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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-ruffus">Debian Med / python-ruffus</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-ruffus/commit/ab77b638a49683a3a092d03c8ab78ba1b1c14495">ab77b638</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-22T18:12:35Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove Python2 module
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-ruffus/commit/bc4d36abb8323c6cc9b713e2c43fb7bae1c85f3c">bc4d36ab</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-22T18:12:47Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-ruffus/commit/efe9d53b0e9e770585ce0aff46840c7c3071be30">efe9d53b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-22T18:12:52Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.4.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-ruffus/commit/a92d3b437265a1e9d542093534b3d6ee0824dd6c">a92d3b43</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-22T18:12:52Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">R-U: rename d/tests/control.autodep8 to d/tests/control
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-ruffus/commit/33613004aae0d85cf3a6240d126eb82516492486">33613004</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-22T18:12:52Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">R-U: autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-ruffus/commit/1daa74b3f7b973a276c20e36f94bfd49054aa9a5">1daa74b3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-22T18:12:56Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Bug-Database, Repository, Repository-Browse.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-ruffus/commit/a31619fa89a5180c04bd9923f5d30de368308500">a31619fa</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-22T18:37:46Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fiy doc-base file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-ruffus/commit/4acf6976c74b65297baaaed82cdd4c0cdd9c8fae">4acf6976</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-22T19:03:46Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Run only Python3 testscript in autopkgtest
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-ruffus/commit/4d8c6b825b2d3359ce394d0c29328bbe950244f5">4d8c6b82</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-22T19:11:35Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>9 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="deleted-file">
−
debian/compat
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#80cd9e4ef2459be69eee211a2d622d62ca7a2aeb">
debian/python-ruffus-doc.doc-base.html
</a>
</li>
<li class="file-stats">
<a href="#88137b03d990e147c3434567fb8ad48f95dab39a">
debian/python-ruffus-doc.doc-base.pdf
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control.autodep8
→
debian/tests/control
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
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</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/python-ruffus/compare/8d9294dc2e3535ca60869d08d483b3699d54576c...4d8c6b825b2d3359ce394d0c29328bbe950244f5#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" 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="LC1" class="line" lang="plaintext">python-ruffus (2.8.1-5) unstable; urgency=medium</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="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" 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="LC3" class="line" lang="plaintext"> * Remove Python2 module</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="plaintext"> Closes: #938152</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="plaintext"> * debhelper-compat 12</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="plaintext"> * Standards-Version: 4.4.1</span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="plaintext"> * rename debian/tests/control.autodep8 to debian/tests/control</span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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="LC8" class="line" lang="plaintext"> * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g</span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Database, Repository, Repository-</span>
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<td class="diff-line-num new new_line" data-linenumber="10" 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="LC10" class="line" lang="plaintext"> Browse.</span>
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<td class="diff-line-num new new_line" data-linenumber="11" 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="LC11" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="12" 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="LC12" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Sun, 22 Dec 2019 20:04:05 +0100</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">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">python-ruffus (2.8.1-4) unstable; urgency=medium</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"> * Enable reproducible build by removing non-deterministic temporary temp</span>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/python-ruffus/compare/8d9294dc2e3535ca60869d08d483b3699d54576c...4d8c6b825b2d3359ce394d0c29328bbe950244f5#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">11</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/python-ruffus/compare/8d9294dc2e3535ca60869d08d483b3699d54576c...4d8c6b825b2d3359ce394d0c29328bbe950244f5#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">@@ -4,40 +4,19 @@ Uploaders: Andreas Tille <tille@debian.org></td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: python</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Testsuite: autopkgtest-pkg-python</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right"> (>= 11~</span>),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right">-compat (= 12</span>),</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> python-all,</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> python-setuptools,</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> python-pytest,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python3-all,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> python3-setuptools,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> python3-sphinx,</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> python3-sphinx-rtd-theme,</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> python3-pytest,</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> graphviz</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2</span>.1</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4</span>.1</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/python-ruffus</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/python-ruffus.git</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Homepage: http://www.ruffus.org.uk/</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">Package: python-ruffus</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> ${python:Depends},</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> graphviz</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">Suggests: python-drmaa</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">Description: Python computation pipeline library widely used in bioinformatics</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> Ruffus is designed to allow scientific and other analyses to be automated</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> with the minimum of fuss and the least effort.</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"> * Lightweight: Suitable for the simplest of tasks</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"> * Scalable: Handles even fiendishly complicated pipelines which would cause</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> make or scons to go cross-eyed and recursive.</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"> * Standard Python: No "clever magic", no pre-processing.</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext"> * Unintrusive: Unambitious, lightweight syntax which tries to do this one</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext"> small thing well.</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Package: python3-ruffus</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Depends: ${shlibs:Depends},</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">@@ -14,5 +14,5 @@ Abstract: Python computation pipeline library widely used in bioinformatics</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="html">Section: Science/Biology</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="html">Format: html</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="html">Files: /usr/share/doc/python-ruffus/html</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="html">Index: /usr/share/doc/python-ruffus/html/index.html</span></pre>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="html">Files: /usr/share/doc/python-ruffus<span class="idiff left right">-doc</span>/html</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="html">Index: /usr/share/doc/python-ruffus<span class="idiff left right">-doc</span>/html/index.html</span></pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,4 +14,4 @@ Abstract: Python computation pipeline library widely used in bioinformatics</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Section: Science/Biology</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">Format: pdf</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Files: /usr/share/doc/python-ruffus/ruffus.pdf.gz</span></pre>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Files: /usr/share/doc/python-ruffus<span class="idiff left right">-doc</span>/ruffus.pdf.gz</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/python-ruffus/compare/8d9294dc2e3535ca60869d08d483b3699d54576c...4d8c6b825b2d3359ce394d0c29328bbe950244f5#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -9,7 +9,7 @@ docpkg:=$(DEB_SOURCE)-doc</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">export PYBUILD_NAME=ruffus</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></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"> dh $@ --with python<span class="idiff left right">2,python</span>3,sphinxdoc --buildsystem=pybuild</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> dh $@ --with python3,sphinxdoc --buildsystem=pybuild</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> dh_auto_build</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" 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">@@ -18,6 +18,7 @@ override_dh_auto_build:</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">override_dh_installdocs:</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> dh_installdocs -ppython-ruffus-doc doc/_build/html</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> dh_installdocs -A</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> find debian -name run_all_unit_tests.cmd -delete</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -60,7 +61,6 @@ override_dh_install:</td>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext"> find debian/python3-$(PYBUILD_NAME)/usr/lib/python3*/dist-packages/ruffus/test -name "*.py" -exec sed -i 's+^\(#!/usr/bin/.*python\)[[:space:]]*$$+\13+' \{\} \;</span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext"> # leave only the test starter that fits Python version</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext"> find debian/python3-$(PYBUILD_NAME) -name run_all_unit_tests.cmd -delete</span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext"> find debian/python-$(PYBUILD_NAME) -name run_all_unit_tests3.cmd -delete</span>
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext"> sed -i '1s?^#! */usr/bin/env *python *$$?#!/usr/bin/python3?' `grep -Rl '^#! */usr/bin/env *python *$$' debian/python3-$(PYBUILD_NAME)`</span>
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65
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext"></span>
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext">override_dh_fixperms:</span>
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<a href="https://salsa.debian.org/med-team/python-ruffus/compare/8d9294dc2e3535ca60869d08d483b3699d54576c...4d8c6b825b2d3359ce394d0c29328bbe950244f5#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control.autodep8</strong>
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<a href="https://salsa.debian.org/med-team/python-ruffus/compare/8d9294dc2e3535ca60869d08d483b3699d54576c...4d8c6b825b2d3359ce394d0c29328bbe950244f5#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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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/sh -e</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"></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 class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>python-ruffus</span>
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4
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<pre style="margin: 0;">-<span id="LC4" 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;">$ADTTMP</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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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">ADTTMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" 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;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</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="LC5" 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="sb" 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;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="sb" style="color: #d14;">`</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</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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6
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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;">fi</span></span>
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7
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<td class="diff-line-num new_line old" data-linenumber="8" 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">
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$A<span class="idiff left right">DT</span>TMP</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$A<span class="idiff left right">UTOPKGTEST_</span>TMP</span></span>
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8
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<td class="diff-line-num new_line" data-linenumber="9" 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">
9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir </span>ruffus</span>
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9
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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;">cd </span>ruffus</span>
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10
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/python-ruffus-doc/test <span class="nb" style="color: #0086b3;">.</span></span>
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11
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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;">cd test</span></span>
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12
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell">find <span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: #000080;">-type</span> f <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"*.gz"</span> <span class="nt" style="color: #000080;">-exec</span> <span class="nb" style="color: #0086b3;">gunzip</span> <span class="se" style="color: #d14;">\{\}</span> <span class="se" style="color: #d14;">\;</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># mod +x [a-z]*.py</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;">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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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">HOME</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$ADTTMP</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>testscript <span class="k" style="font-weight: 600;">in </span>run_all_unit_tests<span class="k" style="font-weight: 600;">*</span>.cmd <span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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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;"># exclude tests with known issues ... should not be needed any more since fix_test.patch</span></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;"># sed -i -e 's/\(unittest test_file_name_parameters.*\)\\/\1 true/' \</span></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># -e 's/\(unittest test_ruffus_utility.*\)\\/\1 true/' \</span></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># $testscript</span></span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"> bash <span class="nv" style="color: #008080;">$testscript</span></span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span></pre>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">HOME</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">bash run_all_unit_tests3.cmd</span></pre>
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<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<a href="https://salsa.debian.org/med-team/python-ruffus/compare/8d9294dc2e3535ca60869d08d483b3699d54576c...4d8c6b825b2d3359ce394d0c29328bbe950244f5#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Reference:</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> Author: Leo Goodstadt</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> Title: "Ruffus: A Lightweight Python Library for Computational Pipelines"</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> Journal: Bioinformatics</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> Year: 2010</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> Volume: 26</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> Number: 21</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> Pages: 2778-9</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> DOI: 10.1093/bioinformatics/btq524</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> PMID: 20847218</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> URL: "http://bioinformatics.oxfordjournals.org/content/early/\</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> 2010/09/16/bioinformatics.btq524"</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> ePrint: "http://bioinformatics.oxfordjournals.org/content/early/\</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> 2010/09/16/bioinformatics.btq524.full.pdf+html"</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> Author: Leo Goodstadt</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Title: 'Ruffus: A Lightweight Python Library for Computational Pipelines'</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Journal: Bioinformatics</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Year: 2010</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> Volume: 26</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> Number: 21</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> Pages: 2778-9</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> DOI: 10.1093/bioinformatics/btq524</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> PMID: 20847218</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> URL: http://bioinformatics.oxfordjournals.org/content/early/2010/09/16/bioinformatics.btq524</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> ePrint: http://bioinformatics.oxfordjournals.org/content/early/2010/09/16/bioinformatics.btq524.full.pdf+html</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Registry:</span>
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<td class="diff-line-num new_line old" data-linenumber="14" 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">
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> - Name: OMICtools</span>
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<td class="diff-line-num old old_line" data-linenumber="17" 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">
17
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<td class="diff-line-num new_line old" data-linenumber="14" 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">
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> Entry: OMICS_07398</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="plaintext"> - Name: SciCrunch</span>
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<td class="diff-line-num old old_line" data-linenumber="19" 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">
19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> Entry: NA</span>
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<td class="diff-line-num old old_line" data-linenumber="20" 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">
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<td class="diff-line-num new_line old" data-linenumber="14" 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">
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> - Name: bio.tools</span>
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<td class="diff-line-num old old_line" data-linenumber="21" 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">
21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> Entry: NA</span>
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<td class="diff-line-num new_line old" data-linenumber="14" 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">
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> - Name: conda:bioconda</span>
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<td class="diff-line-num old old_line" data-linenumber="23" 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">
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> Entry: ruffus</span></pre>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">- Name: OMICtools</span>
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<td class="diff-line-num new old_line" data-linenumber="24" 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="LC15" class="line" lang="plaintext"> Entry: OMICS_07398</span>
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<td class="diff-line-num new old_line" data-linenumber="24" 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="LC16" class="line" lang="plaintext">- Name: SciCrunch</span>
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<td class="diff-line-num new new_line" data-linenumber="17" 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="LC17" class="line" lang="plaintext"> Entry: NA</span>
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<td class="diff-line-num new new_line" data-linenumber="18" 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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">- Name: bio.tools</span>
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<td class="diff-line-num new new_line" data-linenumber="19" 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">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> Entry: NA</span>
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<td class="diff-line-num new new_line" data-linenumber="20" 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">
20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">- Name: conda:bioconda</span>
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<td class="diff-line-num new new_line" data-linenumber="21" 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="LC21" class="line" lang="plaintext"> Entry: ruffus</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Bug-Database: https://github.com/bunbun/ruffus/issues</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Repository: https://github.com/bunbun/ruffus.git</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Repository-Browse: https://github.com/bunbun/ruffus</span></pre>
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