</span></span></pre>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell">bash simple_test.sh</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">bash run-tiny.sh</span></pre>
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