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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-cooler">Debian Med / python-cooler</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cooler/-/commit/f91261f00c052164741ea33e787bf84009469952">f91261f0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-14T10:13:14+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install test data
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cooler/-/commit/c67c084b1db739f71f34db017a8c15dc045c8170">c67c084b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-14T10:19:21+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Autopkgtest
</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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</li>
<li class="file-stats">
<a href="#3c500cfc19c6a63abbdadec9ed575221ed334ed6">
<span class="new-file">
+
debian/python3-cooler-examples.install
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</li>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
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</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/python-cooler/-/compare/a796e28a20eb926d1ad74c063a85eecb65d3b742...c67c084b1db739f71f34db017a8c15dc045c8170#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">@@ -37,7 +37,7 @@ Depends: ${python3:Depends},</td>
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">multiprocess</span><span class="p">,</span></span>
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<td class="diff-line-num new_line" data-linenumber="38" 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">
38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">biopython</span><span class="p">,</span></span>
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">pyfaidx</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">p<span class="idiff left right">yp</span>airix</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="40" 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="LC40" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">pairix</span><span class="p">,</span></span>
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41
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<td class="diff-line-num new_line" data-linenumber="41" 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">
41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">asciitree</span><span class="p">,</span></span>
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42
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">yaml</span><span class="p">,</span></span>
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<td class="diff-line-num new_line" data-linenumber="43" 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">
43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">simplejson</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="50" 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="50" 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">@@ -50,3 +50,21 @@ Description: library for a sparse, compressed, binary persistent storage</td>
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">HDF5</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">container</span> <span class="n" style="color: #333;">format</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">cooler</span> <span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">includes</span> <span class="n" style="color: #333;">a</span></span>
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="mosel"> <span class="n" style="color: #333;">suite</span> <span class="k" style="font-weight: 600;">of</span> <span class="nf" style="color: #900; font-weight: 600;">command</span> <span class="n" style="color: #333;">line</span> <span class="n" style="color: #333;">tools</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">Python</span> <span class="n" style="color: #333;">API</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">facilitate</span> <span class="n" style="color: #333;">creating</span><span class="p">,</span></span>
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52
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52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="mosel"> <span class="n" style="color: #333;">querying</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">manipulating</span> <span class="n" style="color: #333;">cooler</span> <span class="n" style="color: #333;">files</span><span class="p">.</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="mosel"></span>
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<td class="diff-line-num new new_line" data-linenumber="54" 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">
54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Package</span><span class="p">:</span> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">cooler</span><span class="p">-</span><span class="n" style="color: #333;">examples</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="mosel"><span class="n" style="color: #333;">Architecture</span><span class="p">:</span> <span class="n" style="color: #333;">all</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="mosel"><span class="n" style="color: #333;">Section</span><span class="p">:</span> <span class="n" style="color: #333;">python</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="mosel"><span class="n" style="color: #333;">Depends</span><span class="p">:</span> <span class="p">${</span><span class="n" style="color: #333;">python3</span><span class="p">:</span><span class="n" style="color: #333;">Depends</span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="mosel"> <span class="p">${</span><span class="n" style="color: #333;">misc</span><span class="p">:</span><span class="n" style="color: #333;">Depends</span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="mosel"><span class="n" style="color: #333;">Enhances</span><span class="p">:</span> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">cooler</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="mosel"><span class="n" style="color: #333;">Description</span><span class="p">:</span> <span class="n" style="color: #333;">library</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">sparse</span><span class="p">,</span> <span class="n" style="color: #333;">compressed</span><span class="p">,</span> <span class="n" style="color: #333;">binary</span> <span class="n" style="color: #333;">persistent</span> <span class="n" style="color: #333;">storage</span> <span class="p">(</span><span class="n" style="color: #333;">examples</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="mosel"> <span class="n" style="color: #333;">Cooler</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">support</span> <span class="n" style="color: #333;">library</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">sparse</span><span class="p">,</span> <span class="n" style="color: #333;">compressed</span><span class="p">,</span> <span class="n" style="color: #333;">binary</span> <span class="n" style="color: #333;">persistent</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="mosel"> <span class="n" style="color: #333;">storage</span> <span class="n" style="color: #333;">format</span><span class="p">,</span> <span class="n" style="color: #333;">also</span> <span class="n" style="color: #333;">called</span> <span class="n" style="color: #333;">cooler</span><span class="p">,</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">store</span> <span class="n" style="color: #333;">genomic</span> <span class="n" style="color: #333;">interaction</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="mosel"> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">such</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">Hi</span><span class="p">-</span><span class="n" style="color: #333;">C</span> <span class="n" style="color: #333;">contact</span> <span class="n" style="color: #333;">matrices</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="mosel"> <span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="mosel"> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">cooler</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">format</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">implementation</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">genomic</span> <span class="n" style="color: #333;">matrix</span> <span class="n" style="color: #333;">data</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">HDF5</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">container</span> <span class="n" style="color: #333;">format</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">cooler</span> <span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">includes</span> <span class="n" style="color: #333;">a</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="mosel"> <span class="n" style="color: #333;">suite</span> <span class="k" style="font-weight: 600;">of</span> <span class="nf" style="color: #900; font-weight: 600;">command</span> <span class="n" style="color: #333;">line</span> <span class="n" style="color: #333;">tools</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">Python</span> <span class="n" style="color: #333;">API</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">facilitate</span> <span class="n" style="color: #333;">creating</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="mosel"> <span class="n" style="color: #333;">querying</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">manipulating</span> <span class="n" style="color: #333;">cooler</span> <span class="n" style="color: #333;">files</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="mosel"> <span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="mosel"> <span class="n" style="color: #333;">This</span> <span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">contains</span> <span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">example</span> <span class="n" style="color: #333;">data</span><span class="p">.</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-cooler/-/compare/a796e28a20eb926d1ad74c063a85eecb65d3b742...c67c084b1db739f71f34db017a8c15dc045c8170#3c500cfc19c6a63abbdadec9ed575221ed334ed6"><strong>debian/python3-cooler-examples.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">tests</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">python3</span><span class="o" style="font-weight: 600;">-</span><span class="nx">cooler</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-cooler/-/compare/a796e28a20eb926d1ad74c063a85eecb65d3b742...c67c084b1db739f71f34db017a8c15dc045c8170#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Depends: @</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @<span class="idiff left right">, python3-pytest, python3-mock</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<a href="https://salsa.debian.org/med-team/python-cooler/-/compare/a796e28a20eb926d1ad74c063a85eecb65d3b742...c67c084b1db739f71f34db017a8c15dc045c8170#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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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"></span>
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4
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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">python3-cooler</span></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LC_ALL</span><span class="o" style="font-weight: 600;">=</span>C.UTF-8</span>
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7
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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="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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8
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8
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<pre style="margin: 0;"> <span id="LC8" 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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9
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<pre style="margin: 0;">-<span id="LC9" 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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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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12
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9
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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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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13
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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14
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/<span class="idiff left">examples/</span><span class="k" style="font-weight: 600;"><span class="idiff right">*</span></span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/<span class="idiff left right">tests</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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16
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"></span>
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17
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</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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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"></span>
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19
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<pre style="margin: 0;">-<span id="LC19" 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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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell">pytest-3</span></pre>
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