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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/q2-feature-classifier">Debian Med / q2-feature-classifier</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-feature-classifier/-/commit/3229570ca91ca056044fe39e233a16948a246b21">3229570c</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-01-27T18:37:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add build dir to PYTHONPATH
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-feature-classifier/-/commit/9068af8aede8389510cf1d68015bc343bce6d641">9068af8a</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-01-27T19:48:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add vsearch.patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-feature-classifier/-/commit/6fd5232640025887a07b99df9b32a0a24aca2e32">6fd52326</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-01-27T19:52:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">vsearch.patch dep3 header
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-feature-classifier/-/commit/bb5186c8ce72d8ec8088db7f85246209950c38b5">bb5186c8</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-01-27T19:52:26+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update changelog
</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<span class="new-file">
+
debian/patches/series
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<li class="file-stats">
<a href="#d0dece1c828ff9df104f5fab31819f5024c0c528">
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+
debian/patches/vsearch.patch
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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-feature-classifier/-/compare/2a328d9d9885f043056ca7e7e22eb5c40ef10817...bb5186c8ce72d8ec8088db7f85246209950c38b5#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15" 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="15" 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">@@ -15,6 +15,10 @@ q2-feature-classifier (2020.11.1-1) UNRELEASED; urgency=medium</td>
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<td class="diff-line-num new_line" data-linenumber="15" 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="LC15" class="line" lang="plaintext"> * Build-Depends: q2-taxa</span>
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<td class="diff-line-num old_line" data-linenumber="16" 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="LC16" class="line" lang="plaintext"> Closes: #974839</span>
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<td class="diff-line-num old_line" data-linenumber="17" 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="LC17" class="line" lang="plaintext"></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">
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> [ Étienne Mollier ]</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">
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> * Add build directory to PYTHONPATH for dh_auto_test.</span>
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<td class="diff-line-num new old_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">
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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">
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> * Add vsearch.patch to fix --search_exact invalid options.</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> -- Liubov Chuprikova <chuprikovalv@gmail.com> Sat, 07 Sep 2019 13:41:46 +0200</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">q2-feature-classifier (2019.4.0-1) unstable; urgency=medium</span>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/q2-feature-classifier/-/compare/2a328d9d9885f043056ca7e7e22eb5c40ef10817...bb5186c8ce72d8ec8088db7f85246209950c38b5#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">vsearch.patch</span></pre>
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<li id="d0dece1c828ff9df104f5fab31819f5024c0c528">
<a href="https://salsa.debian.org/med-team/q2-feature-classifier/-/compare/2a328d9d9885f043056ca7e7e22eb5c40ef10817...bb5186c8ce72d8ec8088db7f85246209950c38b5#d0dece1c828ff9df104f5fab31819f5024c0c528"><strong>debian/patches/vsearch.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: fix failure to invoke vsearch --search_exact</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> TODO: confirm simply dropping options is the proper approach</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Étienne Mollier <etienne.mollier@mailoo.org></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Last-Update: 2021-01-27</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- q2-feature-classifier.orig/q2_feature_classifier/_vsearch.py</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ q2-feature-classifier/q2_feature_classifier/_vsearch.py</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">@@ -50,6 +50,15 @@</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> '--threads', str(threads)]</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> if search_exact:</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> cmd[1] = '--search_exact'</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # These options are not compatible with a --search_exact command.</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cmd.remove('--id')</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cmd.remove(str(perc_identity))</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cmd.remove('--maxaccepts')</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cmd.remove(str(maxaccepts))</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cmd.remove('--maxrejects')</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cmd.remove(str(maxrejects))</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cmd.remove('--query_cov')</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cmd.remove(str(query_cov))</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> if top_hits_only:</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> cmd.append('--top_hits_only')</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> if output_no_hits:</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/q2-feature-classifier/-/compare/2a328d9d9885f043056ca7e7e22eb5c40ef10817...bb5186c8ce72d8ec8088db7f85246209950c38b5#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" 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">@@ -14,6 +14,7 @@ export PYBUILD_BEFORE_INSTALL=rm -rvf {build_dir}/q2-feature-classifier.egg-* \</td>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> PYTHONPATH=$(CURDIR) \</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> dh_auto_test -- -s custom --test-args="cd {build_dir}; py.test-3 --cov=q2_feature_classifier"</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">endif</span>
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