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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/circlator">Debian Med / circlator</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/circlator/-/commit/d744eecaaf9f1340673eea50b30f7026a14b651a">d744eeca</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-11-30T14:55:12+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Rewrite test
</pre>
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<strong><a href="https://salsa.debian.org/med-team/circlator/-/commit/5855b2c40b24a1e65d2b33d4ee72911cf3a9433d">5855b2c4</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-11-30T15:21:18+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix tests
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<h4>8 changed files:</h4>
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<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
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debian/README.test
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
debian/docs
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<a href="#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c">
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debian/examples
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debian/rules
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<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
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debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/circlator/-/compare/85828934d7a403a329ffb56c4a1630c7d19ca1ca...5855b2c40b24a1e65d2b33d4ee72911cf3a9433d#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nc" style="color: #458; font-weight: 600;">Notes</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">how</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">package</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">tested</span><span class="mf" style="color: #099;">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2" 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="LC2" class="line" lang="php"><span class="err" style="color: #a61717; background-color: #e3d2d2;">────────────────────────────────────────</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"></span>
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<td class="diff-line-num new new_line" data-linenumber="4" 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="LC4" class="line" lang="php"><span class="nc" style="color: #458; font-weight: 600;">This</span> <span class="n" style="color: #333;">package</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">tested</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">running</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">provided</span> <span class="n" style="color: #333;">test</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5" 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="LC5" class="line" lang="php"></span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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="LC6" class="line" lang="php"> <span class="n" style="color: #333;">sh</span> <span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">unit</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">test</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="php"><span class="n" style="color: #333;">in</span> <span class="n" style="color: #333;">order</span> <span class="n" style="color: #333;">to</span> <span class="n" style="color: #333;">confirm</span> <span class="n" style="color: #333;">its</span> <span class="n" style="color: #333;">integrity</span><span class="mf" style="color: #099;">.</span></span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/circlator/-/compare/85828934d7a403a329ffb56c4a1630c7d19ca1ca...5855b2c40b24a1e65d2b33d4ee72911cf3a9433d#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">circlator (1.5.6-2) UNRELEASED; 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"> * Rewrite autopkgtest</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Closes: #976100</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Depends: canu (instead of Suggests)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Skip some failing tests in autopkgtest</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 30 Nov 2020 14:37:58 +0100</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">circlator (1.5.6-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * Afif removed himself from Uploaders (thanks for your work on this)</span>
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<a href="https://salsa.debian.org/med-team/circlator/-/compare/85828934d7a403a329ffb56c4a1630c7d19ca1ca...5855b2c40b24a1e65d2b33d4ee72911cf3a9433d#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">@@ -31,8 +31,8 @@ Depends: ${misc:Depends},</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> bwa (>= 0.7.12),</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> mummer,</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> samtools,</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"> spades</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"><span class="idiff left right">Suggests:</span> canu</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> spades<span class="idiff left right">,</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"><span class="idiff left right"> </span> canu</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">Description: circularize genome assemblies</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> Circlator is a tool to automate assembly circularization for bacterial and</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> small eukaryotic genomes and produce accurate linear representations of</span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">README.md</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/tests/run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/README.test</span></pre>
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<a href="https://salsa.debian.org/med-team/circlator/-/compare/85828934d7a403a329ffb56c4a1630c7d19ca1ca...5855b2c40b24a1e65d2b33d4ee72911cf3a9433d#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c"><strong>debian/examples</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">circlator/tests/*.py</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">circlator/tests/data</span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</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">#DH_VERBOSE = 1</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"><span class="idiff left right">#</span>include /usr/share/dpkg/default.mk</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">include /usr/share/dpkg/default.mk</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="LC6" class="line" lang="plaintext">export LC_ALL=C.UTF-8</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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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">@@ -12,3 +12,7 @@ override_dh_auto_test:</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> PYTHONPATH=$(CURDIR) nosetests3 -v --where=circlator/tests</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">endif</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">override_dh_installexamples:</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> dh_installexamples</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> cd debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/examples && tar caf data.tar.xz data && rm -rf data</span></pre>
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<a href="https://salsa.debian.org/med-team/circlator/-/compare/85828934d7a403a329ffb56c4a1630c7d19ca1ca...5855b2c40b24a1e65d2b33d4ee72911cf3a9433d#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Test-Command: cd $ADTTMP && circlator test test-dir</span>
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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: @, python3-nose</span>
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2
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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/circlator/-/compare/85828934d7a403a329ffb56c4a1630c7d19ca1ca...5855b2c40b24a1e65d2b33d4ee72911cf3a9433d#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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2
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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 class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-x</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>circlator</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC7" 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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8
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<pre style="margin: 0;">+<span id="LC8" 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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9
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<pre style="margin: 0;">+<span id="LC9" 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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10
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<pre style="margin: 0;">+<span id="LC10" 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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</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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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">tar </span>xaf data.tar.xz</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-i</span> <span class="s2" style="color: #d14;">"s/data_dir = os.path.join(modules_dir, 'tests', 'data')/data_dir = os.path.join(os.getcwd(), 'data')/"</span> <span class="k" style="font-weight: 600;">*</span>.py</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell">nosetests3 <span class="nt" style="color: #000080;">-v</span> <span class="nb" style="color: #0086b3;">.</span></span></pre>
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