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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/q2-feature-classifier">Debian Med / q2-feature-classifier</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-feature-classifier/-/commit/55ef240e9a46112de08db228e89fd595e55f420d">55ef240e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-01T12:43:42+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2021.8.0</pre>
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<h4>24 changed files:</h4>
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.github/workflows/ci.yml
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<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
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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">
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ci/recipe/conda_build_config.yaml
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<a href="#22fbe0b68848772d4b1c45f0d62dcd71a06cde00">
ci/recipe/meta.yaml
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<li class="file-stats">
<a href="#d399100d954b34407a7fab64d234f2f353e084f7">
q2_feature_classifier/__init__.py
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<li class="file-stats">
<a href="#1ce0eef8581985aad1e3a575a326710b569c677e">
q2_feature_classifier/_blast.py
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<li class="file-stats">
<a href="#51782921baee3f3292d09d4edb05c90bb30e5458">
q2_feature_classifier/_consensus_assignment.py
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<li class="file-stats">
<a href="#094a1aa475cfaf7797a2658ec9dd513ef4fa1524">
q2_feature_classifier/_cutter.py
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<a href="#a983074a9a2caf11735d1d54cef2229d079a453b">
q2_feature_classifier/_skl.py
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<li class="file-stats">
<a href="#71ef0c2491ce3a86a4eb9be230cd72759b8b3fbe">
q2_feature_classifier/_taxonomic_classifier.py
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<a href="#e1b612463caf8bb74f319ce3000e7a5fe7ccc722">
q2_feature_classifier/_version.py
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<a href="#755fedce54140c1dd2a4118628932cf48cc68dc1">
q2_feature_classifier/_vsearch.py
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<li class="file-stats">
<a href="#8b429ca6f0ecc3f6f870bba70ce4d821c711e1a6">
q2_feature_classifier/classifier.py
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<a href="#755f4579ecc3f3c0aa4fb3990012d35e2ef52a20">
q2_feature_classifier/custom.py
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<a href="#72570e58b033315f467b9016c41bd184ded95a2d">
q2_feature_classifier/plugin_setup.py
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<a href="#3aadb3d24bf2fb8e9de04f7f8f2672ad9039c647">
q2_feature_classifier/tests/__init__.py
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<a href="#43c534546ab6a7d5ef0423b90cd0e1b64c1614f7">
q2_feature_classifier/tests/test_classifier.py
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<li class="file-stats">
<a href="#9119ec5d547606e633f235bfd8d07e884992502a">
q2_feature_classifier/tests/test_consensus_assignment.py
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<a href="#999afd5f0a1e64a2e7576675f1e80bc18ef7890e">
q2_feature_classifier/tests/test_custom.py
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<a href="#715a2480ca561cb9e6668f29875ac268c86dba44">
q2_feature_classifier/tests/test_cutter.py
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<a href="#d1ace7f5ea694e1686443cb8424bc9921f057f2b">
q2_feature_classifier/tests/test_taxonomic_classifier.py
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<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<h4>Changes:</h4>
<li id="899ce9c202bf7bb5480e72836c3edc773c9c4244">
<a href="https://salsa.debian.org/med-team/q2-feature-classifier/-/commit/55ef240e9a46112de08db228e89fd595e55f420d#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="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">push</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">branches</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="LC12" class="line" lang="yaml"></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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<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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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"></span>
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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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42
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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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<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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<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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47
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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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48
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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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49
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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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51
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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-feature-classifier</span></span>
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53
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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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54
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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_feature_classifier</span></span>
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55
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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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<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/q2-feature-classifier/-/commit/55ef240e9a46112de08db228e89fd595e55f420d#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 $MINICONDA_PREFIX</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">export PATH="$MINICONDA_PREFIX/bin:$PATH"</span></span>
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10
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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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15
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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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<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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21
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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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<a href="https://salsa.debian.org/med-team/q2-feature-classifier/-/commit/55ef240e9a46112de08db228e89fd595e55f420d#0398ccd0f49298b10a3d76a47800d2ebecd49859"><strong>LICENSE</strong></a>
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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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<a href="https://salsa.debian.org/med-team/q2-feature-classifier/-/commit/55ef240e9a46112de08db228e89fd595e55f420d#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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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-feature-classifier</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-feature-classifier.svg?branch=master</span><span class="p">)</span>](https://travis-ci.org/qiime2/q2-feature-classifier)</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-feature-classifier/-/commit/55ef240e9a46112de08db228e89fd595e55f420d#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-feature-classifier/-/commit/55ef240e9a46112de08db228e89fd595e55f420d#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-feature-classifier</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" 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">@@ -19,20 +18,28 @@ requirements:</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC19" 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="LC20" 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;">scikit-learn 0.2<span class="idiff left right">3</span>.1</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;">scikit-learn <span class="idiff left">==</span>0.2<span class="idiff right">4</span>.1</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;">joblib</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;">scikit-bio</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;">biom-format >=2.1.5,<2.2.0</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;">blast >=2.6.0</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># There are issues with 2.8.2, and no OS X builds exist after 2.7.0</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">vsearch <=2.7.0</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 {{ <span class="idiff left right">release</span> }}.*</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;">q2-types {{ <span class="idiff left right">release</span> }}.*</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-quality-control {{ <span class="idiff left right">release</span> }}.*</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;">q2-taxa {{ <span class="idiff left right">release</span> }}.*</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">q2-feature-table {{ <span class="idiff left right">release</span> }}.*</span></span>
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<pre style="margin: 0;">+<span id="LC28" 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="LC29" 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="LC30" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">q2-quality-control {{ <span class="idiff left right">qiime2_epoch</span> }}.*</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-taxa {{ <span class="idiff left right">qiime2_epoch</span> }}.*</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;">q2-feature-table {{ <span class="idiff left right">qiime2_epoch</span> }}.*</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;">test</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC35" 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="LC36" 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="LC37" 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="LC38" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">q2-quality-control >={{ q2_quality_control }}</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">q2-taxa >={{ q2_taxa }}</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">q2-feature-table >={{ q2_feature_table }}</span></span>
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<pre style="margin: 0;">+<span id="LC41" 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="LC43" 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="LC44" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">q2_feature_classifier</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">qiime2.plugins.feature_classifier</span></span>
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<a href="https://salsa.debian.org/med-team/q2-feature-classifier/-/commit/55ef240e9a46112de08db228e89fd595e55f420d#d399100d954b34407a7fab64d234f2f353e084f7"><strong>q2_feature_classifier/__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-feature-classifier/-/commit/55ef240e9a46112de08db228e89fd595e55f420d#1ce0eef8581985aad1e3a575a326710b569c677e"><strong>q2_feature_classifier/_blast.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-feature-classifier/-/commit/55ef240e9a46112de08db228e89fd595e55f420d#51782921baee3f3292d09d4edb05c90bb30e5458"><strong>q2_feature_classifier/_consensus_assignment.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-feature-classifier/-/commit/55ef240e9a46112de08db228e89fd595e55f420d#094a1aa475cfaf7797a2658ec9dd513ef4fa1524"><strong>q2_feature_classifier/_cutter.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="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-feature-classifier/-/commit/55ef240e9a46112de08db228e89fd595e55f420d#71ef0c2491ce3a86a4eb9be230cd72759b8b3fbe"><strong>q2_feature_classifier/_taxonomic_classifier.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-feature-classifier/-/commit/55ef240e9a46112de08db228e89fd595e55f420d#e1b612463caf8bb74f319ce3000e7a5fe7ccc722"><strong>q2_feature_classifier/_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;">"9<span class="idiff left right">77304e2f5b04d9b36edce8f978282e524957e64</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 20:44:56</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;">"9<span class="idiff left right">eb351f285c83f247214317a0db456f983bd5b25</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 18:35:30</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-feature-classifier/-/commit/55ef240e9a46112de08db228e89fd595e55f420d#755fedce54140c1dd2a4118628932cf48cc68dc1"><strong>q2_feature_classifier/_vsearch.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">@@ -77,7 +77,7 @@ def classify_hybrid_vsearch_sklearn(ctx,</td>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">min_consensus</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.51</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">maxhits</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'all'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">maxrejects</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'all'</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;">reads_per_batch</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;"><span class="idiff left right">0</span></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;">reads_per_batch</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;"><span class="idiff left right">'auto'</span></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;">confidence</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.7</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;">read_orientation</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'auto'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">threads</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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<a href="https://salsa.debian.org/med-team/q2-feature-classifier/-/commit/55ef240e9a46112de08db228e89fd595e55f420d#8b429ca6f0ecc3f6f870bba70ce4d821c711e1a6"><strong>q2_feature_classifier/classifier.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">@@ -199,13 +199,13 @@ def _autotune_reads_per_batch(reads, n_jobs):</td>
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">classify_sklearn</span><span class="p">(</span><span class="n" style="color: #333;">reads</span><span class="p">:</span> <span class="n" style="color: #333;">DNAFASTAFormat</span><span class="p">,</span> <span class="n" style="color: #333;">classifier</span><span class="p">:</span> <span class="n" style="color: #333;">Pipeline</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">reads_per_batch</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">,</span> <span class="n" style="color: #333;">n_jobs</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</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="LC202" class="line" lang="python"> <span class="n" style="color: #333;">reads_per_batch</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">'auto'</span></span><span class="p">,</span> <span class="n" style="color: #333;">n_jobs</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</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="LC203" class="line" lang="python"> <span class="n" style="color: #333;">pre_dispatch</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'2*n_jobs'</span><span class="p">,</span> <span class="n" style="color: #333;">confidence</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">float</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.7</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"> <span class="n" style="color: #333;">read_orientation</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'auto'</span></span>
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python"> <span class="p">)</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>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># autotune reads per batch</span></span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">reads_per_batch</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">reads_per_batch</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;"><span class="idiff left right">'auto'</span></span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">reads_per_batch</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_autotune_reads_per_batch</span><span class="p">(</span><span class="n" style="color: #333;">reads</span><span class="p">,</span> <span class="n" style="color: #333;">n_jobs</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># transform reads to DNAIterator</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">@@ -233,7 +233,7 @@ def classify_sklearn(reads: DNAFASTAFormat, classifier: Pipeline,</td>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="python"><span class="n" style="color: #333;">_classify_parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="python"> <span class="s" style="color: #d14;">'reads_per_batch'</span><span class="p">:</span> <span class="n" style="color: #333;">Int</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">Range</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"> <span class="s" style="color: #d14;">'reads_per_batch'</span><span class="p">:</span> <span class="n" style="color: #333;">Int</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">Range</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left">1</span></span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">|</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Str</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Choices</span></span><span class="p"><span class="idiff">([</span></span><span class="s" style="color: #d14;"><span class="idiff">'auto'</span></span><span class="p"><span class="idiff right">])</span>,</span></span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="python"> <span class="s" style="color: #d14;">'n_jobs'</span><span class="p">:</span> <span class="n" style="color: #333;">Int</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="python"> <span class="s" style="color: #d14;">'pre_dispatch'</span><span class="p">:</span> <span class="n" style="color: #333;">Str</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python"> <span class="s" style="color: #d14;">'confidence'</span><span class="p">:</span> <span class="n" style="color: #333;">Float</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">Range</span><span class="p">(</span></span>
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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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<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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<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="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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<a href="https://salsa.debian.org/med-team/q2-feature-classifier/-/commit/55ef240e9a46112de08db228e89fd595e55f420d#43c534546ab6a7d5ef0423b90cd0e1b64c1614f7"><strong>q2_feature_classifier/tests/test_classifier.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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<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-feature-classifier/-/commit/55ef240e9a46112de08db228e89fd595e55f420d#999afd5f0a1e64a2e7576675f1e80bc18ef7890e"><strong>q2_feature_classifier/tests/test_custom.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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<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-feature-classifier/-/commit/55ef240e9a46112de08db228e89fd595e55f420d#d1ace7f5ea694e1686443cb8424bc9921f057f2b"><strong>q2_feature_classifier/tests/test_taxonomic_classifier.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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<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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