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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/q2-taxa">Debian Med / q2-taxa</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-taxa/-/commit/e8554fbd9f33a4df3237fe687a84f294c8e7daa4">e8554fbd</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-09-29T14:15:31+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2021.8.0+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-taxa/-/commit/ca130aec7cd397ba0c303cc63654e4f65870d387">ca130aec</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-09-29T14:15:31+02:00</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/q2-taxa/-/commit/3fcb499f57f85ce902b15f57276504330251ad8a">3fcb499f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-09-29T14:15:31+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2021.8.0+dfsg'
Update to upstream version '2021.8.0+dfsg'
with Debian dir a48523944e829ac2d406e106c8ee3b41fc8f844f</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-taxa/-/commit/80dca528bddb9abd19e2b80dc1a89098e09676ec">80dca528</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-09-29T14:15:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.6.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-taxa/-/commit/150c7f1c5dcda92ba4a352eb362dc18ff9b8f1b6">150c7f1c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-09-29T14:21:05+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Versioned (Build-)Depends from qiime and its modules (>= 2021.8.0-1)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-taxa/-/commit/83cddb66837d5ca1621f88d32235e913babb86a6">83cddb66</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-09-29T14:45:53+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix Versions and upload to unstable
</pre>
</li>
</ul>
<h4>21 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#899ce9c202bf7bb5480e72836c3edc773c9c4244">
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+
.github/workflows/ci.yml
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<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
<span class="deleted-file">
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.travis.yml
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<li class="file-stats">
<a href="#0398ccd0f49298b10a3d76a47800d2ebecd49859">
LICENSE
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<a href="#243f1ef343e8375e9296d24d5fc49b37a3869bcc">
<span class="deleted-file">
−
ci/recipe/conda_build_config.yaml
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<li class="file-stats">
<a href="#22fbe0b68848772d4b1c45f0d62dcd71a06cde00">
ci/recipe/meta.yaml
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<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="#8efffbd84b4a963cace9c72f98a047e357a96ec9">
q2_taxa/__init__.py
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<li class="file-stats">
<a href="#89b5aedf9522dc397b71d18ad2a42ebb4a5453e1">
q2_taxa/_method.py
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<li class="file-stats">
<a href="#64d397f51ea3c6a4f5e5e433a24eee8c1d36d6b6">
q2_taxa/_util.py
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<li class="file-stats">
<a href="#1d474d05be0b5c09809046c47577874bc381d4d5">
q2_taxa/_version.py
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<li class="file-stats">
<a href="#8833ba7fa943e1c897add380821376320a7b5009">
q2_taxa/_visualizer.py
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<li class="file-stats">
<a href="#58926e8b6cd387d9c1c814ed77d97bc4a63414ee">
q2_taxa/assets/barplot/index.html
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<li class="file-stats">
<a href="#ef9c2a53b88c77db627dc1e45857c38d4553e0ec">
q2_taxa/assets/barplot/src/render.js
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<li class="file-stats">
<a href="#cd41f5831ac254dd647b66317881b6dcc8e22fd6">
q2_taxa/plugin_setup.py
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<li class="file-stats">
<a href="#30850f68a53ca950a201908fe0fcde12fd212b98">
q2_taxa/tests/__init__.py
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<li class="file-stats">
<a href="#ad565400ff000b14c664f87d21d9ab071aa49607">
q2_taxa/tests/test_methods.py
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<li class="file-stats">
<a href="#ef79b0dcac45299a8293c4be36beb8554ad36e4f">
q2_taxa/tests/test_plugin_setup.py
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<li class="file-stats">
<a href="#869562bce194beffa1fa021e505679c5968d987a">
q2_taxa/tests/test_visualizer.py
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<h4>Changes:</h4>
<li id="899ce9c202bf7bb5480e72836c3edc773c9c4244">
<a href="https://salsa.debian.org/med-team/q2-taxa/-/compare/a8e78df1d12563fec666639d4a2dde550244de37...83cddb66837d5ca1621f88d32235e913babb86a6#899ce9c202bf7bb5480e72836c3edc773c9c4244"><strong>.github/workflows/ci.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># This file is automatically generated by busywork.qiime2.org and</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># template-repos - any manual edits made to this file will be erased when</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># busywork performs maintenance updates.</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"><span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">ci</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">pull_request</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">master</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"> <span class="na" style="color: #008080;">lint</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"> <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">ubuntu-latest</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">checkout source</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/checkout@v2</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">set up python </span><span class="m" style="color: #099;">3.8</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/setup-python@v1</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> <span class="na" style="color: #008080;">python-version</span><span class="pi">:</span> <span class="m" style="color: #099;">3.8</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">install dependencies</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">python -m pip install --upgrade pip</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">lint</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"> <span class="s" style="color: #d14;">pip install -q https://github.com/qiime2/q2lint/archive/master.zip</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="s" style="color: #d14;">q2lint</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <span class="s" style="color: #d14;">pip install -q flake8</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"> <span class="s" style="color: #d14;">flake8</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="yaml"> <span class="na" style="color: #008080;">build-and-test</span><span class="pi">:</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="yaml"> <span class="na" style="color: #008080;">needs</span><span class="pi">:</span> <span class="s" style="color: #d14;">lint</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="yaml"> <span class="na" style="color: #008080;">strategy</span><span class="pi">:</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="yaml"> <span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="yaml"> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="pi">[</span><span class="nv" style="color: #008080;">ubuntu-latest</span><span class="pi">,</span> <span class="nv" style="color: #008080;">macos-latest</span><span class="pi">]</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="yaml"> <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ matrix.os }}</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">checkout source</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/checkout@v2</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="yaml"> <span class="na" style="color: #008080;">fetch-depth</span><span class="pi">:</span> <span class="m" style="color: #099;">0</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">set up git repo for versioneer</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">git fetch --depth=1 origin +refs/tags/*:refs/tags/*</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">qiime2/action-library-packaging@alpha1</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="yaml"> <span class="na" style="color: #008080;">package-name</span><span class="pi">:</span> <span class="s" style="color: #d14;">q2-taxa</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="yaml"> <span class="na" style="color: #008080;">build-target</span><span class="pi">:</span> <span class="s" style="color: #d14;">dev</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="yaml"> <span class="na" style="color: #008080;">additional-tests</span><span class="pi">:</span> <span class="s" style="color: #d14;">py.test --pyargs q2_taxa</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="yaml"> <span class="na" style="color: #008080;">library-token</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ secrets.LIBRARY_TOKEN }}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2-taxa/-/compare/a8e78df1d12563fec666639d4a2dde550244de37...83cddb66837d5ca1621f88d32235e913babb86a6#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">dist</span><span class="pi">:</span> <span class="s" style="color: #d14;">trusty</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">sudo</span><span class="pi">:</span> <span class="no" style="color: #008080;">false</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">python</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="yaml"><span class="na" style="color: #008080;">before_install</span><span class="pi">:</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">export MPLBACKEND='Agg'</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">wget -q https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">export MINICONDA_PREFIX="$HOME/miniconda"</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">bash miniconda.sh -b -p $MINICONDA_PREFIX</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">export PATH="$MINICONDA_PREFIX/bin:$PATH"</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda config --set always_yes yes</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda update -q conda</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda info -a</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">wget -q https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py36-linux-conda.yml</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda env create -q -n test-env --file qiime2-latest-py36-linux-conda.yml</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">source activate test-env</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda install -q pytest-cov</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pip install -q flake8 coveralls</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pip install -q https://github.com/qiime2/q2lint/archive/master.zip</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make install</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make lint</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make test-cov</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="yaml"><span class="na" style="color: #008080;">after_success</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">coveralls</span></span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">BSD 3-Clause License</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Copyright (c) 2016-202<span class="idiff left right">0</span>, QIIME 2 development team.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Copyright (c) 2016-202<span class="idiff left right">1</span>, QIIME 2 development team.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">All rights reserved.</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Redistribution and use in source and binary forms, with or without</span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># q2-taxa</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/qiime2/q2-taxa.svg?branch=master</span><span class="p">)</span>](https://travis-ci.org/qiime2/q2-taxa)</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Coverage Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://coveralls.io/repos/github/qiime2/q2-taxa/badge.svg?branch=master</span><span class="p">)</span>](https://coveralls.io/github/qiime2/q2-taxa?branch=master)</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="p">![](</span><span class="sx" style="color: #d14;">https://github.com/qiime2/q2-taxa/workflows/ci/badge.svg</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="markdown">This is a QIIME 2 plugin. For details on QIIME 2, see https://qiime2.org.</span></pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown">This is a QIIME 2 plugin. For details on QIIME 2, see https://qiime2.org.</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-taxa/-/compare/a8e78df1d12563fec666639d4a2dde550244de37...83cddb66837d5ca1621f88d32235e913babb86a6#243f1ef343e8375e9296d24d5fc49b37a3869bcc"><strong>ci/recipe/conda_build_config.yaml</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">python</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="yaml"> <span class="pi">-</span> <span class="m" style="color: #099;">3.6</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2-taxa/-/compare/a8e78df1d12563fec666639d4a2dde550244de37...83cddb66837d5ca1621f88d32235e913babb86a6#22fbe0b68848772d4b1c45f0d62dcd71a06cde00"><strong>ci/recipe/meta.yaml</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="yaml"><span class="pi">{</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">%</span> <span class="nv" style="color: #008080;">set data = load_setup_py_data() %</span><span class="pi">}</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="yaml"><span class="pi">{</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">%</span> <span class="nv" style="color: #008080;">set version = data.get('version') or 'placehold' %</span><span class="pi">}</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="yaml"><span class="pi">{</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">%</span> <span class="nv" style="color: #008080;">set release = '.'.join(version.split('.')</span><span class="pi">[:</span><span class="nv" style="color: #008080;">2</span><span class="pi">]</span><span class="nv" style="color: #008080;">) %</span><span class="pi">}</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="yaml"><span class="na" style="color: #008080;">package</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">q2-taxa</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="21" 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">@@ -21,11 +20,17 @@ requirements:</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python {{ python }}</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pandas</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">qiime2 {{ <span class="idiff left right">release</span> }}.*</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">q2templates {{ <span class="idiff left right">release</span> }}.*</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">q2-types {{ <span class="idiff left right">release</span> }}.*</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">qiime2 {{ <span class="idiff left right">qiime2_epoch</span> }}.*</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">q2templates {{ <span class="idiff left right">qiime2_epoch</span> }}.*</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">q2-types {{ <span class="idiff left right">qiime2_epoch</span> }}.*</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="yaml"><span class="na" style="color: #008080;">test</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="na" style="color: #008080;">requires</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">qiime2 >={{ qiime2 }}</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">q2templates >={{ q2templates }}</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">q2-types >={{ q2_types }}</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pytest</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="yaml"> <span class="na" style="color: #008080;">imports</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">q2_taxa</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">qiime2.plugins.taxa</span></span>
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<a href="https://salsa.debian.org/med-team/q2-taxa/-/compare/a8e78df1d12563fec666639d4a2dde550244de37...83cddb66837d5ca1621f88d32235e913babb86a6#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">q2-taxa (2020.11.1+dfsg-3) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">q2-taxa (2021.8.0+dfsg-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"> * Team upload.</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"> [ Steffen Moeller ]</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Fixed d/u/watch - now finds new version to download</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">@@ -6,7 +8,11 @@ q2-taxa (2020.11.1+dfsg-3) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> [ Nilesh Patra ]</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * d/salsa-ci.yml: Disable build on i386 due to missing python3-skbio</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="LC9" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Mon, 26 Jul 2021 00:43:56 +0530</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Standards-Version: 4.6.0 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * Versioned (Build-)Depends from qiime and its modules (>= 2021.8.0)</span>
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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"> -- Andreas Tille <tille@debian.org> Wed, 29 Sep 2021 14:21:11 +0200</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">q2-taxa (2020.11.1+dfsg-2) unstable; urgency=medium</span>
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<a href="https://salsa.debian.org/med-team/q2-taxa/-/compare/a8e78df1d12563fec666639d4a2dde550244de37...83cddb66837d5ca1621f88d32235e913babb86a6#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,9 +11,9 @@ Build-Depends: debhelper-compat (= 13),</td>
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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;">pytest</span><span class="p">-</span><span class="n" style="color: #333;">cov</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;">pandas</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;">nodejs</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;">qiime</span> <span class="p">(>=</span> <span class="m" style="color: #099;">202<span class="idiff left right">0.11</span>.0</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;">q2templates</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="mosel"> <span class="n" style="color: #333;">q2</span><span class="p">-</span><span class="n" style="color: #333;">types</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;">qiime</span> <span class="p">(>=</span> <span class="m" style="color: #099;">202<span class="idiff left right">1.8</span>.0</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;">q2templates</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">2021.8.0</span></span><span class="p"><span class="idiff right">)</span>,</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="mosel"> <span class="n" style="color: #333;">q2</span><span class="p">-</span><span class="n" style="color: #333;">types</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">2021.8.0</span></span><span class="p"><span class="idiff right">)</span>,</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="mosel"> <span class="n" style="color: #333;">node</span><span class="p">-</span><span class="n" style="color: #333;">webpack</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="mosel"> <span class="n" style="color: #333;">node</span><span class="p">-</span><span class="n" style="color: #333;">uglifyjs</span><span class="p">-</span><span class="n" style="color: #333;">webpack</span><span class="p">-</span><span class="n" style="color: #333;">plugin</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="mosel"> <span class="n" style="color: #333;">node</span><span class="p">-</span><span class="n" style="color: #333;">babel</span><span class="p">-</span><span class="n" style="color: #333;">loader</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">@@ -21,7 +21,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="mosel"> <span class="n" style="color: #333;">node</span><span class="p">-</span><span class="n" style="color: #333;">natural</span><span class="p">-</span><span class="n" style="color: #333;">sort</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="mosel"> <span class="n" style="color: #333;">node</span><span class="p">-</span><span class="n" style="color: #333;">thenby</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="mosel"> <span class="n" style="color: #333;">node</span><span class="p">-</span><span class="n" style="color: #333;">d3</span></span>
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<pre style="margin: 0;">-<span id="LC24" 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.<span class="idiff left right">5.1</span></span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" 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.<span class="idiff left right">6.0</span></span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="mosel"><span class="n" style="color: #333;">Vcs</span><span class="p">-</span><span class="n" style="color: #333;">Browser</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</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 class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">q2</span><span class="p">-</span><span class="n" style="color: #333;">taxa</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="mosel"><span class="n" style="color: #333;">Vcs</span><span class="p">-</span><span class="n" style="color: #333;">Git</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</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 class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">q2</span><span class="p">-</span><span class="n" style="color: #333;">taxa</span><span class="p">.</span><span class="n" style="color: #333;">git</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="mosel"><span class="n" style="color: #333;">Homepage</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">qiime2</span><span class="p">.</span><span class="n" style="color: #333;">org</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">@@ -33,9 +33,9 @@ Depends: ${shlibs:Depends},</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="mosel"> <span class="p">${</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="LC34" 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="LC35" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">pandas</span><span class="p">,</span></span>
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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="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="mosel"> <span class="n" style="color: #333;">q2templates</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="mosel"> <span class="n" style="color: #333;">q2</span><span class="p">-</span><span class="n" style="color: #333;">types</span><span class="p">,</span></span>
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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="idiff left"> </span><span class="p"><span class="idiff">(>=</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">2021.8.0</span></span><span class="p"><span class="idiff right">)</span>,</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="mosel"> <span class="n" style="color: #333;">q2templates</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">2021.8.0</span></span><span class="p"><span class="idiff right">)</span>,</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="mosel"> <span class="n" style="color: #333;">q2</span><span class="p">-</span><span class="n" style="color: #333;">types</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">2021.8.0</span></span><span class="p"><span class="idiff right">)</span>,</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="mosel"> <span class="n" style="color: #333;">node</span><span class="p">-</span><span class="n" style="color: #333;">d3</span><span class="p">-</span><span class="n" style="color: #333;">scale</span><span class="p">-</span><span class="n" style="color: #333;">chromatic</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;">node</span><span class="p">-</span><span class="n" style="color: #333;">natural</span><span class="p">-</span><span class="n" style="color: #333;">sort</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="mosel"> <span class="n" style="color: #333;">node</span><span class="p">-</span><span class="n" style="color: #333;">thenby</span></span>
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<a href="https://salsa.debian.org/med-team/q2-taxa/-/compare/a8e78df1d12563fec666639d4a2dde550244de37...83cddb66837d5ca1621f88d32235e913babb86a6#8efffbd84b4a963cace9c72f98a047e357a96ec9"><strong>q2_taxa/__init__.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-202<span class="idiff left right">0</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-202<span class="idiff left right">1</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<a href="https://salsa.debian.org/med-team/q2-taxa/-/compare/a8e78df1d12563fec666639d4a2dde550244de37...83cddb66837d5ca1621f88d32235e913babb86a6#89b5aedf9522dc397b71d18ad2a42ebb4a5453e1"><strong>q2_taxa/_method.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-202<span class="idiff left right">0</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-202<span class="idiff left right">1</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</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">@@ -7,13 +7,14 @@</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pd</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">biom</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">qiime2</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._util</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">_collapse_table</span><span class="p">,</span> <span class="n" style="color: #333;">_get_max_level</span></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">collapse</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">:</span> <span class="n" style="color: #333;"><span class="idiff left">pd</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">DataFram</span>e</span><span class="p">,</span> <span class="n" style="color: #333;">taxonomy</span><span class="p">:</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">Series</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">level</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;"><span class="idiff left">pd</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">DataFram</span>e</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">collapse</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">:</span> <span class="n" style="color: #333;"><span class="idiff left">biom</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">Tabl</span>e</span><span class="p">,</span> <span class="n" style="color: #333;">taxonomy</span><span class="p">:</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">Series</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">level</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;"><span class="idiff left">biom</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">Tabl</span>e</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">level</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">'Requested level of %d is too low. Must be greater '</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">'than or equal to 1.'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">level</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/q2-taxa/-/compare/a8e78df1d12563fec666639d4a2dde550244de37...83cddb66837d5ca1621f88d32235e913babb86a6#64d397f51ea3c6a4f5e5e433a24eee8c1d36d6b6"><strong>q2_taxa/_util.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-202<span class="idiff left right">0</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-202<span class="idiff left right">1</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</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">@@ -12,7 +12,7 @@ def _get_max_level(taxonomy):</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_collapse_table</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">,</span> <span class="n" style="color: #333;">taxonomy</span><span class="p">,</span> <span class="n" style="color: #333;">level</span><span class="p">,</span> <span class="n" style="color: #333;">max_observed_level</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">table_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">columns</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">table_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">ids</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">axis</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff">'observation'</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">taxonomy_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">taxonomy</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">missing_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_ids</span><span class="p">.</span><span class="n" style="color: #333;">difference</span><span class="p">(</span><span class="n" style="color: #333;">taxonomy_ids</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">missing_ids</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</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">@@ -21,15 +21,15 @@ def _collapse_table(table, taxonomy, level, max_observed_level):</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_collapse</span><span class="p">(</span><span class="n" style="color: #333;">tax</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_collapse</span><span class="p">(</span><span class="n" style="color: #333;">id_</span><span class="p">,</span> <span class="n" style="color: #333;">md</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">tax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">taxonomy</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">id_</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">tax</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tax</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">';'</span><span class="p">)]</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">tax</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">max_observed_level</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">padding</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'__'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">max_observed_level</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">tax</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">tax</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="n" style="color: #333;">padding</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="s" style="color: #d14;">';'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">tax</span><span class="p">[:</span><span class="n" style="color: #333;">level</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">table</span><span class="p">.</span><span class="n" style="color: #333;">columns</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">taxonomy</span><span class="p">.</span><span class="nb" style="color: #0086b3;">apply</span><span class="p">(</span><span class="n" style="color: #333;">_collapse</span><span class="p">)[</span><span class="n" style="color: #333;">table</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">table</span><span class="p">.</span><span class="n" style="color: #333;">groupby</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">,</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">).</span><span class="n" style="color: #333;">agg</span><span class="p">(</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">table</span><span class="p">.</span><span class="n" style="color: #333;">collapse</span><span class="p">(</span><span class="n" style="color: #333;">_collapse</span><span class="p">,</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'observation'</span><span class="p">,</span> <span class="n" style="color: #333;">norm</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_extract_to_level</span><span class="p">(</span><span class="n" style="color: #333;">taxonomy</span><span class="p">,</span> <span class="n" style="color: #333;">table</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">@@ -40,6 +40,7 @@ def _extract_to_level(taxonomy, table):</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Collapse table at specified level</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">level</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">max_obs_lvl</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">collapsed_table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_collapse_table</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">,</span> <span class="n" style="color: #333;">taxonomy</span><span class="p">,</span> <span class="n" style="color: #333;">level</span><span class="p">,</span> <span class="n" style="color: #333;">max_obs_lvl</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">collapsed_tables</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">collapsed_table</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">as_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collapsed_table</span><span class="p">.</span><span class="n" style="color: #333;">transpose</span><span class="p">().</span><span class="n" style="color: #333;">to_dataframe</span><span class="p">(</span><span class="n" style="color: #333;">dense</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">collapsed_tables</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">as_df</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">collapsed_tables</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2-taxa/-/compare/a8e78df1d12563fec666639d4a2dde550244de37...83cddb66837d5ca1621f88d32235e913babb86a6#1d474d05be0b5c09809046c47577874bc381d4d5"><strong>q2_taxa/_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;">" (tag: 202<span class="idiff left right">0.11.1</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;">"14<span class="idiff left right">99d2d7a5f0bd958e19f8b2fffb6205e8fe50ad</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;">"202<span class="idiff left right">0-12-05 20:44:48</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;">" (tag: 202<span class="idiff left right">1.8.0</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">b</span>14<span class="idiff right">8b8ec248a63b43e8986ea74fe727dde0c07bb</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;">"202<span class="idiff left right">1-09-09 18:35:31</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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<a href="https://salsa.debian.org/med-team/q2-taxa/-/compare/a8e78df1d12563fec666639d4a2dde550244de37...83cddb66837d5ca1621f88d32235e913babb86a6#8833ba7fa943e1c897add380821376320a7b5009"><strong>q2_taxa/_visualizer.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-202<span class="idiff left right">0</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-202<span class="idiff left right">1</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</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">@@ -11,6 +11,7 @@ import os.path</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pkg_resources</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">shutil</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">biom</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pd</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">q2templates</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"></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">@@ -22,13 +23,19 @@ from ._util import _extract_to_level</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="n" style="color: #333;">TEMPLATES</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pkg_resources</span><span class="p">.</span><span class="n" style="color: #333;">resource_filename</span><span class="p">(</span><span class="s" style="color: #d14;">'q2_taxa'</span><span class="p">,</span> <span class="s" style="color: #d14;">'assets'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">barplot</span><span class="p">(</span><span class="n" style="color: #333;">output_dir</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">table</span><span class="p">:</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">,</span> <span class="n" style="color: #333;">taxonomy</span><span class="p">:</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">Series</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span><span class="p">:</span> <span class="n" style="color: #333;">Metadata</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">ids_not_in_metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">ids</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">barplot</span><span class="p">(</span><span class="n" style="color: #333;">output_dir</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">table</span><span class="p">:</span> <span class="n" style="color: #333;">biom</span><span class="p">.</span><span class="n" style="color: #333;">Table</span><span class="p">,</span> <span class="n" style="color: #333;">taxonomy</span><span class="p">:</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">Series</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span><span class="p">:</span> <span class="n" style="color: #333;">Metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">metadata</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Metadata</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">({</span><span class="s" style="color: #d14;">'id'</span><span class="p">:</span> <span class="n" style="color: #333;">table</span><span class="p">.</span><span class="n" style="color: #333;">ids</span><span class="p">(</span><span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'sample'</span><span class="p">)}).</span><span class="n" style="color: #333;">set_index</span><span class="p">(</span><span class="s" style="color: #d14;">'id'</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">ids_not_in_metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">.</span><span class="n" style="color: #333;">ids</span><span class="p">(</span><span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'sample'</span><span class="p">))</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">ids</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ids_not_in_metadata</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">'Sample IDs found in the table are missing in the '</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="sa">f</span><span class="s" style="color: #d14;">'metadata: </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">ids_not_in_metadata</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">!</span><span class="n" style="color: #333;">r</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">.'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">num_metadata_cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">column_count</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">to_dataframe</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">jsonp_files</span><span class="p">,</span> <span class="n" style="color: #333;">csv_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[],</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">collapsed_tables</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_extract_to_level</span><span class="p">(</span><span class="n" style="color: #333;">taxonomy</span><span class="p">,</span> <span class="n" style="color: #333;">table</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">@@ -62,7 +69,9 @@ def barplot(output_dir: str, table: pd.DataFrame, taxonomy: pd.Series,</td>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Now that the tables have been collapsed, write out the index template</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">TEMPLATES</span><span class="p">,</span> <span class="s" style="color: #d14;">'barplot'</span><span class="p">,</span> <span class="s" style="color: #d14;">'index.html'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">q2templates</span><span class="p">.</span><span class="n" style="color: #333;">render</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="n" style="color: #333;">context</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'jsonp_files'</span><span class="p">:</span> <span class="n" style="color: #333;">jsonp_files</span><span class="p">})</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">q2templates</span><span class="p">.</span><span class="n" style="color: #333;">render</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">output_dir</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">context</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'jsonp_files'</span><span class="p">:</span> <span class="n" style="color: #333;">jsonp_files</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="s" style="color: #d14;">'num_metadata_cols'</span><span class="p">:</span> <span class="n" style="color: #333;">num_metadata_cols</span><span class="p">})</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Copy assets for rendering figure</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">copytree</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">TEMPLATES</span><span class="p">,</span> <span class="s" style="color: #d14;">'barplot'</span><span class="p">,</span> <span class="s" style="color: #d14;">'dist'</span><span class="p">),</span></span>
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<a href="https://salsa.debian.org/med-team/q2-taxa/-/compare/a8e78df1d12563fec666639d4a2dde550244de37...83cddb66837d5ca1621f88d32235e913babb86a6#58926e8b6cd387d9c1c814ed77d97bc4a63414ee"><strong>q2_taxa/assets/barplot/index.html</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">@@ -45,4 +45,5 @@</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="html"> <span class="nt" style="color: #000080;"><script </span><span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">'{{ level }}?callback=load_data'</span><span class="nt" style="color: #000080;">></script></span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="html"> {% endfor %}</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="html"> <span class="nt" style="color: #000080;"><script </span><span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">'dist/bundle.js'</span><span class="nt" style="color: #000080;">></script></span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="html"> <span class="nt" style="color: #000080;"><p></span>Number of sample metadata columns provided: {{ num_metadata_cols }}<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="html">{% endblock %}</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-taxa/-/compare/a8e78df1d12563fec666639d4a2dde550244de37...83cddb66837d5ca1621f88d32235e913babb86a6#ef9c2a53b88c77db627dc1e45857c38d4553e0ec"><strong>q2_taxa/assets/barplot/src/render.js</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">@@ -34,7 +34,10 @@ export default function render(svg, colorScheme, xOrdering, dataMeta, barWidth)</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">const</span> <span class="nx">range</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[];</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">const</span> <span class="nx">domain</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[];</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kd" style="font-weight: 600;">let</span> <span class="nx">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nx">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nx">keys</span><span class="p">.</span><span class="nx">length</span><span class="p">;</span> <span class="nx">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="javascript"> <span class="nx">range</span><span class="p">.</span><span class="nx">push</span><span class="p">(</span><span class="nx">scheme</span><span class="p">.</span><span class="nx">scheme</span><span class="p">[</span><span class="nx">i</span> <span class="o" style="font-weight: 600;">%</span> <span class="nx">scheme</span><span class="p">.</span><span class="nx">scheme</span><span class="p">.</span><span class="nx">length</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="javascript"> <span class="c1" style="color: #998; font-style: italic;">// Assign colors from the "end" of the color scheme, which causes the</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="javascript"> <span class="c1" style="color: #998; font-style: italic;">// color scheme to consistently give the topmost value in the barplot the</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="javascript"> <span class="c1" style="color: #998; font-style: italic;">// same color (https://github.com/qiime2/q2-taxa/issues/111)</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="javascript"> <span class="nx">range</span><span class="p">.</span><span class="nx">push</span><span class="p">(</span><span class="nx">scheme</span><span class="p">.</span><span class="nx">scheme</span><span class="p">[(</span><span class="nx">keys</span><span class="p">.</span><span class="nx">length</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="nx">i</span><span class="p">)</span> <span class="o" style="font-weight: 600;">%</span> <span class="nx">scheme</span><span class="p">.</span><span class="nx">scheme</span><span class="p">.</span><span class="nx">length</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="javascript"> <span class="nx">domain</span><span class="p">.</span><span class="nx">push</span><span class="p">(</span><span class="nx">i</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="javascript"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="javascript"> <span class="nx">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">scaleOrdinal</span><span class="p">(</span><span class="nx">range</span><span class="p">).</span><span class="nx">domain</span><span class="p">(</span><span class="nx">domain</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/q2-taxa/-/compare/a8e78df1d12563fec666639d4a2dde550244de37...83cddb66837d5ca1621f88d32235e913babb86a6#cd41f5831ac254dd647b66317881b6dcc8e22fd6"><strong>q2_taxa/plugin_setup.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-202<span class="idiff left right">0</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-202<span class="idiff left right">1</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<a href="https://salsa.debian.org/med-team/q2-taxa/-/compare/a8e78df1d12563fec666639d4a2dde550244de37...83cddb66837d5ca1621f88d32235e913babb86a6#30850f68a53ca950a201908fe0fcde12fd212b98"><strong>q2_taxa/tests/__init__.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-202<span class="idiff left right">0</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-202<span class="idiff left right">1</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<a href="https://salsa.debian.org/med-team/q2-taxa/-/compare/a8e78df1d12563fec666639d4a2dde550244de37...83cddb66837d5ca1621f88d32235e913babb86a6#ad565400ff000b14c664f87d21d9ab071aa49607"><strong>q2_taxa/tests/test_methods.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-202<span class="idiff left right">0</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-202<span class="idiff left right">1</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</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">@@ -8,8 +8,10 @@</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">unittest</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">biom</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pd</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas.<span class="idiff left right">util.</span>testing</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pdt</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas.testing</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pdt</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">qiime2</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2_taxa</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">collapse</span><span class="p">,</span> <span class="n" style="color: #333;">filter_table</span><span class="p">,</span> <span class="n" style="color: #333;">filter_seqs</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">@@ -31,63 +33,70 @@ class CollapseTests(unittest.TestCase):</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">check_index_type</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">check_column_type</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">check_frame_type</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">check_less_precise</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">check_names</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">by_blocks</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">check_exact</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assert_index_equal</span><span class="p">(</span><span class="n" style="color: #333;">left</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">right</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_collapse</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">([[</span><span class="mf" style="color: #099;">2.0</span><span class="p">,</span> <span class="mf" style="color: #099;">2.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">9.0</span><span class="p">,</span> <span class="mf" style="color: #099;">8.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">4.0</span><span class="p">]],</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'D'</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'feat1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'feat2'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">biom</span><span class="p">.</span><span class="n" style="color: #333;">Table</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([[</span><span class="mf" style="color: #099;">2.0</span><span class="p">,</span> <span class="mf" style="color: #099;">2.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">9.0</span><span class="p">,</span> <span class="mf" style="color: #099;">8.0</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="p">[</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">4.0</span><span class="p">]]),</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'D'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'feat1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'feat2'</span><span class="p">]).</span><span class="n" style="color: #333;">transpose</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">taxonomy</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">Series</span><span class="p">([</span><span class="s" style="color: #d14;">'a; b; c'</span><span class="p">,</span> <span class="s" style="color: #d14;">'a; b; d'</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'feat1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'feat2'</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">actual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collapse</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">,</span> <span class="n" style="color: #333;">taxonomy</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">([[</span><span class="mf" style="color: #099;">4.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">2.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">17.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">4.0</span><span class="p">]],</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'D'</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'a'</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assert_data_frame_almost_equal</span><span class="p">(</span><span class="n" style="color: #333;">actual</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">actual</span><span class="p">.</span><span class="n" style="color: #333;">del_metadata</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">biom</span><span class="p">.</span><span class="n" style="color: #333;">Table</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([[</span><span class="mf" style="color: #099;">4.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">2.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">17.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">4.0</span><span class="p">]]),</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'D'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'a'</span><span class="p">]).</span><span class="n" style="color: #333;">transpose</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">actual</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">actual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collapse</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">,</span> <span class="n" style="color: #333;">taxonomy</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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54
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">([[</span><span class="mf" style="color: #099;">4.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">2.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">17.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">4.0</span><span class="p">]],</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'D'</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'a;b'</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assert_data_frame_almost_equal</span><span class="p">(</span><span class="n" style="color: #333;">actual</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">actual</span><span class="p">.</span><span class="n" style="color: #333;">del_metadata</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">biom</span><span class="p">.</span><span class="n" style="color: #333;">Table</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([[</span><span class="mf" style="color: #099;">4.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">2.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">17.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">4.0</span><span class="p">]]),</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'D'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'a;b'</span><span class="p">]).</span><span class="n" style="color: #333;">transpose</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">actual</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">actual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collapse</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">,</span> <span class="n" style="color: #333;">taxonomy</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">([[</span><span class="mf" style="color: #099;">2.0</span><span class="p">,</span> <span class="mf" style="color: #099;">2.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">9.0</span><span class="p">,</span> <span class="mf" style="color: #099;">8.0</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"> <span class="p">[</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">4.0</span><span class="p">]],</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'D'</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'a;b;c'</span><span class="p">,</span> <span class="s" style="color: #d14;">'a;b;d'</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assert_data_frame_almost_equal</span><span class="p">(</span><span class="n" style="color: #333;">actual</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">actual</span><span class="p">.</span><span class="n" style="color: #333;">del_metadata</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">biom</span><span class="p">.</span><span class="n" style="color: #333;">Table</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([[</span><span class="mf" style="color: #099;">2.0</span><span class="p">,</span> <span class="mf" style="color: #099;">2.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">9.0</span><span class="p">,</span> <span class="mf" style="color: #099;">8.0</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="p">[</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">4.0</span><span class="p">]]),</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'D'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'a;b;c'</span><span class="p">,</span> <span class="s" style="color: #d14;">'a;b;d'</span><span class="p">]).</span><span class="n" style="color: #333;">transpose</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">actual</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_collapse_missing_level</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">([[</span><span class="mf" style="color: #099;">2.0</span><span class="p">,</span> <span class="mf" style="color: #099;">2.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">9.0</span><span class="p">,</span> <span class="mf" style="color: #099;">8.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">4.0</span><span class="p">]],</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'D'</span><span class="p">],</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'feat1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'feat2'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">biom</span><span class="p">.</span><span class="n" style="color: #333;">Table</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([[</span><span class="mf" style="color: #099;">2.0</span><span class="p">,</span> <span class="mf" style="color: #099;">2.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">9.0</span><span class="p">,</span> <span class="mf" style="color: #099;">8.0</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="p">[</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">4.0</span><span class="p">]]),</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'D'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'feat1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'feat2'</span><span class="p">]).</span><span class="n" style="color: #333;">transpose</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">taxonomy</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">Series</span><span class="p">([</span><span class="s" style="color: #d14;">'a; b'</span><span class="p">,</span> <span class="s" style="color: #d14;">'a; b; d'</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'feat1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'feat2'</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">actual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collapse</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">,</span> <span class="n" style="color: #333;">taxonomy</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">([[</span><span class="mf" style="color: #099;">4.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">2.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">17.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">4.0</span><span class="p">]],</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'D'</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'a'</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assert_data_frame_almost_equal</span><span class="p">(</span><span class="n" style="color: #333;">actual</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">actual</span><span class="p">.</span><span class="n" style="color: #333;">del_metadata</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">biom</span><span class="p">.</span><span class="n" style="color: #333;">Table</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([[</span><span class="mf" style="color: #099;">4.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">2.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">17.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">4.0</span><span class="p">]]),</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'D'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'a'</span><span class="p">]).</span><span class="n" style="color: #333;">transpose</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">actual</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">actual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collapse</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">,</span> <span class="n" style="color: #333;">taxonomy</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">([[</span><span class="mf" style="color: #099;">4.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">2.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">17.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">4.0</span><span class="p">]],</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'D'</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'a;b'</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assert_data_frame_almost_equal</span><span class="p">(</span><span class="n" style="color: #333;">actual</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">actual</span><span class="p">.</span><span class="n" style="color: #333;">del_metadata</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">biom</span><span class="p">.</span><span class="n" style="color: #333;">Table</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([[</span><span class="mf" style="color: #099;">4.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">2.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">17.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">4.0</span><span class="p">]]),</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'D'</span><span class="p">],</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'a;b'</span><span class="p">]).</span><span class="n" style="color: #333;">transpose</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">actual</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">actual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collapse</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">,</span> <span class="n" style="color: #333;">taxonomy</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">([[</span><span class="mf" style="color: #099;">2.0</span><span class="p">,</span> <span class="mf" style="color: #099;">2.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">9.0</span><span class="p">,</span> <span class="mf" style="color: #099;">8.0</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"> <span class="p">[</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">4.0</span><span class="p">]],</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'D'</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'a;b;__'</span><span class="p">,</span> <span class="s" style="color: #d14;">'a;b;d'</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assert_data_frame_almost_equal</span><span class="p">(</span><span class="n" style="color: #333;">actual</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">actual</span><span class="p">.</span><span class="n" style="color: #333;">del_metadata</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">biom</span><span class="p">.</span><span class="n" style="color: #333;">Table</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([[</span><span class="mf" style="color: #099;">2.0</span><span class="p">,</span> <span class="mf" style="color: #099;">2.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">9.0</span><span class="p">,</span> <span class="mf" style="color: #099;">8.0</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="p">[</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">4.0</span><span class="p">]]),</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'D'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'a;b;__'</span><span class="p">,</span> <span class="s" style="color: #d14;">'a;b;d'</span><span class="p">]).</span><span class="n" style="color: #333;">transpose</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">actual</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_collapse_bad_level</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">([[</span><span class="mf" style="color: #099;">2.0</span><span class="p">,</span> <span class="mf" style="color: #099;">2.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">9.0</span><span class="p">,</span> <span class="mf" style="color: #099;">8.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">4.0</span><span class="p">]],</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="102" 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="111" 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">@@ -102,12 +111,12 @@ class CollapseTests(unittest.TestCase):</td>
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102
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">collapse</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">,</span> <span class="n" style="color: #333;">taxonomy</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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103
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_collapse_missing_table_ids_in_taxonomy</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">pd</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">DataFrame</span></span><span class="p">([[</span><span class="mf" style="color: #099;">2.0</span><span class="p">,</span> <span class="mf" style="color: #099;">2.0</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"> <span class="p">[</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="p">[</span><span class="mf" style="color: #099;">9.0</span><span class="p">,</span> <span class="mf" style="color: #099;">8.0</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"> <span class="p">[</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">4.0</span><span class="p">]],</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">index</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span></span><span class="p">[</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'D'</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">columns</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span></span><span class="p">[</span><span class="s" style="color: #d14;">'feat1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'feat2'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">biom</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">Table</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">array</span></span><span class="p">([[</span><span class="mf" style="color: #099;">2.0</span><span class="p">,</span> <span class="mf" style="color: #099;">2.0</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="idiff left right"> </span><span class="p">[</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="idiff left right"> </span><span class="p">[</span><span class="mf" style="color: #099;">9.0</span><span class="p">,</span> <span class="mf" style="color: #099;">8.0</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="idiff left"> </span><span class="p">[</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">4.0</span><span class="p">]]<span class="idiff right">)</span>,</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'D'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'feat1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'feat2'</span><span class="p">])<span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">transpose</span></span><span class="p"><span class="idiff right">()</span></span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">taxonomy</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">Series</span><span class="p">([</span><span class="s" style="color: #d14;">'a; b; c'</span><span class="p">,</span> <span class="s" style="color: #d14;">'a; b; d'</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'feat1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'feat3'</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">'missing.*feat2'</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/q2-taxa/-/compare/a8e78df1d12563fec666639d4a2dde550244de37...83cddb66837d5ca1621f88d32235e913babb86a6#ef79b0dcac45299a8293c4be36beb8554ad36e4f"><strong>q2_taxa/tests/test_plugin_setup.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-202<span class="idiff left right">0</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-202<span class="idiff left right">1</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<a href="https://salsa.debian.org/med-team/q2-taxa/-/compare/a8e78df1d12563fec666639d4a2dde550244de37...83cddb66837d5ca1621f88d32235e913babb86a6#869562bce194beffa1fa021e505679c5968d987a"><strong>q2_taxa/tests/test_visualizer.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-202<span class="idiff left right">0</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-202<span class="idiff left right">1</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</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">@@ -10,6 +10,8 @@ import os</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">tempfile</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">unittest</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">biom</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pd</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">qiime2</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"></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">@@ -19,10 +21,10 @@ from q2_taxa import barplot</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BarplotTests</span><span class="p">(</span><span class="n" style="color: #333;">unittest</span><span class="p">.</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">pd</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">DataFrame</span></span><span class="p">([[</span><span class="mf" style="color: #099;">2.0</span><span class="p">,</span> <span class="mf" style="color: #099;">2.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">9.0</span><span class="p">,</span> <span class="mf" style="color: #099;">8.0</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="p">[</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">4.0</span><span class="p">]],</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">index</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span></span><span class="p">[</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'D'</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">columns</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span></span><span class="p">[</span><span class="s" style="color: #d14;">'feat1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'feat2'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">biom</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">Table</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">array</span></span><span class="p">([[</span><span class="mf" style="color: #099;">2.0</span><span class="p">,</span> <span class="mf" style="color: #099;">2.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">9.0</span><span class="p">,</span> <span class="mf" style="color: #099;">8.0</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="idiff left"> </span><span class="p">[</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">4.0</span><span class="p">]]<span class="idiff right">)</span>,</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'D'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'feat1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'feat2'</span><span class="p">])<span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">transpose</span></span><span class="p"><span class="idiff right">()</span></span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">taxonomy</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">Series</span><span class="p">([</span><span class="s" style="color: #d14;">'a; b; c'</span><span class="p">,</span> <span class="s" style="color: #d14;">'a; b; d'</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'feat1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'feat2'</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"></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">@@ -39,6 +41,7 @@ class BarplotTests(unittest.TestCase):</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">index_fp</span><span class="p">).</span><span class="n" style="color: #333;">read</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">csv_lvl3_fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'level-3.csv'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">csv_lvl3_fp</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="s" style="color: #d14;">'val1'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">csv_lvl3_fp</span><span class="p">).</span><span class="n" style="color: #333;">read</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_barplot_metadata_extra_id</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qiime2</span><span class="p">.</span><span class="n" style="color: #333;">Metadata</span><span class="p">(</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="65" 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">@@ -62,3 +65,14 @@ class BarplotTests(unittest.TestCase):</td>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">tempfile</span><span class="p">.</span><span class="n" style="color: #333;">TemporaryDirectory</span><span class="p">()</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">output_dir</span><span class="p">:</span></span>
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">'missing.*D'</span><span class="p">):</span></span>
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">barplot</span><span class="p">(</span><span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">table</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">taxonomy</span><span class="p">,</span> <span class="n" style="color: #333;">metadata</span><span class="p">)</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_barplot_no_metadata</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">tempfile</span><span class="p">.</span><span class="n" style="color: #333;">TemporaryDirectory</span><span class="p">()</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">output_dir</span><span class="p">:</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">barplot</span><span class="p">(</span><span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">table</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">taxonomy</span><span class="p">)</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">index_fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'index.html'</span><span class="p">)</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">index_fp</span><span class="p">))</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="s" style="color: #d14;">"src='level-1.jsonp?callback=load_data'"</span> <span class="ow" style="font-weight: 600;">in</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">index_fp</span><span class="p">).</span><span class="n" style="color: #333;">read</span><span class="p">())</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">csv_lvl3_fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'level-3.csv'</span><span class="p">)</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">csv_lvl3_fp</span><span class="p">))</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="s" style="color: #d14;">'val1'</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">csv_lvl3_fp</span><span class="p">).</span><span class="n" style="color: #333;">read</span><span class="p">())</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2-taxa/-/compare/a8e78df1d12563fec666639d4a2dde550244de37...83cddb66837d5ca1621f88d32235e913babb86a6#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-202<span class="idiff left right">0</span>, QIIME 2 development team.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-202<span class="idiff left right">1</span>, QIIME 2 development team.</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</span></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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