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GitLab

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<h3>

Nilesh Patra pushed to branch upstream

at <a href="https://salsa.debian.org/med-team/augur">Debian Med / augur</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/augur/-/commit/56d7c1d2b650a8de5ce66522aef0118e7ecd3325">56d7c1d2</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-10-19T16:50:14+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 13.0.2</pre>

</li>

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<h4>6 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">

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−

.travis.yml

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</a>

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<li class="file-stats">

<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">

CHANGES.md

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<li class="file-stats">

<a href="#a1a05fb3eb681edc11e8c987f65967f416af0ee1">

augur/__version__.py

</a>

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<li class="file-stats">

<a href="#5aa84eddf9e5286c15160859a367e2b67129d7d8">

augur/tree.py

</a>

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<li class="file-stats">

<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">

setup.py

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<li class="file-stats">

<a href="#f94db01b058d7708a7469ee090e80b78c49de97a">

tests/functional/tree.t

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<h4>Changes:</h4>

<li id="dea01dd89a3b602828e630677fde5d77c06441c8">

<a href="https://salsa.debian.org/med-team/augur/-/commit/56d7c1d2b650a8de5ce66522aef0118e7ecd3325#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong>

deleted

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="s" style="color: #d14;">~> </span><span class="m" style="color: #099;">1.0</span></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">generic</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="c1" style="color: #998; font-style: italic;"># See <https://docs.travis-ci.com/user/build-stages/> for more information on</span></span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># how build stages work.</span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="yaml"><span class="na" style="color: #008080;">stages</span><span class="pi">:</span></span>

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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;">test</span></span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml"></span>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="yaml">  <span class="c1" style="color: #998; font-style: italic;"># See <https://docs.travis-ci.com/user/conditions-v1> for more on the "if" syntax.</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC10" 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;">deploy</span></span>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml">    <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">branch = release and type != pull_request</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;">include</span><span class="pi">:</span></span>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="yaml">    <span class="pi">-</span> <span class="nl">&test</span></span>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml">      <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s" style="color: #d14;">test</span></span>

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<pre style="margin: 0;">-<span id="LC17" 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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<pre style="margin: 0;">-<span id="LC18" class="line" lang="yaml">      <span class="na" style="color: #008080;">python</span><span class="pi">:</span> <span class="m" style="color: #099;">3.6</span></span>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="yaml">      <span class="na" style="color: #008080;">before_install</span><span class="pi">:</span></span>

</pre>

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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;">wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;</span></span>

</pre>

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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;">bash miniconda.sh -b -p $HOME/miniconda</span></span>

</pre>

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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;">export PATH="$HOME/miniconda/bin:$PATH"</span></span>

</pre>

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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;">hash -r</span></span>

</pre>

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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;">conda config --set always_yes yes --set changeps1 no</span></span>

</pre>

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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;">conda update -q conda</span></span>

</pre>

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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;">conda info -a</span></span>

</pre>

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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;">conda create -n augur -c bioconda python=$TRAVIS_PYTHON_VERSION mafft raxml fasttree iqtree vcftools pip</span></span>

</pre>

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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;">source activate augur</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="yaml">      <span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>

</pre>

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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;">pip install -e .[dev]</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="yaml">      <span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>

</pre>

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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 -c pytest.python3.ini  --cov-report= --cov=augur)</span></span>

</pre>

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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;">(cram --shell=/bin/bash tests/functional/*.t tests/builds/*.t)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="yaml">        <span class="pi">-</span> <span class="s" style="color: #d14;">(bash tests/builds/runner.sh)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="yaml">      <span class="na" style="color: #008080;">after_success</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="yaml">        <span class="c1" style="color: #998; font-style: italic;"># upload to codecov</span></span>

</pre>

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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;">bash <(curl -s https://codecov.io/bash) -f "!*.gcov" -X gcov -e TRAVIS_PYTHON_VERSION -y ci/codecov.yml|| echo "Codecov did not collect coverage reports"</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="yaml"></span>

</pre>

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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;"><<</span><span class="pi">:</span> <span class="nv" style="color: #008080;">*test</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="yaml">      <span class="na" style="color: #008080;">python</span><span class="pi">:</span> <span class="m" style="color: #099;">3.7</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;"><<</span><span class="pi">:</span> <span class="nv" style="color: #008080;">*test</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="yaml">      <span class="na" style="color: #008080;">python</span><span class="pi">:</span> <span class="m" style="color: #099;">3.8</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="yaml"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="yaml">    <span class="pi">-</span> <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s" style="color: #d14;">deploy</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="yaml">      <span class="na" style="color: #008080;">script</span><span class="pi">:</span> <span class="s" style="color: #d14;">./devel/travis-rebuild-docker-image</span></span></pre>

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<br>

</li>

<li id="7facec255884dc55d3818e4dfbea89b1bdd7f49e">

<a href="https://salsa.debian.org/med-team/augur/-/commit/56d7c1d2b650a8de5ce66522aef0118e7ecd3325#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.md</strong></a>

<hr>

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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">@@ -3,6 +3,16 @@</td>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## __NEXT__</span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 13.0.2 (12 October 2021)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Bug Fixes</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p">*</span> dependencies: Support latest versions of BioPython. <span class="p">[</span><span class="nv" style="color: #008080;">#777</span><span class="p">][]</span> (@huddlej)</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p">*</span> tree: Allow users to specify arbitrary IQ-TREE models. <span class="p">[</span><span class="nv" style="color: #008080;">#776</span><span class="p">][]</span> (@huddlej)</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">#776</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/776</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">#777</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/777</span></span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"></span>

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6

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 13.0.1 (1 October 2021)</span></span>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"></span>

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8

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Bug Fixes</span></span>

</pre>

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<li id="a1a05fb3eb681edc11e8c987f65967f416af0ee1">

<a href="https://salsa.debian.org/med-team/augur/-/commit/56d7c1d2b650a8de5ce66522aef0118e7ecd3325#a1a05fb3eb681edc11e8c987f65967f416af0ee1"><strong>augur/__version__.py</strong></a>

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1

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<td class="new_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'13.0.<span class="idiff left right">1</span>'</span></span>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'13.0.<span class="idiff left right">2</span>'</span></span>

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2

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<td class="new_line diff-line-num" data-linenumber="2" 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">

2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>

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4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">is_augur_version_compatible</span><span class="p">(</span><span class="n" style="color: #333;">version</span><span class="p">):</span></span>

</pre>

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<br>

</li>

<li id="5aa84eddf9e5286c15160859a367e2b67129d7d8">

<a href="https://salsa.debian.org/med-team/augur/-/commit/56d7c1d2b650a8de5ce66522aef0118e7ecd3325#5aa84eddf9e5286c15160859a367e2b67129d7d8"><strong>augur/tree.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="191" 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="191" 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">@@ -191,19 +191,19 @@ def build_iqtree(aln_file, out_file, substitution_model="GTR", clean_up=True, nt</td>

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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python">            <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span></span>

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python">        <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python"></span>

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<td class="old_line diff-line-num old" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">substitution_model</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">none</span>"</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">substitution_model</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</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>

</pre>

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<td class="old_line diff-line-num" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python">        <span class="n" style="color: #333;">call</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">iqtree</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fast_opts</span><span class="p">,</span> <span class="s" style="color: #d14;">"-nt"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">nthreads</span><span class="p">),</span> <span class="s" style="color: #d14;">"-s"</span><span class="p">,</span> <span class="n" style="color: #333;">shquote</span><span class="p">(</span><span class="n" style="color: #333;">tmp_aln_file</span><span class="p">),</span></span>

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<td class="old_line diff-line-num" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python">                <span class="s" style="color: #d14;">"-m"</span><span class="p">,</span> <span class="n" style="color: #333;">substitution_model</span><span class="p">,</span> <span class="n" style="color: #333;">tree_builder_args</span><span class="p">,</span> <span class="s" style="color: #d14;">">"</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC198" class="line" lang="python">        <span class="n" style="color: #333;">call</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">iqtree</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fast_opts</span><span class="p">,</span> <span class="s" style="color: #d14;">"-nt"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">nthreads</span><span class="p">),</span> <span class="s" style="color: #d14;">"-s"</span><span class="p">,</span> <span class="n" style="color: #333;">shquote</span><span class="p">(</span><span class="n" style="color: #333;">tmp_aln_file</span><span class="p">),</span> <span class="n" style="color: #333;">tree_builder_args</span><span class="p">,</span> <span class="s" style="color: #d14;">">"</span><span class="p">,</span> <span class="n" style="color: #333;">shquote</span><span class="p">(</span><span class="n" style="color: #333;">log_file</span><span class="p">)]</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

198

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python">        <span class="n" style="color: #333;">call</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">iqtree</span><span class="p"><span class="idiff left right">,</span></span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fast_opts</span><span class="p">,</span> <span class="s" style="color: #d14;">"-nt"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">nthreads</span><span class="p">),</span> <span class="s" style="color: #d14;">"-s"</span><span class="p">,</span> <span class="n" style="color: #333;">shquote</span><span class="p">(</span><span class="n" style="color: #333;">tmp_aln_file</span><span class="p">),</span> <span class="n" style="color: #333;">tree_builder_args</span><span class="p">,</span> <span class="s" style="color: #d14;">">"</span><span class="p">,</span> <span class="n" style="color: #333;">shquote</span><span class="p">(</span><span class="n" style="color: #333;">log_file</span><span class="p">)]</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="199" 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">

199

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<td class="new_line diff-line-num" data-linenumber="199" 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">

199

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="200" 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">

200

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<td class="new_line diff-line-num" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="python">    <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</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;">call</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="201" 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">

201

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<td class="new_line diff-line-num" data-linenumber="201" 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">

201

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="202" 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">

202

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<td class="new_line diff-line-num" data-linenumber="202" 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">

202

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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Building a tree via:</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="203" 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">

203

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<td class="new_line diff-line-num" data-linenumber="203" 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">

203

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python">          <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">Nguyen et al: IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies."</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python">          <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">Mol. Biol. Evol., 32:268-274. https://doi.org/10.1093/molbev/msu300</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

205

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<td class="new_line diff-line-num old" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC205" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">substitution_model</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"<span class="idiff left right">none</span>"</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC206" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Conducting a model test... see <span class="idiff left right">iqtree.log</span> for the result. You can specify this with --substitution-model in future runs."</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

205

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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">substitution_model</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

206

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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="sa"><span class="idiff left">f</span></span><span class="s" style="color: #d14;">"Conducting a model test... see <span class="idiff">'</span></span><span class="si" style="color: #d14;"><span class="idiff">{</span></span><span class="n" style="color: #333;"><span class="idiff">shquote</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">log_file</span></span><span class="p"><span class="idiff">)</span></span><span class="si" style="color: #d14;"><span class="idiff">}</span></span><span class="s" style="color: #d14;"><span class="idiff right">'</span> for the result. You can specify this with --substitution-model in future runs."</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="207" 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">

207

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<td class="new_line diff-line-num" data-linenumber="207" 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">

207

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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="208" 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">

208

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<td class="new_line diff-line-num" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC208" class="line" lang="python">    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python">        <span class="n" style="color: #333;">run_shell_command</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">raise_errors</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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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">@@ -216,10 +216,6 @@ def build_iqtree(aln_file, out_file, substitution_model="GTR", clean_up=True, nt</td>

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="python">            <span class="n" style="color: #333;">n</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp_name</span></span>

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#this allows the user to check intermediate output, as tree.nwk will be</span></span>

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">clean_up</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC219" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;">#allow user to see chosen model if modeltest was run</span></span>

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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">substitution_model</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'none'</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python">                <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">copyfile</span><span class="p">(</span><span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">out_file</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="n" style="color: #333;">out_file</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 class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="s" style="color: #d14;">"iqtree.log"</span><span class="p">))</span></span>

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<pre style="margin: 0;">-<span id="LC222" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</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;">isfile</span><span class="p">(</span><span class="n" style="color: #333;">tmp_aln_file</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="python">                <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">tmp_aln_file</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="344" 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">@@ -344,8 +340,8 @@ def register_arguments(parser):</td>

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<pre style="margin: 0;"> <span id="LC340" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--alignment'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-a'</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"alignment in fasta or VCF format"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC341" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--method'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'iqtree'</span><span class="p">,</span> <span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"fasttree"</span><span class="p">,</span> <span class="s" style="color: #d14;">"raxml"</span><span class="p">,</span> <span class="s" style="color: #d14;">"iqtree"</span><span class="p">],</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"tree builder to use"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC342" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--output'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-o'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'file name to write tree to'</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC347" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--substitution-model'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"GTR"</span><span class="p">,</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">choices</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"HKY"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"GTR"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"HKY+G"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"GTR+G"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"GTR+R10"</span></span><span class="p"><span class="idiff right">],</span></span></span>

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<td class="new_line diff-line-num old" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC348" class="line" lang="python">                                <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'substitution model to use. Specify </span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;"><span class="idiff left right">none</span></span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;"> to run ModelTest. Currently, only available for IQTREE.'</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC343" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--substitution-model'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"GTR"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC344" class="line" lang="python">                                <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'substitution model to use. Specify </span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;"><span class="idiff left right">auto</span></span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;"> to run ModelTest. Currently, only available for IQTREE.'</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC345" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--nthreads'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">nthreads_value</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC346" class="line" lang="python">                                <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"number of threads to use; specifying the value 'auto' will cause the number of available CPU cores on your system, if determinable, to be used"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--vcf-reference'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'fasta file of the sequence the VCF was mapped to'</span><span class="p">)</span></span>

</pre>

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<br>

</li>

<li id="8e2edce0d507e1297474f25c00cae94258db38d8">

<a href="https://salsa.debian.org/med-team/augur/-/commit/56d7c1d2b650a8de5ce66522aef0118e7ecd3325#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="48" 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="48" 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">@@ -48,7 +48,7 @@ setuptools.setup(</td>

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<td class="new_line diff-line-num" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python">    <span class="n" style="color: #333;">python_requires</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'>={}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</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="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">n</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">min_version</span><span class="p">)),</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python">    <span class="n" style="color: #333;">install_requires</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python">        <span class="s" style="color: #d14;">"bcbio-gff >=0.6.0, ==0.6.*"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python">        <span class="s" style="color: #d14;">"biopython >=1.67, <span class="idiff left"><</span>=1.7<span class="idiff right">6</span>"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python">        <span class="s" style="color: #d14;">"biopython >=1.67, <span class="idiff left">!</span>=1.7<span class="idiff right">7, !=1.78</span>"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python">        <span class="s" style="color: #d14;">"jsonschema >=3.0.0, ==3.*"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python">        <span class="s" style="color: #d14;">"packaging >=19.2"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python">        <span class="s" style="color: #d14;">"pandas >=1.0.0, ==1.*"</span><span class="p">,</span></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="f94db01b058d7708a7469ee090e80b78c49de97a">

<a href="https://salsa.debian.org/med-team/augur/-/commit/56d7c1d2b650a8de5ce66522aef0118e7ecd3325#f94db01b058d7708a7469ee090e80b78c49de97a"><strong>tests/functional/tree.t</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="20" 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="20" 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">@@ -20,6 +20,15 @@ Try building a tree with IQ-TREE with more threads (4) than there are input sequ</td>

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<td class="old_line diff-line-num" data-linenumber="20" 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">

20

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20

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="perl">  <span class="o" style="font-weight: 600;">></span>  <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">nthreads</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">></span> <span class="sr" style="color: #009926;">/dev/null</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" 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">

21

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<td class="new_line diff-line-num" 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">

21

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="perl">  <span class="nv" style="color: #008080;">WARNING:</span> <span class="nv" style="color: #008080;">more</span> <span class="nv" style="color: #008080;">threads</span> <span class="nv" style="color: #008080;">requested</span> <span class="nv" style="color: #008080;">than</span> <span class="nv" style="color: #008080;">there</span> <span class="nv" style="color: #008080;">are</span> <span class="nv" style="color: #008080;">sequences</span><span class="p">;</span> <span class="nv" style="color: #008080;">falling</span> <span class="nv" style="color: #008080;">back</span> <span class="nv" style="color: #008080;">to</span> <span class="nv" style="color: #008080;">IQ</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">TREE</span><span class="p">'</span><span class="s1" style="color: #d14;">s `-nt AUTO` mode.</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="22" 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">

22

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<td class="new_line diff-line-num" data-linenumber="22" 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">

22

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC22" class="line" lang="perl"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

23

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC23" class="line" lang="perl"><span class="s1" style="color: #d14;">Try building a tree with IQ-TREE using its ModelTest functionality, by supplying a substitution model of "auto".</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

24

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC24" class="line" lang="perl"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

25

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC25" class="line" lang="perl"><span class="s1" style="color: #d14;">  $ ${AUGUR} tree \</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

26

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC26" class="line" lang="perl"><span class="s1" style="color: #d14;">  >  --alignment tree/aligned.fasta \</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

27

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC27" class="line" lang="perl"><span class="s1" style="color: #d14;">  >  --method iqtree \</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

28

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC28" class="line" lang="perl"><span class="s1" style="color: #d14;">  >  --substitution-model auto \</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

29

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC29" class="line" lang="perl"><span class="s1" style="color: #d14;">  >  --output "$TMP/tree_raw.nwk" \</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

30

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC30" class="line" lang="perl"><span class="s1" style="color: #d14;">  >  --nthreads 1 > /dev/null</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

31

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC31" class="line" lang="perl"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="23" 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">

23

</td>

<td class="new_line diff-line-num" data-linenumber="32" 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">

32

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC32" class="line" lang="perl"><span class="s1" style="color: #d14;">Clean up tree log files.</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="24" 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">

24

</td>

<td class="new_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

33

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC33" class="line" lang="perl"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="25" 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">

25

</td>

<td class="new_line diff-line-num" data-linenumber="34" 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">

34

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC34" class="line" lang="perl"><span class="s1" style="color: #d14;">  $ rm -f tree/*.log</span></span>

</pre>

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