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<h3>
Étienne Mollier 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/b3e374b18583c404c3e389b6d1c91c0fc51d9d9d">b3e374b1</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-12-12T11:09:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">More tests to run-unit-test
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2cli/-/commit/6c15489ad00b994894d50732d7afb92e181a0092">6c15489a</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-12-12T11:09:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2cli/-/commit/392b6192bbfd42e4aea8270427887f6e323e94df">392b6192</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-12-12T11:09:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2020.11.1</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2cli/-/commit/b18ee1c79f7042f7cab602f51ba49445508b3bed">b18ee1c7</a></strong>
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<span>by Étienne Mollier</span>
<i>at 2020-12-12T11:09:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2020.11.1'
Update to upstream version '2020.11.1'
with Debian dir 8376effb30321c7d254e7a67d2711de25a1fd64d</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2cli/-/commit/3e6e61996497242a32d576bf774a143f576527ee">3e6e6199</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-12-12T11:10:54+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2cli/-/commit/cacfaaace41ce9bf6e8fb6f14b0b22ac7c7d99f0">cacfaaac</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-12-12T11:16:49+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add myself to uploaders
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2cli/-/commit/11329ddefefe2f70f7c54b029ef5f6ed4f1d9fe3">11329dde</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-12-12T11:19:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bump dependency on qiime (>= 2020.11.1)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2cli/-/commit/31849e00479ac2300aa1e31e59b1870515379398">31849e00</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-12-12T12:41:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">improved autopkgtest coverage
</pre>
</li>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
</a>
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<li class="file-stats">
<a href="#ba66450cf2f4739dc96974820c344fd32edb89f0">
q2cli/_version.py
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/q2cli/-/compare/aef444bbfd5c9ac840367a8d6f2f9e221527c44b...31849e00479ac2300aa1e31e59b1870515379398#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">q2cli (2020.11.1-1) unstable; 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"> * Added enough tests do drop the "superficial" marker. (Closes: #976271)</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Add myself to Uploaders.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Bump dependency on qiime (>= 2020.11.1)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Étienne Mollier <etienne.mollier@mailoo.org> Sat, 12 Dec 2020 11:09:49 +0100</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">q2cli (2020.11.0-1) unstable; urgency=medium</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"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/q2cli/-/compare/aef444bbfd5c9ac840367a8d6f2f9e221527c44b...31849e00479ac2300aa1e31e59b1870515379398#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">Source</span><span class="p">:</span> <span class="n" style="color: #333;">q2cli</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="mosel"><span class="n" style="color: #333;">Maintainer</span><span class="p">:</span> <span class="n" style="color: #333;">Debian</span> <span class="n" style="color: #333;">Med</span> <span class="n" style="color: #333;">Packaging</span> <span class="n" style="color: #333;">Team</span> <span class="p"><</span><span class="n" style="color: #333;">debian</span><span class="p">-</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">packaging</span><span class="p">@</span><span class="n" style="color: #333;">lists</span><span class="p">.</span><span class="n" style="color: #333;">alioth</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">></span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="mosel"><span class="n" style="color: #333;">Uploaders</span><span class="p">:</span> <span class="n" style="color: #333;">Liubov</span> <span class="n" style="color: #333;">Chuprikova</span> <span class="p"><</span><span class="n" style="color: #333;">chuprikovalv</span><span class="p">@</span><span class="n" style="color: #333;">gmail</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="mosel"><span class="n" style="color: #333;">Uploaders</span><span class="p">:</span> <span class="n" style="color: #333;">Liubov</span> <span class="n" style="color: #333;">Chuprikova</span> <span class="p"><</span><span class="n" style="color: #333;">chuprikovalv</span><span class="p">@</span><span class="n" style="color: #333;">gmail</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">>,</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="mosel"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">É</span><span class="n" style="color: #333;">tienne</span> <span class="n" style="color: #333;">Mollier</span> <span class="p"><</span><span class="n" style="color: #333;">etienne</span><span class="p">.</span><span class="n" style="color: #333;">mollier</span><span class="p">@</span><span class="n" style="color: #333;">mailoo</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">></span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="mosel"><span class="n" style="color: #333;">Section</span><span class="p">:</span> <span class="n" style="color: #333;">science</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="mosel"><span class="n" style="color: #333;">Priority</span><span class="p">:</span> <span class="n" style="color: #333;">optional</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="mosel"><span class="n" style="color: #333;">Build</span><span class="p">-</span><span class="n" style="color: #333;">Depends</span><span class="p">:</span> <span class="n" style="color: #333;">debhelper</span><span class="p">-</span><span class="n" style="color: #333;">compat</span> <span class="p">(=</span> <span class="m" style="color: #099;">13</span><span class="p">),</span></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">@@ -8,7 +9,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">,</span></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><span class="c1" style="color: #998; font-style: italic;">!nocheck>,</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;">setuptools</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;">qiime</span> <span class="p">(>=</span> <span class="m" style="color: #099;">2020.11.<span class="idiff left right">0</span></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;">qiime</span> <span class="p">(>=</span> <span class="m" style="color: #099;">2020.11.<span class="idiff left right">1</span></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;">click</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">nose</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="mosel"><span class="n" style="color: #333;">Standards</span><span class="p">-</span><span class="k" style="font-weight: 600;">Version</span><span class="p">:</span> <span class="m" style="color: #099;">4.5.1</span></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">@@ -22,7 +23,7 @@ Architecture: all</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="mosel"><span class="n" style="color: #333;">Depends</span><span class="p">:</span> <span class="p">${</span><span class="n" style="color: #333;">shlibs</span><span class="p">:</span><span class="n" style="color: #333;">Depends</span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="mosel"> <span class="p">${</span><span class="n" style="color: #333;">misc</span><span class="p">:</span><span class="n" style="color: #333;">Depends</span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="mosel"> <span class="p">${</span><span class="n" style="color: #333;">python3</span><span class="p">:</span><span class="n" style="color: #333;">Depends</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;">qiime</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="mosel"> <span class="n" style="color: #333;">qiime</span><span class="idiff left"> </span><span class="p"><span class="idiff">(>=</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">2020.11.1</span></span><span class="p"><span class="idiff right">)</span>,</span></span>
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<pre style="margin: 0;"> <span id="LC27" 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="LC28" 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="LC29" class="line" lang="mosel"><span class="n" style="color: #333;">Description</span><span class="p">:</span> <span class="n" style="color: #333;">Click</span><span class="p">-</span><span class="n" style="color: #333;">based</span> <span class="nf" style="color: #900; font-weight: 600;">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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<a href="https://salsa.debian.org/med-team/q2cli/-/compare/aef444bbfd5c9ac840367a8d6f2f9e221527c44b...31849e00479ac2300aa1e31e59b1870515379398#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Depends: @</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr<span class="idiff left right">, superficial</span></span></pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @<span class="idiff left right">, q2-sample-classifier, q2-feature-table, file</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/q2cli/-/compare/aef444bbfd5c9ac840367a8d6f2f9e221527c44b...31849e00479ac2300aa1e31e59b1870515379398#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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">@@ -11,6 +11,118 @@ cd "${AUTOPKGTEST_TMP}"</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"></span>
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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: #008080;">HOME</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">HOME</span><span class="k" style="font-weight: 600;">:-</span><span class="nv" style="color: #008080;">$PWD</span><span class="k" style="font-weight: 600;">}</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">/usr/bin/qiime <span class="nt" style="color: #000080;">--help</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nv" style="color: #008080;">QZA_SAMPLE</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"/usr/lib/python3/dist-packages/q2_sample_classifier/tests/data/vaw.qza"</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-r</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$QZA_SAMPLE</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;">></span>&2 <span class="o" style="font-weight: 600;"><<-</span><span class="no" style="color: #008080;">ERR</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="sh" style="color: #d14;"> error: could not find sample data: </span><span class="nv" style="color: #008080;">$QZA_SAMPLE</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="sh" style="color: #d14;"> Please install the following package:</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="sh" style="color: #d14;"> - q2-sample-classifier</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="sh" style="color: #d14;"> - q2-feature-table</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="no" style="color: #008080;"> ERR</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># TODO: same tests but with recommended dependencies!</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># This is important since there is a huge change of behavior, and</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># extensions may potentially break the qiime command as I am seeing with</span></span>
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<td class="diff-line-num new new_line" data-linenumber="29" 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">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># python3-sklearn at the moment.</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-v</span></span>
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<td class="diff-line-num new new_line" data-linenumber="31" 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">
31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># 0. the basics</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"> qiime <span class="nt" style="color: #000080;">--version</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># 1. help messages</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"> qiime <span class="nt" style="color: #000080;">--help</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"> qiime info <span class="nt" style="color: #000080;">--help</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"> qiime tools <span class="nt" style="color: #000080;">--help</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"> qiime dev <span class="nt" style="color: #000080;">--help</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"> qiime tools citations <span class="nt" style="color: #000080;">--help</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"> qiime tools <span class="nb" style="color: #0086b3;">export</span> <span class="nt" style="color: #000080;">--help</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"> qiime tools extract <span class="nt" style="color: #000080;">--help</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"> qiime tools import <span class="nt" style="color: #000080;">--help</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"> qiime tools inspect-metadata <span class="nt" style="color: #000080;">--help</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"> qiime tools peek <span class="nt" style="color: #000080;">--help</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"> qiime tools validate <span class="nt" style="color: #000080;">--help</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"> qiime tools view <span class="nt" style="color: #000080;">--help</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"> qiime dev export-default-theme <span class="nt" style="color: #000080;">--help</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"> qiime dev import-theme <span class="nt" style="color: #000080;">--help</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"> qiime dev refresh-cache <span class="nt" style="color: #000080;">--help</span></span>
</pre>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell"> qiime dev reset-theme <span class="nt" style="color: #000080;">--help</span></span>
</pre>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># 2. info command</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell"> qiime info</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># 3. tools commands</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"> qiime tools</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell"> qiime tools citations <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$QZA_SAMPLE</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">></span> citations.bib</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell"> file citations.bib | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-qi</span> <span class="s1" style="color: #d14;">'bibtex'</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="shell"> qiime tools <span class="nb" style="color: #0086b3;">export</span> <span class="nt" style="color: #000080;">--input-path</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$QZA_SAMPLE</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">--output-path</span> <span class="nb" style="color: #0086b3;">.</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell"> file feature-table.biom | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-qi</span> <span class="s1" style="color: #d14;">'Hierarchical Data Format'</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="shell"> qiime tools extract <span class="nt" style="color: #000080;">--input-path</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$QZA_SAMPLE</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cd </span>861451cc-c250-43fc-818a-ddc2159dbe25</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">md5sum</span> <span class="nt" style="color: #000080;">--check</span> checksums.md5</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cd</span> -</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="shell"> qiime tools inspect-metadata <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$QZA_SAMPLE</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">--tsv</span> <span class="o" style="font-weight: 600;">></span> metadata.tsv</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="shell"> qiime tools inspect-metadata <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$QZA_SAMPLE</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">--no-tsv</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="shell"> qiime tools peek <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$QZA_SAMPLE</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="shell"> qiime tools import <span class="nt" style="color: #000080;">--show-importable-types</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="shell"> qiime tools import <span class="nt" style="color: #000080;">--show-importable-formats</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="shell"> qiime tools import <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="shell"> <span class="nt" style="color: #000080;">--type</span> <span class="s1" style="color: #d14;">'FeatureTable[Frequency]'</span> <span class="se" style="color: #d14;">\</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="shell"> <span class="nt" style="color: #000080;">--input-path</span> <span class="s1" style="color: #d14;">'861451cc-c250-43fc-818a-ddc2159dbe25/data'</span> <span class="se" style="color: #d14;">\</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="shell"> <span class="nt" style="color: #000080;">--output-path</span> artifact.qza</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="shell"> file artifact.qza | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-qi</span> <span class="s1" style="color: #d14;">'zip archive data'</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="shell"></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="shell"> qiime tools validate artifact.qza</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="shell"></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># TODO test qiime tools view, missing Vizualization data at the moment,</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># most likely available under the form of *.qvz files.</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="shell"></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># 4. dev commands</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="shell"> qiime dev</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="shell"> qiime dev export-default-theme <span class="nt" style="color: #000080;">--output-path</span> file.theme</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="shell"> diff file.theme - <span class="o" style="font-weight: 600;"><<-</span><span class="no" style="color: #008080;">END</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="shell"><span class="sh" style="color: #d14;"> [option]</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="shell"><span class="sh" style="color: #d14;"> fg = blue</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="shell"></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="shell"><span class="sh" style="color: #d14;"> [type]</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="shell"><span class="sh" style="color: #d14;"> fg = green</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="shell"></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="shell"><span class="sh" style="color: #d14;"> [default_arg]</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="shell"><span class="sh" style="color: #d14;"> fg = magenta</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="shell"></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="shell"><span class="sh" style="color: #d14;"> [command]</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="shell"><span class="sh" style="color: #d14;"> fg = blue</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num new new_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">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="shell"><span class="sh" style="color: #d14;"> [emphasis]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="104" 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">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="shell"><span class="sh" style="color: #d14;"> underline = True</span></span>
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<td class="diff-line-num new new_line" data-linenumber="105" 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">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="106" 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">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="shell"><span class="sh" style="color: #d14;"> [problem]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="107" 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">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="shell"><span class="sh" style="color: #d14;"> fg = yellow</span></span>
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<td class="diff-line-num new new_line" data-linenumber="108" 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">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="109" 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">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="shell"><span class="sh" style="color: #d14;"> [warning]</span></span>
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<td class="diff-line-num new old_line" data-linenumber="15" 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="110" 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">
110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="shell"><span class="sh" style="color: #d14;"> fg = yellow</span></span>
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<td class="diff-line-num new new_line" data-linenumber="111" 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">
111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="shell"><span class="sh" style="color: #d14;"> bold = True</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="113" 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">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="shell"><span class="sh" style="color: #d14;"> [error]</span></span>
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<td class="diff-line-num new old_line" data-linenumber="15" 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="114" 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">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="shell"><span class="sh" style="color: #d14;"> fg = red</span></span>
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<td class="diff-line-num new new_line" data-linenumber="115" 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">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="shell"><span class="sh" style="color: #d14;"> bold = True</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="117" 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">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="shell"><span class="sh" style="color: #d14;"> [required]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="118" 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">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="shell"><span class="sh" style="color: #d14;"> underline = True</span></span>
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<td class="diff-line-num new new_line" data-linenumber="119" 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">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="120" 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">
120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="shell"><span class="sh" style="color: #d14;"> [success]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="121" 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">
121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="shell"><span class="sh" style="color: #d14;"> fg = green</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="123" 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">
123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="shell"><span class="no" style="color: #008080;"> END</span></span>
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<td class="diff-line-num new new_line" data-linenumber="124" 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">
124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="shell"> qiime dev import-theme <span class="nt" style="color: #000080;">--theme</span> file.theme</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="125" 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">
125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="shell"> qiime dev refresh-cache</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="15" 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="126" 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">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">yes</span> | qiime dev reset-theme</span>
</pre>
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<td class="diff-line-num 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">
15
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<td class="diff-line-num new_line" data-linenumber="127" 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">
127
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC127" class="line" lang="shell"></span>
</pre>
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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">
16
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<pre style="margin: 0;"> <span id="LC128" 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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<a href="https://salsa.debian.org/med-team/q2cli/-/compare/aef444bbfd5c9ac840367a8d6f2f9e221527c44b...31849e00479ac2300aa1e31e59b1870515379398#ba66450cf2f4739dc96974820c344fd32edb89f0"><strong>q2cli/_version.py</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">@@ -23,9 +23,9 @@ def get_keywords():</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># setup.py/versioneer.py will grep for the variable names, so they must</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># each be defined on a line of their own. _version.py will just call</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># get_keywords().</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">git_refnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" (<span class="idiff left right">HEAD -> master, tag: 2020.11.0</span>)"</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">git_full</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">e09576b507ecee9df78ed142aacad6dd595654ca</span>"</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">git_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2020-1<span class="idiff left right">1-25 17:13:09</span> +0000"</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">git_refnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" (<span class="idiff left right">tag: 2020.11.1</span>)"</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">git_full</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">cf25aa05a20ac823fb1f447d244f6801d083a713</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">git_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2020-1<span class="idiff left right">2-05 20:44:48</span> +0000"</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">keywords</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"refnames"</span><span class="p">:</span> <span class="n" style="color: #333;">git_refnames</span><span class="p">,</span> <span class="s" style="color: #d14;">"full"</span><span class="p">:</span> <span class="n" style="color: #333;">git_full</span><span class="p">,</span> <span class="s" style="color: #d14;">"date"</span><span class="p">:</span> <span class="n" style="color: #333;">git_date</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">keywords</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"></span>
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