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<h3>
Liubov Chuprikova pushed to branch master
at <a href="https://salsa.debian.org/med-team/q2-types">Debian Med / q2-types</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-types/commit/8a867119d1120dfa4b8e6f5163a2ed4a9a1a3ad3">8a867119</a></strong>
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<span>by Liubov Chuprikova</span>
<i>at 2019-03-28T18:41:27Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Make build time tests to pass
</pre>
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<strong><a href="https://salsa.debian.org/med-team/q2-types/commit/31a459a93673271174a3c06701d6dee73b87049e">31a459a9</a></strong>
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<span>by Liubov Chuprikova</span>
<i>at 2019-03-28T18:41:59Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add ITP bug number
</pre>
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/q2-types/compare/22b9e03ad66724b5f8aca88700d348eaeda4cce7...31a459a93673271174a3c06701d6dee73b87049e#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">q2-types (2019.1.0-1) 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: #<span class="idiff left right"><bug></span>)</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #<span class="idiff left right">925931</span>)</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"> -- Liubov Chuprikova <chuprikovalv@gmail.com> Mon, 25 Mar 2019 19:56:36 +0100</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/q2-types/compare/22b9e03ad66724b5f8aca88700d348eaeda4cce7...31a459a93673271174a3c06701d6dee73b87049e#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7" 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">@@ -7,7 +7,7 @@ Build-Depends: debhelper (>= 12~),</td>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="mosel"> <span class="n" style="color: #333;">dh</span><span class="p">-</span><span class="n" style="color: #333;">python</span><span class="p">,</span></span>
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<td class="diff-line-num new_line" data-linenumber="8" 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">
8
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">,</span></span>
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<td class="diff-line-num 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">
9
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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">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" 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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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> python3-pytest,</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">pytest</span><span class="p"><span class="idiff left">-</span></span><span class="n" style="color: #333;"><span class="idiff right">cov</span></span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">biom</span><span class="p">-</span><span class="n" style="color: #333;">format</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">skbio</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">ijson</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="33" 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">@@ -33,4 +33,24 @@ Depends: ${shlibs:Depends},</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="mosel"> <span class="n" style="color: #333;">libopenblas</span><span class="p">-</span><span class="n" style="color: #333;">base</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="mosel"> <span class="n" style="color: #333;">qiime</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="mosel"><span class="n" style="color: #333;">Description</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;">plugin</span> <span class="n" style="color: #333;">defining</span> <span class="n" style="color: #333;">types</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">microbiome</span> <span class="n" style="color: #333;">analysis</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> <long_description></span></pre>
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<pre style="margin: 0;">+<span id="LC36" 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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<pre style="margin: 0;">+<span id="LC37" 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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<pre style="margin: 0;">+<span id="LC38" 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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<pre style="margin: 0;">+<span id="LC39" class="line" lang="mosel"> <span class="n" style="color: #333;">publication</span><span class="p">-</span><span class="n" style="color: #333;">quality</span> <span class="n" style="color: #333;">figures</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">statistical</span> <span class="n" style="color: #333;">results</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="mosel"> <span class="n" style="color: #333;">Key</span> <span class="n" style="color: #333;">features</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Integrated</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">automatic</span> <span class="n" style="color: #333;">tracking</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">provenance</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Semantic</span> <span class="n" style="color: #333;">type</span> <span class="nf" style="color: #900; font-weight: 600;">system</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Plugin</span> <span class="nf" style="color: #900; font-weight: 600;">system</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">extending</span> <span class="n" style="color: #333;">microbiome</span> <span class="n" style="color: #333;">analysis</span> <span class="n" style="color: #333;">functionality</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Support</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">multiple</span> <span class="n" style="color: #333;">types</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">user</span> <span class="n" style="color: #333;">interfaces</span> <span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">g</span><span class="p">.</span> <span class="n" style="color: #333;">API</span><span class="p">,</span> <span class="nf" style="color: #900; font-weight: 600;">command</span> <span class="n" style="color: #333;">line</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="mosel"> <span class="n" style="color: #333;">graphical</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="mosel"> <span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC47" 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;">complete</span> <span class="n" style="color: #333;">redesign</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">rewrite</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">1</span> <span class="n" style="color: #333;">microbiome</span> <span class="n" style="color: #333;">analysis</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="mosel"> <span class="n" style="color: #333;">pipeline</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;">will</span> <span class="n" style="color: #333;">address</span> <span class="n" style="color: #333;">many</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">limitations</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">while</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="mosel"> <span class="n" style="color: #333;">retaining</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">features</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">makes</span> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">1</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">powerful</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">widely</span><span class="p">-</span><span class="n" style="color: #333;">used</span> <span class="n" style="color: #333;">analysis</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="mosel"> <span class="n" style="color: #333;">pipeline</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="mosel"> <span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC52" 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;">currently</span> <span class="n" style="color: #333;">supports</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">initial</span> <span class="k" style="font-weight: 600;">end</span><span class="p">-</span><span class="k" style="font-weight: 600;">to</span><span class="p">-</span><span class="k" style="font-weight: 600;">end</span> <span class="n" style="color: #333;">microbiome</span> <span class="n" style="color: #333;">analysis</span> <span class="n" style="color: #333;">pipeline</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="mosel"> <span class="n" style="color: #333;">New</span> <span class="n" style="color: #333;">functionality</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">regularly</span> <span class="n" style="color: #333;">become</span> <span class="n" style="color: #333;">available</span> <span class="n" style="color: #333;">through</span> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">plugins</span><span class="p">.</span> <span class="n" style="color: #333;">You</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="mosel"> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">view</span> <span class="n" style="color: #333;">a</span> <span class="k" style="font-weight: 600;">list</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">plugins</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">currently</span> <span class="n" style="color: #333;">available</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">plugin</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="mosel"> <span class="n" style="color: #333;">availability</span> <span class="n" style="color: #333;">page</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">future</span> <span class="n" style="color: #333;">plugins</span> <span class="n" style="color: #333;">page</span> <span class="n" style="color: #333;">lists</span> <span class="n" style="color: #333;">plugins</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">being</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="mosel"> <span class="n" style="color: #333;">developed</span><span class="p">.</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2-types/compare/22b9e03ad66724b5f8aca88700d348eaeda4cce7...31a459a93673271174a3c06701d6dee73b87049e#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">@@ -17,15 +17,15 @@ include /usr/share/dpkg/default.mk</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"># for hardening you might like to uncomment this:</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"># export DEB_BUILD_MAINT_OPTIONS=hardening=+all</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="LC20" class="line" lang="plaintext"># For testing, we need .egg-info so the entry points are available.</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">export PYBUILD_BEFORE_TEST=python{version} setup.py develop --install-dir {build_dir}</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"># Delete .egg-info and other files that were generated along with .egg-info</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">export PYBUILD_AFTER_TEST=rm -rf {build_dir}/q2-types.egg-* {build_dir}/site.py \</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> {build_dir}/.coverage* {build_dir}/easy-install.pth</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> dh $@ --with python3 --buildsystem=pybuild</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">#override_dh_auto_test:</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"># do_stuff_for_testing</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">#endif</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> dh_auto_test -- -s custom --test-args="cd {build_dir}; py.test-3 --cov=q2_types"</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"></span></pre>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">### If you **really** can not use uscan (even not with mode=git) use a debian/get-orig-script</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">#get-orig-source:</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"># . debian/get-orig-source</span></pre>
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