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<h3>
Liubov Chuprikova pushed to branch master
at <a href="https://salsa.debian.org/med-team/q2cli">Debian Med / q2cli</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2cli/commit/effd46a1b089568a2b44d423182d47deea1c8a91">effd46a1</a></strong>
<div>
<span>by Liubov Chuprikova</span>
<i>at 2019-03-23T15:39:53Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add a simple autopkgtest
</pre>
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<h4>2 changed files:</h4>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/q2cli/commit/effd46a1b089568a2b44d423182d47deea1c8a91#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">@@ -23,7 +23,7 @@ Depends: ${shlibs:Depends},</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="mosel"> <span class="n" style="color: #333;">qiime</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">setuptools</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">click</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="mosel"><span class="n" style="color: #333;">Description</span><span class="p">:</span> <span class="n" style="color: #333;">Command</span> <span class="n" style="color: #333;">line</span> <span class="n" style="color: #333;">interface</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span></span>
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<td class="diff-line-num new old_line" data-linenumber="27" 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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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="mosel"><span class="n" style="color: #333;">Description</span><span class="p">:</span> <span class="n" style="color: #333;">C<span class="idiff left">lick</span></span><span class="p"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">based</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff right">c</span>ommand</span> <span class="n" style="color: #333;">line</span> <span class="n" style="color: #333;">interface</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span></span>
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27
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<td class="diff-line-num new_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">
27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="mosel"> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">powerful</span><span class="p">,</span> <span class="n" style="color: #333;">extensible</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">decentralized</span> <span class="n" style="color: #333;">microbiome</span> <span class="n" style="color: #333;">analysis</span></span>
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28
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<td class="diff-line-num new_line" data-linenumber="28" 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="LC28" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">package</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">focus</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">data</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">analysis</span> <span class="n" style="color: #333;">transparency</span><span class="p">.</span> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">enables</span></span>
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="mosel"> <span class="n" style="color: #333;">researchers</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">start</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">analysis</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">raw</span> <span class="n" style="color: #333;">DNA</span> <span class="n" style="color: #333;">sequence</span> <span class="n" style="color: #333;">data</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">finish</span> <span class="k" style="font-weight: 600;">with</span></span>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/q2cli/commit/effd46a1b089568a2b44d423182d47deea1c8a91#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: navy;">-e</span></span>
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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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3
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<pre style="margin: 0;"> <span id="LC2" 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: teal;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#PACKAGENAME#</span></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nv" style="color: teal;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="idiff left right">q2cli</span></span>
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5
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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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6
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<pre style="margin: 0;"> <span id="LC5" 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: teal;">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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7
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: navy;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: navy;">-test</span>.XXXXXX<span class="k" style="font-weight: 600;">)</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" 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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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;"># later is on purpose.</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;"># shellcheck disable=SC2064</span></span>
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11
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7
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<pre style="margin: 0;"> <span id="LC7" 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;">${</span><span class="nv" style="color: teal;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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12
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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13
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: navy;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">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;">${</span><span class="nv" style="color: teal;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"></span>
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16
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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17
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"></span>
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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;">#do_stuff_to_test_package#</span></span></pre>
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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;">export </span><span class="nv" style="color: teal;">HOME</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">HOME</span><span class="k" style="font-weight: 600;">:-</span><span class="nv" style="color: teal;">$PWD</span><span class="k" style="font-weight: 600;">}</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell">/usr/bin/qiime <span class="nt" style="color: navy;">--help</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"></span>
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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;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">RESULTS: OK</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span></span></pre>
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