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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/paleomix">Debian Med / paleomix</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/paleomix/-/commit/7f5d705d9bcb3dcab5db6ce3077bbebb99da5f07">7f5d705d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-01T10:27:44+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Renamed lintian tag
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/paleomix/-/commit/d7334280ae59c8aaaf7e3be3270a9de173e38146">d7334280</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-01T10:31:47+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix manpage
</pre>
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<strong><a href="https://salsa.debian.org/med-team/paleomix/-/commit/775d3d767543959e8f91f04033a94cc2a5401c82">775d3d76</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-09-01T10:42:15+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix autopkgtest
</pre>
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#efc7fe57b5983b0283c6410fceef7e74f687aeb5">
debian/lintian-overrides
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<li class="file-stats">
<a href="#a8995c9d073ffaa58c9c9e41e4c10af6f9d1fedb">
debian/mans/phylo_pipeline.1
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
</a>
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</ul>
<h4>Changes:</h4>
<li id="efc7fe57b5983b0283c6410fceef7e74f687aeb5">
<a href="https://salsa.debian.org/med-team/paleomix/-/compare/57a985f8ecd748125d4092744117b65543cb271b...775d3d767543959e8f91f04033a94cc2a5401c82#efc7fe57b5983b0283c6410fceef7e74f687aeb5"><strong>debian/lintian-overrides</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"># Those zero byte files are needed in tests and there was extra means done to move these into the package</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">paleomix: zero-byte-file-in-doc-directory usr/share/doc/paleomix/tests/data/*</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"># The different compression methods are part of the test suite</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">paleomix: <span class="idiff left right">duplicated-compressed-fil</span>e usr/share/doc/paleomix/tests/data/fasta_file.fasta*</span></pre>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">paleomix: <span class="idiff left right">compressed-duplicat</span>e usr/share/doc/paleomix/tests/data/fasta_file.fasta*</span></pre>
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<li id="a8995c9d073ffaa58c9c9e41e4c10af6f9d1fedb">
<a href="https://salsa.debian.org/med-team/paleomix/-/compare/57a985f8ecd748125d4092744117b65543cb271b...775d3d767543959e8f91f04033a94cc2a5401c82#a8995c9d073ffaa58c9c9e41e4c10af6f9d1fedb"><strong>debian/mans/phylo_pipeline.1</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -99,7 +99,7 @@ tree is printed, and no tasks are executed.</td>
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<td class="diff-line-num new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext">\fB\-\-temp\-root\fR=\fI\,TEMP_ROOT\/\fR</span>
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<td class="diff-line-num old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="plaintext">Location for temporary files and folders</span>
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<td class="diff-line-num old old_line" data-linenumber="102" 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="LC102" class="line" lang="plaintext">[/tmp/<span class="idiff left right">tillea</span>/phylo_pipeline]</span>
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<td class="diff-line-num new old_line" data-linenumber="103" 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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<td class="diff-line-num new new_line" data-linenumber="102" 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="LC102" class="line" lang="plaintext">[/tmp/<span class="idiff left right">USERNAME</span>/phylo_pipeline]</span>
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<td class="diff-line-num old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="plaintext">\fB\-\-samples\-root\fR=\fI\,SAMPLES_ROOT\/\fR</span>
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<td class="diff-line-num old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="plaintext">Location of BAM files for each sample [./data/samples]</span>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/paleomix/-/compare/57a985f8ecd748125d4092744117b65543cb271b...775d3d767543959e8f91f04033a94cc2a5401c82#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,6 +9,7 @@ if [ "$AUTOPKGTEST_TMP" = "" ] ; then</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/tests <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/README.rst <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="22" 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">@@ -22,4 +23,4 @@ done</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## tox needs to run in source dir and relies on files only available in full source</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># tox</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## so rather run some test that is part of the tox test suite</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell">nosetests <span class="nt" style="color: #000080;">--with-coverage</span> <span class="nt" style="color: #000080;">--cover-erase</span> <span class="nt" style="color: #000080;">--cover-inclusive</span> <span class="nt" style="color: #000080;">--cover-tests</span> <span class="nt" style="color: #000080;">--cover-package</span> paleomix .</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">\ No newline at end of file</td>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell">pytest-3</span></pre>
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