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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/lumpy-sv">Debian Med / lumpy-sv</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/lumpy-sv/-/commit/eaa7dcc371f34b5b2e36be610ee08008218b0a19">eaa7dcc3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-01T22:19:24+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bamkit is about to be uploaded to new
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<strong><a href="https://salsa.debian.org/med-team/lumpy-sv/-/commit/dee6e8cfc972f767126986f06ec5de51d402615e">dee6e8cf</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-06-01T23:05:16+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove autopkgtest template
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<strong><a href="https://salsa.debian.org/med-team/lumpy-sv/-/commit/e64a65545fbf60c5c98965bc1d00d416b2f9582c">e64a6554</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-06-01T23:20:10+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adapt check to Python3
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<h4>8 changed files:</h4>
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debian/README.test
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#8d695f5062616d175c0a919bfe84431505824645">
debian/etc/lumpyexpress.config
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<a href="#68d8c5c6babbf5cf109b2584c454449dbff75772">
debian/install
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<a href="#6864ced7557ec33a7ee70c7b0c75b076f84f4fac">
debian/patches/lumpyexpress.config.patch
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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/lumpy-sv/-/compare/1112e38314b113869a3f4b9748ce484113c9c107...e64a65545fbf60c5c98965bc1d00d416b2f9582c#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="php"><span class="nx">Notes</span> <span class="nx">on</span> <span class="nx">how</span> <span class="nx">this</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span><span class="o" style="font-weight: 600;">.</span></span>
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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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<pre style="margin: 0;">-<span id="LC4" class="line" lang="php"><span class="nx">This</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span> <span class="nx">by</span> <span class="nx">running</span> <span class="nx">the</span> <span class="nx">provided</span> <span class="nx">test</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="php"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="php"> <span class="nx">sh</span> <span class="nx">run</span><span class="o" style="font-weight: 600;">-</span><span class="nx">unit</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>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="php"><span class="nx">in</span> <span class="nx">order</span> <span class="nx">to</span> <span class="nx">confirm</span> <span class="nx">its</span> <span class="nx">integrity</span><span class="o" style="font-weight: 600;">.</span></span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/lumpy-sv/-/compare/1112e38314b113869a3f4b9748ce484113c9c107...e64a65545fbf60c5c98965bc1d00d416b2f9582c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">lumpy-sv (0.3.0+dfsg-<span class="idiff left right">2</span>) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">lumpy-sv (0.3.0+dfsg-<span class="idiff left right">1</span>) 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"> * Initial release (Closes: #961998)</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> TODO: https://salsa.debian.org/med-team/bamkit</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 01 Jun 2020 21:58:38 +0200</span></pre>
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<a href="https://salsa.debian.org/med-team/lumpy-sv/-/compare/1112e38314b113869a3f4b9748ce484113c9c107...e64a65545fbf60c5c98965bc1d00d416b2f9582c#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="27" 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">@@ -27,7 +27,8 @@ Depends: ${shlibs:Depends},</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> samtools,</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> python3,</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> python3-pysam,</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> python3-numpy</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> python3-numpy,</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> bamkit</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">Recommends: sambamba</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">Description: general probabilistic framework for structural variant discovery</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> LUMPY, a novel SV discovery framework that naturally integrates multiple</span>
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<a href="https://salsa.debian.org/med-team/lumpy-sv/-/compare/1112e38314b113869a3f4b9748ce484113c9c107...e64a65545fbf60c5c98965bc1d00d416b2f9582c#8d695f5062616d175c0a919bfe84431505824645"><strong>debian/etc/lumpyexpress.config</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">@@ -8,6 +8,6 @@ SAMTOOLS=/usr/bin/samtools</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="conf"><span class="n" style="color: #333;">PYTHON</span>=/<span class="n" style="color: #333;">usr</span>/<span class="n" style="color: #333;">bin</span>/<span class="n" style="color: #333;">python3</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="conf"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="conf"><span class="n" style="color: #333;">PAIREND_DISTRO</span>=/<span class="n" style="color: #333;">usr</span>/<span class="n" style="color: #333;">share</span>/<span class="n" style="color: #333;">lumpy</span>-<span class="n" style="color: #333;">sv</span>/<span class="n" style="color: #333;">scripts</span>/<span class="n" style="color: #333;">pairend_distro</span>.<span class="n" style="color: #333;">py</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="conf"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#BAMGROUPREADS=/usr/share/lumpy-sv/scripts</span>/bamkit/bamgroupreads.py</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="conf"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#BAMFILTERRG=/usr/share/lumpy-sv/scripts</span>/bamkit/bamfilterrg.py</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="conf"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#BAMLIBS=/usr/share/lumpy-sv/scripts</span>/bamkit/bamlibs.py</span></span></pre>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="conf"><span class="n" style="color: #333;"><span class="idiff left">BAMGROUPREADS</span></span><span class="idiff">=/</span><span class="n" style="color: #333;"><span class="idiff">usr</span></span><span class="idiff">/</span><span class="n" style="color: #333;"><span class="idiff right">share</span></span>/<span class="n" style="color: #333;">bamkit</span>/<span class="n" style="color: #333;">bamgroupreads</span>.<span class="n" style="color: #333;">py</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="conf"><span class="n" style="color: #333;"><span class="idiff left">BAMFILTERRG</span></span><span class="idiff">=/</span><span class="n" style="color: #333;"><span class="idiff">usr</span></span><span class="idiff">/</span><span class="n" style="color: #333;"><span class="idiff right">share</span></span>/<span class="n" style="color: #333;">bamkit</span>/<span class="n" style="color: #333;">bamfilterrg</span>.<span class="n" style="color: #333;">py</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="conf"><span class="n" style="color: #333;"><span class="idiff left">BAMLIBS</span></span><span class="idiff">=/</span><span class="n" style="color: #333;"><span class="idiff">usr</span></span><span class="idiff">/</span><span class="n" style="color: #333;"><span class="idiff right">share</span></span>/<span class="n" style="color: #333;">bamkit</span>/<span class="n" style="color: #333;">bamlibs</span>.<span class="n" style="color: #333;">py</span></span></pre>
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<a href="https://salsa.debian.org/med-team/lumpy-sv/-/compare/1112e38314b113869a3f4b9748ce484113c9c107...e64a65545fbf60c5c98965bc1d00d416b2f9582c#68d8c5c6babbf5cf109b2584c454449dbff75772"><strong>debian/install</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">debian/etc/lumpyexpress.config etc/lumpy</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/etc/lumpyexpress.config etc/lumpy<span class="idiff left right">-sv</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">scripts usr/share/lumpy-sv</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">bin/lumpy usr/bin</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">bin/lumpy_filter usr/bin</span>
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<a href="https://salsa.debian.org/med-team/lumpy-sv/-/compare/1112e38314b113869a3f4b9748ce484113c9c107...e64a65545fbf60c5c98965bc1d00d416b2f9582c#6864ced7557ec33a7ee70c7b0c75b076f84f4fac"><strong>debian/patches/lumpyexpress.config.patch</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">@@ -21,6 +21,17 @@ Description: Adapt paths to Debian locations</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> # For testing if the full BAM is actually a CRAM!</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"> HEXDUMP=`which hexdump || true`</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="p">@@ -92,8 +92,8 @@</span> check_python_modules() {</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> PYTHON_TEST=$1</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> echo -e "\nChecking for required python modules ($PYTHON_TEST)..."</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $PYTHON_TEST -c "import imp; imp.find_module('pysam')"</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $PYTHON_TEST -c "import imp; imp.find_module('numpy')"</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $PYTHON_TEST -c "import importlib; importlib.util.find_spec('pysam')"</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $PYTHON_TEST -c "import importlib; importlib.util.find_spec('numpy')"</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> ## usage</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"><span class="p">@@ -126,7 +126,7 @@</span> options:</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"> # set defaults</span>
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<a href="https://salsa.debian.org/med-team/lumpy-sv/-/compare/1112e38314b113869a3f4b9748ce484113c9c107...e64a65545fbf60c5c98965bc1d00d416b2f9582c#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Depends: @</span>
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3
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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/lumpy-sv/-/compare/1112e38314b113869a3f4b9748ce484113c9c107...e64a65545fbf60c5c98965bc1d00d416b2f9582c#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong>
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1
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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>
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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;">#PACKAGENAME#</span></span>
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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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<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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<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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<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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<pre style="margin: 0;">-<span id="LC12" 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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell"></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</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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