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<h3>
Nilesh Patra pushed to branch master
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/ef1986b803fb6290fa9fcd2dbca44803c5b64c8b">ef1986b8</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-01-18T19:34:19+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/augur/-/commit/884cbf1f30c78e9114e8c256d94584002411c4e6">884cbf1f</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-01-18T19:34:20+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 10.3.0</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/augur/-/commit/e24f8c1dda80aab7794b78cea63333fc1e279451">e24f8c1d</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-01-18T19:35:06+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/10.3.0'
Update to upstream version '10.3.0'
with Debian dir fce2fb4db65e3697b2ffa611af592babb6febbc5</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/augur/-/commit/d80b50c3679d73a836b9dcd304426a3edf8c0238">d80b50c3</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-01-18T14:10:50+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
</pre>
</li>
</ul>
<h4>13 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
</a>
</li>
<li class="file-stats">
<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">
CHANGES.md
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#a1a05fb3eb681edc11e8c987f65967f416af0ee1">
augur/__version__.py
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<li class="file-stats">
<a href="#6f472ebe2f0cdadd2929544cafb4b0e1fb8a0290">
augur/frequencies.py
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<li class="file-stats">
<a href="#a2755cb286db6c4fda7886a509ef645586f42c72">
augur/frequency_estimators.py
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<li class="file-stats">
<a href="#f4919502f59714aa98c2d5c8a78855a31c295c88">
<span class="new-file">
+
codecov.yml
</span>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#f0eca249c61d71d1d8e29cf4012012da7dadbad8">
paper/paper.bib
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<li class="file-stats">
<a href="#30cbbea27bb1efbfe6e3017b073e19e61ebced6f">
paper/paper.md
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<li class="file-stats">
<a href="#225cc818de93cbf949f751310621362b4d1d00f3">
scripts/identify_emerging_clades.py
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<li class="file-stats">
<a href="#081890624636fe474b1df86be458d3200baa3001">
scripts/verify_meta_json.py
</a>
</li>
<li class="file-stats">
<a href="#9db30a8891be7b63bf8fe1f26d0ffb472e77c96b">
tests/test_frequencies.py
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/augur/-/compare/bb58b81e4f3a2a198c5ddd2fa4709917a654e7c6...d80b50c3679d73a836b9dcd304426a3edf8c0238#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,7 +24,7 @@ jobs:</td>
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<td class="diff-line-num old_line" 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">
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<td class="diff-line-num new_line" 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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<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>
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<td class="diff-line-num old_line" 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">
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<td class="diff-line-num new_line" 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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<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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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="26" 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="diff-line-num new_line" data-linenumber="26" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<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>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="27" 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="diff-line-num new_line old" data-linenumber="27" 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="LC27" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda <span class="idiff left right">env create -f environment.yml</span></span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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">
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<td class="diff-line-num new new_line" 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">
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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="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda <span class="idiff left right">create -n augur -c bioconda python=$TRAVIS_PYTHON_VERSION mafft raxml fasttree iqtree vcftools pip</span></span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="28" 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="diff-line-num new_line" data-linenumber="28" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<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>
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<td class="diff-line-num old_line" data-linenumber="29" 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="diff-line-num new_line" data-linenumber="29" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC29" class="line" lang="yaml"> <span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="30" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<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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</table>
<br>
</li>
<li id="7facec255884dc55d3818e4dfbea89b1bdd7f49e">
<a href="https://salsa.debian.org/med-team/augur/-/compare/bb58b81e4f3a2a198c5ddd2fa4709917a654e7c6...d80b50c3679d73a836b9dcd304426a3edf8c0238#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.md</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" 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">@@ -3,6 +3,24 @@</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<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>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" 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;">## 10.3.0 (14 January 2021)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="8" 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="LC8" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Bug Fixes</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p">*</span> scripts: Fix typo in <span class="sb" style="color: #d14;">`verify_meta_json.py`</span> <span class="p">[</span><span class="nv" style="color: #008080;">#656</span><span class="p">][]</span> (@felixonmars)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p">*</span> CI: Use the expected Python version in conda environments <span class="p">[</span><span class="nv" style="color: #008080;">#658</span><span class="p">][]</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"><span class="p">*</span> CI: Minimize codecov feedback <span class="p">[</span><span class="nv" style="color: #008080;">#661</span><span class="p">][]</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Features</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"><span class="p">*</span> frequencies: Add <span class="sb" style="color: #d14;">`--pivot-interval-units`</span> argument with support for weekly pivots <span class="p">[</span><span class="nv" style="color: #008080;">#660</span><span class="p">][]</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"><span class="p">*</span> frequencies: Add support for ISO dates for <span class="sb" style="color: #d14;">`--min-date`</span> and <span class="sb" style="color: #d14;">`--max-date`</span> arguments <span class="p">[</span><span class="nv" style="color: #008080;">#660</span><span class="p">][]</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">#656</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/656</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">#658</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/658</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">#660</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/660</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">#661</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/661</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 10.2.0 (1 January 2021)</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Features</span></span>
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<a href="https://salsa.debian.org/med-team/augur/-/compare/bb58b81e4f3a2a198c5ddd2fa4709917a654e7c6...d80b50c3679d73a836b9dcd304426a3edf8c0238#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</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">@@ -3,6 +3,7 @@</td>
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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;">![install with bioconda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat</span><span class="p">)</span>](http://bioconda.github.io/recipes/augur/README.html)</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Documentation Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://readthedocs.org/projects/nextstrain-augur/badge/?version=latest</span><span class="p">)</span>](https://nextstrain-augur.readthedocs.io/en/stable/?badge=latest)</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![License: AGPL v3</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/License-AGPL%20v3-blue.svg</span><span class="p">)</span>](https://www.gnu.org/licenses/agpl-3.0)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![DOI</span><span class="p">](</span><span class="sx" style="color: #d14;">https://joss.theoj.org/papers/10.21105/joss.02906/status.svg</span><span class="p">)</span>](https://doi.org/10.21105/joss.02906)</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## About Nextstrain</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"></span>
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<a href="https://salsa.debian.org/med-team/augur/-/compare/bb58b81e4f3a2a198c5ddd2fa4709917a654e7c6...d80b50c3679d73a836b9dcd304426a3edf8c0238#a1a05fb3eb681edc11e8c987f65967f416af0ee1"><strong>augur/__version__.py</strong></a>
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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;">'10.<span class="idiff left right">2</span>.0'</span></span>
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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;">'10.<span class="idiff left right">3</span>.0'</span></span>
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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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<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>
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<a href="https://salsa.debian.org/med-team/augur/-/compare/bb58b81e4f3a2a198c5ddd2fa4709917a654e7c6...d80b50c3679d73a836b9dcd304426a3edf8c0238#6f472ebe2f0cdadd2929544cafb4b0e1fb8a0290"><strong>augur/frequencies.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">@@ -2,10 +2,12 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="s" style="color: #d14;">infer frequencies of mutations or clades</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">json</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="p">,</span> <span class="n" style="color: #333;">sys</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">datetime</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">defaultdict</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Phylo</span><span class="p">,</span> <span class="n" style="color: #333;">AlignIO</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.Align</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">MultipleSeqAlignment</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">treetime.utils</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.frequency_estimators</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_pivots</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_frequencies</span><span class="p">,</span> <span class="n" style="color: #333;">tree_frequencies</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.frequency_estimators</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">AlignmentKdeFrequencies</span><span class="p">,</span> <span class="n" style="color: #333;">TreeKdeFrequencies</span><span class="p">,</span> <span class="n" style="color: #333;">TreeKdeFrequenciesError</span></span>
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<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,11 +23,13 @@ def register_arguments(parser):</td>
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<pre style="margin: 0;"> <span id="LC23" 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;">'--regions'</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;">nargs</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;">default</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'global'</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC24" 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;">"region to subsample to"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">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;">"--pivot-interval"</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;">int</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;">3</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC24" 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 months between pivots"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">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;">'--min-date'</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;">float</span><span class="p">,</span></span>
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26
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<pre style="margin: 0;">-<span id="LC26" 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;">"minimal pivot value"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">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;">'--max-date'</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;">float</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"maximal pivot value"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"number of units between pivots"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">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;">"--pivot-interval-units"</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;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"months"</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;">'months'</span><span class="p">,</span> <span class="s" style="color: #d14;">'weeks'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"space pivots by months (default) or by weeks"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">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;">'--min-date'</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;">numeric_date</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"date to begin frequencies calculations; may be specified as an Augur-style numeric date (with the year as the integer part) or YYYY-MM-DD"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">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;">'--max-date'</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;">numeric_date</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC32" 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;">"date to end frequencies calculations; may be specified as an Augur-style numeric date (with the year as the integer part) or YYYY-MM-DD"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Tree-specific arguments</span></span>
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<pre style="margin: 0;"> <span id="LC35" 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;">'--tree'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-t'</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>
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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">@@ -104,7 +108,7 @@ def run(args):</td>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">method</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"diffusion"</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># estimate tree frequencies</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">pivots</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_pivots</span><span class="p">(</span><span class="n" style="color: #333;">tps</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">pivot_interval</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">min_date</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">max_date</span><span class="p">)</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">pivots</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_pivots</span><span class="p">(</span><span class="n" style="color: #333;">tps</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">pivot_interval</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">min_date</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">max_date</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">pivot_interval_units</span></span><span class="p">)</span></span>
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108
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"> <span class="n" style="color: #333;">frequency_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"pivots"</span><span class="p">:</span><span class="n" style="color: #333;">format_frequencies</span><span class="p">(</span><span class="n" style="color: #333;">pivots</span><span class="p">)}</span></span>
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109
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">frequency_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"counts"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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110
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="157" 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="161" 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">@@ -157,6 +161,7 @@ def run(args):</td>
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157
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">pivot_frequency</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">pivot_interval</span><span class="p">,</span></span>
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158
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">start_date</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">min_date</span><span class="p">,</span></span>
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159
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="python"> <span class="n" style="color: #333;">end_date</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">max_date</span><span class="p">,</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">pivot_interval_units</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">pivot_interval_units</span><span class="p">,</span></span>
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160
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">weights</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">weights</span><span class="p">,</span></span>
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161
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python"> <span class="n" style="color: #333;">weights_attribute</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">weights_attribute</span><span class="p">,</span></span>
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162
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="python"> <span class="n" style="color: #333;">include_internal_nodes</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">include_internal_nodes</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -190,7 +195,7 @@ def run(args):</td>
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190
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">tps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">mean</span><span class="p">(</span><span class="n" style="color: #333;">dates</span><span class="p">[</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">])</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">seq</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">aln</span><span class="p">])</span></span>
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191
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python"></span>
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192
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">frequencies</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">pivots</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_pivots</span><span class="p">(</span><span class="n" style="color: #333;">tps</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">pivot_interval</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">min_date</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">max_date</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" 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;">pivots</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_pivots</span><span class="p">(</span><span class="n" style="color: #333;">tps</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">pivot_interval</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">min_date</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">max_date</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">pivot_interval_units</span></span><span class="p">)</span></span>
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194
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">frequencies</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"pivots"</span><span class="p">:</span><span class="n" style="color: #333;">format_frequencies</span><span class="p">(</span><span class="n" style="color: #333;">pivots</span><span class="p">)}</span></span>
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="python"></span>
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">method</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"kde"</span><span class="p">:</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -201,6 +206,7 @@ def run(args):</td>
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201
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">pivot_frequency</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">pivot_interval</span><span class="p">,</span></span>
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202
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">start_date</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">min_date</span><span class="p">,</span></span>
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203
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">end_date</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">max_date</span><span class="p">,</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">pivot_interval_units</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">pivot_interval_units</span><span class="p">,</span></span>
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204
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">weights</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">weights</span><span class="p">,</span></span>
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205
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">weights_attribute</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">weights_attribute</span><span class="p">,</span></span>
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206
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">include_internal_nodes</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">include_internal_nodes</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -224,3 +230,19 @@ def run(args):</td>
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224
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230
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="python"></span>
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225
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231
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="python"> <span class="n" style="color: #333;">write_json</span><span class="p">(</span><span class="n" style="color: #333;">frequencies</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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226
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232
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"mutation frequencies written to"</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">,</span> <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;">stdout</span><span class="p">)</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">numeric_date</span><span class="p">(</span><span class="n" style="color: #333;">date</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;">"""</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"><span class="s" style="color: #d14;"> Converts the given *date* string to a :py:class:`float`.</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"><span class="s" style="color: #d14;"> *date* may be given as a number (a float) with year as the integer part, or</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"><span class="s" style="color: #d14;"> in the YYYY-MM-DD (ISO 8601) syntax.</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"><span class="s" style="color: #d14;"> >>> numeric_date("2020.42")</span></span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"><span class="s" style="color: #d14;"> 2020.42</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"><span class="s" style="color: #d14;"> >>> numeric_date("2020-06-04")</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"><span class="s" style="color: #d14;"> 2020.42486...</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC245" 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="LC246" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">date</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">treetime</span><span class="p">.</span><span class="n" style="color: #333;">utils</span><span class="p">.</span><span class="n" style="color: #333;">numeric_date</span><span class="p">(</span><span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">date</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">date</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="mi" style="color: #099;">2</span><span class="p">))))</span></span></pre>
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<a href="https://salsa.debian.org/med-team/augur/-/compare/bb58b81e4f3a2a198c5ddd2fa4709917a654e7c6...d80b50c3679d73a836b9dcd304426a3edf8c0238#a2755cb286db6c4fda7886a509ef645586f42c72"><strong>augur/frequency_estimators.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;"># estimates clade frequencies</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">division</span><span class="p">,</span> <span class="n" style="color: #333;">print_function</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">defaultdict</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">datetime</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pd</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">scipy.interpolate</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">interp1d</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" 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">@@ -18,7 +19,7 @@ class TreeKdeFrequenciesError(Exception):</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_pivots</span><span class="p">(</span><span class="n" style="color: #333;">observations</span><span class="p">,</span> <span class="n" style="color: #333;">pivot_interval</span><span class="p">,</span> <span class="n" style="color: #333;">start_date</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">end_date</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_pivots</span><span class="p">(</span><span class="n" style="color: #333;">observations</span><span class="p">,</span> <span class="n" style="color: #333;">pivot_interval</span><span class="p">,</span> <span class="n" style="color: #333;">start_date</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">end_date</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pivot_interval_units</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff right">"months"</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="s" style="color: #d14;">"""Calculate pivots for a given list of floating point observation dates and</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="s" style="color: #d14;"> interval between pivots.</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -30,11 +31,13 @@ def get_pivots(observations, pivot_interval, start_date=None, end_date=None):</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"><span class="s" style="color: #d14;"> observations : list</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"><span class="s" style="color: #d14;"> a list of observed floating point dates per sample</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"><span class="s" style="color: #d14;"> pivot_interval : int</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"><span class="s" style="color: #d14;"> number of months between pivots</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"><span class="s" style="color: #d14;"> number of months <span class="idiff left right">(or weeks) </span>between pivots</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"><span class="s" style="color: #d14;"> start_date : float</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"><span class="s" style="color: #d14;"> optional start of the pivots interval</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"><span class="s" style="color: #d14;"> end_date : float</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"><span class="s" style="color: #d14;"> optional end of the pivots interval</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"><span class="s" style="color: #d14;"> pivot_interval : str</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"><span class="s" style="color: #d14;"> whether pivots are measured in "months" or in "weeks"</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"><span class="s" style="color: #d14;"> Returns</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"><span class="s" style="color: #d14;"> -------</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">@@ -44,18 +47,27 @@ def get_pivots(observations, pivot_interval, start_date=None, end_date=None):</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Convert months between pivots to pivot frequency.</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">pivot_frequency</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pivot_interval</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">12.0</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pivot_interval_units</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"weeks"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">pivot_frequency</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pivot_interval</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">52.1429</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">pivot_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start_date</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">start_date</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">floor</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">observations</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">pivot_frequency</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pivot_frequency</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">pivot_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end_date</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">end_date</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">ceil</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">observations</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">pivot_frequency</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pivot_frequency</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pivot_interval_units</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"months"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"%sMS"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">pivot_interval</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">pivot_interval_units</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"weeks"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"%sW"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">pivot_interval</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s" style="color: #d14;">"The given interval unit '</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">pivot_interval_units</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">' is not supported."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">datetime_pivots</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;">date_range</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">float_to_datestring</span><span class="p">(</span><span class="n" style="color: #333;">pivot_start</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">float_to_datestring</span><span class="p">(</span><span class="n" style="color: #333;">pivot_end</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">freq</span><span class="o" style="font-weight: 600;"><span class="idiff left">=</span></span><span class="s" style="color: #d14;"><span class="idiff">"%sMS"</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 right">pivot_interval</span></span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">freq</span><span class="idiff left"> </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 right">offset</span></span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">pivots</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="n" style="color: #333;">timestamp_to_float</span><span class="p">(</span><span class="n" style="color: #333;">pivot</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">pivot</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">datetime_pivots</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">around</span><span class="p">(</span><span class="n" style="color: #333;">pivots</span><span class="p">,</span> <span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">around</span><span class="p">(</span><span class="n" style="color: #333;">pivots</span><span class="p">,</span> <span class="mi" style="color: #099;"><span class="idiff left right">4</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">make_pivots</span><span class="p">(</span><span class="n" style="color: #333;">pivots</span><span class="p">,</span> <span class="n" style="color: #333;">tps</span><span class="p">):</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -796,45 +808,33 @@ def test_nested_estimator():</td>
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<pre style="margin: 0;"> <span id="LC808" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC809" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">nested_freq</span></span>
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<pre style="margin: 0;"> <span id="LC810" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC799" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC800" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">float_to_datestring</span><span class="p">(</span><span class="n" style="color: #333;">time</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC801" class="line" lang="python"> <span class="s" style="color: #d14;">"""Convert a floating point date to a date string</span></span>
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<pre style="margin: 0;">-<span id="LC802" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC803" class="line" lang="python"><span class="s" style="color: #d14;"> >>> float_to_datestring(2010.75)</span></span>
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<pre style="margin: 0;">-<span id="LC804" class="line" lang="python"><span class="s" style="color: #d14;"> '2010-10-01'</span></span>
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<pre style="margin: 0;">-<span id="LC805" class="line" lang="python"><span class="s" style="color: #d14;"> >>> float_to_datestring(2011.25)</span></span>
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806
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<pre style="margin: 0;">-<span id="LC806" class="line" lang="python"><span class="s" style="color: #d14;"> '2011-04-01'</span></span>
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<pre style="margin: 0;">-<span id="LC807" class="line" lang="python"><span class="s" style="color: #d14;"> >>> float_to_datestring(2011.0)</span></span>
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808
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<pre style="margin: 0;">-<span id="LC808" class="line" lang="python"><span class="s" style="color: #d14;"> '2011-01-01'</span></span>
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809
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<pre style="margin: 0;">-<span id="LC809" class="line" lang="python"><span class="s" style="color: #d14;"> >>> float_to_datestring(2011.0 + 11.0 / 12)</span></span>
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810
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<pre style="margin: 0;">-<span id="LC810" class="line" lang="python"><span class="s" style="color: #d14;"> '2011-12-01'</span></span>
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<pre style="margin: 0;">-<span id="LC811" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC812" class="line" lang="python"><span class="s" style="color: #d14;"> In some cases, the given float value can be truncated leading to unexpected</span></span>
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<pre style="margin: 0;">-<span id="LC813" class="line" lang="python"><span class="s" style="color: #d14;"> conversion between floating point and integer values. This function should</span></span>
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<pre style="margin: 0;">-<span id="LC814" class="line" lang="python"><span class="s" style="color: #d14;"> account for these errors by rounding months to the nearest integer.</span></span>
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<pre style="margin: 0;">-<span id="LC815" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC816" class="line" lang="python"><span class="s" style="color: #d14;"> >>> float_to_datestring(2011.9166666666665)</span></span>
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817
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<pre style="margin: 0;">-<span id="LC817" class="line" lang="python"><span class="s" style="color: #d14;"> '2011-12-01'</span></span>
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<pre style="margin: 0;">-<span id="LC818" class="line" lang="python"><span class="s" style="color: #d14;"> >>> float_to_datestring(2016.9609856262834)</span></span>
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<pre style="margin: 0;">-<span id="LC819" class="line" lang="python"><span class="s" style="color: #d14;"> '2016-12-01'</span></span>
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">float_to_datestring</span><span class="p">(</span><span class="n" style="color: #333;">numdate</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="python"> <span class="s" style="color: #d14;">"""convert a numeric decimal date to a python datetime object</span></span>
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="python"><span class="s" style="color: #d14;"> Note that this only works for AD dates since the range of datetime objects</span></span>
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="python"><span class="s" style="color: #d14;"> is restricted to year>1.</span></span>
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="python"><span class="s" style="color: #d14;"> Copied from treetime.utils</span></span>
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="python"><span class="s" style="color: #d14;"> Parameters</span></span>
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="python"><span class="s" style="color: #d14;"> ----------</span></span>
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="python"><span class="s" style="color: #d14;"> numdate : float</span></span>
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="python"><span class="s" style="color: #d14;"> numeric date as in 2018.23</span></span>
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="python"><span class="s" style="color: #d14;"> Returns</span></span>
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="python"><span class="s" style="color: #d14;"> -------</span></span>
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="python"><span class="s" style="color: #d14;"> datetime.datetime</span></span>
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="python"><span class="s" style="color: #d14;"> datetime object</span></span>
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<pre style="margin: 0;"> <span id="LC824" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC821" class="line" lang="python"> <span class="n" style="color: #333;">year</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">time</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC822" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC823" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># After accounting for the current year, extract the remainder and convert</span></span>
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<pre style="margin: 0;">-<span id="LC824" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># it to a month using the inverse of the logic used to create the floating</span></span>
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<pre style="margin: 0;">-<span id="LC825" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># point date. If the float date is sufficiently close to the end of the</span></span>
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<pre style="margin: 0;">-<span id="LC826" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># year, rounding can produce a 13th month.</span></span>
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<pre style="margin: 0;">-<span id="LC827" class="line" lang="python"> <span class="n" style="color: #333;">month</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">rint</span><span class="p">(((</span><span class="n" style="color: #333;">time</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">year</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">12</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="mi" style="color: #099;">12</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC829" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Floating point dates do not encode day information, so we always assume</span></span>
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<pre style="margin: 0;">-<span id="LC830" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># they refer to the start of a given month.</span></span>
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<pre style="margin: 0;">-<span id="LC831" class="line" lang="python"> <span class="n" style="color: #333;">day</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC832" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC833" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"%s-%02d-%02d"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">year</span><span class="p">,</span> <span class="n" style="color: #333;">month</span><span class="p">,</span> <span class="n" style="color: #333;">day</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">calendar</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">isleap</span></span>
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="python"> <span class="n" style="color: #333;">days_in_year</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">366</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">isleap</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">numdate</span><span class="p">))</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">365</span></span>
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># add a small number of the time elapsed in a year to avoid</span></span>
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># unexpected behavior for values 1/365, 2/365, etc</span></span>
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="python"> <span class="n" style="color: #333;">days_elapsed</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(((</span><span class="n" style="color: #333;">numdate</span><span class="o" style="font-weight: 600;">%</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mf" style="color: #099;">1e-10</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">days_in_year</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="python"> <span class="n" style="color: #333;">date</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">datetime</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">numdate</span><span class="p">),</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">timedelta</span><span class="p">(</span><span class="n" style="color: #333;">days</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">days_elapsed</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC831" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"%s-%02d-%02d"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">date</span><span class="p">.</span><span class="n" style="color: #333;">year</span><span class="p">,</span> <span class="n" style="color: #333;">date</span><span class="p">.</span><span class="n" style="color: #333;">month</span><span class="p">,</span> <span class="n" style="color: #333;">date</span><span class="p">.</span><span class="n" style="color: #333;">day</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC833" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC834" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">timestamp_to_float</span><span class="p">(</span><span class="n" style="color: #333;">time</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC835" class="line" lang="python"> <span class="s" style="color: #d14;">"""Convert a pandas timestamp to a floating point date.</span></span>
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="python"><span class="s" style="color: #d14;"> This is not entirely accurate as it doesn't account for months with different</span></span>
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="python"><span class="s" style="color: #d14;"> numbers of days, but should be close enough to be accurate for weekly pivots.</span></span>
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<pre style="margin: 0;"> <span id="LC838" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC839" class="line" lang="python"><span class="s" style="color: #d14;"> >>> import datetime</span></span>
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<pre style="margin: 0;"> <span id="LC840" class="line" lang="python"><span class="s" style="color: #d14;"> >>> time = datetime.date(2010, 10, 1)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -848,7 +848,7 @@ def timestamp_to_float(time):</td>
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<pre style="margin: 0;"> <span id="LC848" class="line" lang="python"><span class="s" style="color: #d14;"> >>> timestamp_to_float(datetime.date(2011, 12, 1)) == (2011.0 + 11.0 / 12)</span></span>
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<pre style="margin: 0;"> <span id="LC849" class="line" lang="python"><span class="s" style="color: #d14;"> True</span></span>
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<pre style="margin: 0;"> <span id="LC850" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC851" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">year</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">((</span><span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">month</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">12.0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC851" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">year</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">((</span><span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">month</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">12.0</span><span class="p">)</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="p"><span class="idiff">((</span></span><span class="n" style="color: #333;"><span class="idiff">time</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">day</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff">365.25</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC852" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC853" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC854" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">KdeFrequencies</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -858,8 +858,10 @@ class KdeFrequencies(object):</td>
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<pre style="margin: 0;"> <span id="LC858" class="line" lang="python"><span class="s" style="color: #d14;"> each clade in the tree.</span></span>
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<pre style="margin: 0;"> <span id="LC859" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC860" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">sigma_narrow</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">12.0</span><span class="p">,</span> <span class="n" style="color: #333;">sigma_wide</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">12.0</span><span class="p">,</span> <span class="n" style="color: #333;">proportion_wide</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.2</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC861" class="line" lang="python"> <span class="n" style="color: #333;">pivot_frequency</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">start_date</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">end_date</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">weights</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">weights_attribute</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC862" class="line" lang="python"> <span class="n" style="color: #333;">node_filters</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">max_date</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">include_internal_nodes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">censored</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="python"> <span class="n" style="color: #333;">pivot_frequency</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">start_date</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">end_date</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="python"> <span class="n" style="color: #333;">pivot_interval_units</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"months"</span><span class="p">,</span> <span class="n" style="color: #333;">weights</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">weights_attribute</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="python"> <span class="n" style="color: #333;">node_filters</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">max_date</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">include_internal_nodes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="python"> <span class="n" style="color: #333;">censored</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC865" class="line" lang="python"> <span class="s" style="color: #d14;">"""Define parameters for KDE-based frequency estimation.</span></span>
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<pre style="margin: 0;"> <span id="LC866" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC867" class="line" lang="python"><span class="s" style="color: #d14;"> Args:</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">@@ -869,6 +871,7 @@ class KdeFrequencies(object):</td>
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<pre style="margin: 0;"> <span id="LC871" class="line" lang="python"><span class="s" style="color: #d14;"> pivot_frequency (int): Number of months between pivots</span></span>
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<pre style="margin: 0;"> <span id="LC872" class="line" lang="python"><span class="s" style="color: #d14;"> start_date (float): start of the pivots interval</span></span>
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<pre style="margin: 0;"> <span id="LC873" class="line" lang="python"><span class="s" style="color: #d14;"> end_date (float): end of the pivots interval</span></span>
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="python"><span class="s" style="color: #d14;"> pivot_interval_units (str): Whether pivot intervals are measured in "months" or "weeks"</span></span>
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<pre style="margin: 0;"> <span id="LC875" class="line" lang="python"><span class="s" style="color: #d14;"> weights (dict): Numerical weights indexed by attribute values and applied to individual tips</span></span>
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<pre style="margin: 0;"> <span id="LC876" class="line" lang="python"><span class="s" style="color: #d14;"> weights_attribute (str): Attribute annotated on tips of a tree to use for weighting</span></span>
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<pre style="margin: 0;"> <span id="LC877" class="line" lang="python"><span class="s" style="color: #d14;"> node_filters (dict): Mapping of node attribute names (keys) to a list of valid values to keep</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">@@ -886,6 +889,7 @@ class KdeFrequencies(object):</td>
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<pre style="margin: 0;"> <span id="LC889" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pivot_frequency</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pivot_frequency</span></span>
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<pre style="margin: 0;"> <span id="LC890" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">start_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start_date</span></span>
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<pre style="margin: 0;"> <span id="LC891" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">end_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end_date</span></span>
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<pre style="margin: 0;">+<span id="LC892" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pivot_interval_units</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pivot_interval_units</span></span>
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<pre style="margin: 0;"> <span id="LC893" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">weights</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">weights</span></span>
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<pre style="margin: 0;"> <span id="LC894" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">weights_attribute</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">weights_attribute</span></span>
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<pre style="margin: 0;"> <span id="LC895" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">node_filters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">node_filters</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">@@ -907,6 +911,7 @@ class KdeFrequencies(object):</td>
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<pre style="margin: 0;"> <span id="LC911" class="line" lang="python"> <span class="s" style="color: #d14;">"pivot_frequency"</span><span class="p">:</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pivot_frequency</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC912" class="line" lang="python"> <span class="s" style="color: #d14;">"start_date"</span><span class="p">:</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">start_date</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC913" class="line" lang="python"> <span class="s" style="color: #d14;">"end_date"</span><span class="p">:</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">end_date</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC914" class="line" lang="python"> <span class="s" style="color: #d14;">"pivot_interval_units"</span><span class="p">:</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pivot_interval_units</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC915" class="line" lang="python"> <span class="s" style="color: #d14;">"weights"</span><span class="p">:</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">weights</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC916" class="line" lang="python"> <span class="s" style="color: #d14;">"weights_attribute"</span><span class="p">:</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">weights_attribute</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC917" class="line" lang="python"> <span class="s" style="color: #d14;">"max_date"</span><span class="p">:</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">max_date</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1121,7 +1126,8 @@ class TreeKdeFrequencies(KdeFrequencies):</td>
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<pre style="margin: 0;"> <span id="LC1126" class="line" lang="python"> <span class="n" style="color: #333;">observations</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC1127" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pivot_frequency</span><span class="p">,</span></span>
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1128
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<pre style="margin: 0;"> <span id="LC1128" class="line" lang="python"> <span class="n" style="color: #333;">start_date</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">start_date</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1124" class="line" lang="python"> <span class="n" style="color: #333;">end_date</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">end_date</span></span>
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<pre style="margin: 0;">+<span id="LC1129" class="line" lang="python"> <span class="n" style="color: #333;">end_date</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">end_date</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1130" class="line" lang="python"> <span class="n" style="color: #333;">pivot_interval_units</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pivot_interval_units</span></span>
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<pre style="margin: 0;"> <span id="LC1131" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1132" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC1133" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># If weights are defined, calculate frequencies for all tips by their</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">@@ -1208,7 +1214,8 @@ class AlignmentKdeFrequencies(KdeFrequencies):</td>
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<pre style="margin: 0;"> <span id="LC1214" class="line" lang="python"> <span class="n" style="color: #333;">observations</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC1215" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pivot_frequency</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC1216" class="line" lang="python"> <span class="n" style="color: #333;">start_date</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">start_date</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1211" class="line" lang="python"> <span class="n" style="color: #333;">end_date</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">end_date</span></span>
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<pre style="margin: 0;">+<span id="LC1217" class="line" lang="python"> <span class="n" style="color: #333;">end_date</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">end_date</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1218" class="line" lang="python"> <span class="n" style="color: #333;">pivot_interval_units</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pivot_interval_units</span></span>
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<pre style="margin: 0;"> <span id="LC1219" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1220" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC1221" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Pair alignment sequence indices with observation dates.</span></span>
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<a href="https://salsa.debian.org/med-team/augur/-/compare/bb58b81e4f3a2a198c5ddd2fa4709917a654e7c6...d80b50c3679d73a836b9dcd304426a3edf8c0238#f4919502f59714aa98c2d5c8a78855a31c295c88"><strong>codecov.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">comment</span><span class="pi">:</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;"># Only post a codecov comment if coverage changes.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="na" style="color: #008080;">require_changes</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"><span class="na" style="color: #008080;">coverage</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">status</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Disable GitHub checks for code coverage that make otherwise valid builds fail.</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">project</span><span class="pi">:</span> <span class="s" style="color: #d14;">off</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">patch</span><span class="pi">:</span> <span class="s" style="color: #d14;">off</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"><span class="na" style="color: #008080;">github_checks</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Disable inline annotations of code coverage in pull requests.</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"> <span class="na" style="color: #008080;">annotations</span><span class="pi">:</span> <span class="no" style="color: #008080;">false</span></span></pre>
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<a href="https://salsa.debian.org/med-team/augur/-/compare/bb58b81e4f3a2a198c5ddd2fa4709917a654e7c6...d80b50c3679d73a836b9dcd304426a3edf8c0238#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">augur (10.3.0-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Nilesh Patra <npatra974@gmail.com> Mon, 18 Jan 2021 19:35:13 +0530</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">augur (10.2.0-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * New upstream version</span>
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<a href="https://salsa.debian.org/med-team/augur/-/compare/bb58b81e4f3a2a198c5ddd2fa4709917a654e7c6...d80b50c3679d73a836b9dcd304426a3edf8c0238#f0eca249c61d71d1d8e29cf4012012da7dadbad8"><strong>paper/paper.bib</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">@@ -40,7 +40,7 @@</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="bibtex"> <span class="na" style="color: #008080;">number</span> <span class="p">=</span> <span class="s" style="color: #d14;">{32}</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="bibtex"> <span class="na" style="color: #008080;">urldate</span> <span class="p">=</span> <span class="s" style="color: #d14;">{2020-08-26}</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="bibtex"> <span class="na" style="color: #008080;">journal</span> <span class="p">=</span> <span class="s" style="color: #d14;">{Eurosurveillance}</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="bibtex"> <span class="na" style="color: #008080;">author</span> <span class="p">=</span> <span class="s" style="color: #d14;">{Alm, Erik and Broberg, Eeva K. and Connor, Thomas and Hodcroft, Emma B. and Komissarov, Andrey B. and Maurer-Stroh, Sebastian and Melidou, Angeliki and Neher, Richard A. and O’Toole, Áine and Pereyaslov, Dmitriy and <span class="idiff left right">Group, The WHO European Region sequencing laboratories {and} GISAID EpiCoV</span>}</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="bibtex"> <span class="na" style="color: #008080;">author</span> <span class="p">=</span> <span class="s" style="color: #d14;">{Alm, Erik and Broberg, Eeva K. and Connor, Thomas and Hodcroft, Emma B. and Komissarov, Andrey B. and Maurer-Stroh, Sebastian and Melidou, Angeliki and Neher, Richard A. and O’Toole, Áine and Pereyaslov, Dmitriy and <span class="idiff left right">The WHO European Region Sequencing Laboratories {and} GISAID EpiCoV Group,</span>}</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="bibtex"> <span class="na" style="color: #008080;">month</span> <span class="p">=</span> <span class="nv" style="color: #008080;">aug</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="bibtex"> <span class="na" style="color: #008080;">year</span> <span class="p">=</span> <span class="s" style="color: #d14;">{2020}</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="bibtex"> <span class="na" style="color: #008080;">note</span> <span class="p">=</span> <span class="s" style="color: #d14;">{Publisher: European Centre for Disease Prevention and Control}</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/augur/-/compare/bb58b81e4f3a2a198c5ddd2fa4709917a654e7c6...d80b50c3679d73a836b9dcd304426a3edf8c0238#30cbbea27bb1efbfe6e3017b073e19e61ebced6f"><strong>paper/paper.md</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">@@ -17,34 +17,39 @@ authors:</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Thomas R. Sibley</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"> <span class="na" style="color: #008080;">affiliation</span><span class="pi">:</span> <span class="m" style="color: #099;">2</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"> <span class="na" style="color: #008080;">orcid</span><span class="pi">:</span> <span class="s" style="color: #d14;">0000-0001-5269-2297</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Jover Lee</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"> <span class="na" style="color: #008080;">affiliation</span><span class="pi">:</span> <span class="m" style="color: #099;">2</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"> <span class="na" style="color: #008080;">orcid</span><span class="pi">:</span> <span class="s" style="color: #d14;">0000-0002-2391-0512</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Kairsten Fay</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"> <span class="na" style="color: #008080;">affiliation</span><span class="pi">:</span> <span class="m" style="color: #099;">2</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"> <span class="na" style="color: #008080;">orcid</span><span class="pi">:</span> <span class="s" style="color: #d14;">0000-0002-6529-9205</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Misja Ilcisin</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"> <span class="na" style="color: #008080;">affiliation</span><span class="pi">:</span> <span class="m" style="color: #099;">2</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown"> <span class="na" style="color: #008080;">orcid</span><span class="pi">:</span> <span class="s" style="color: #d14;">0000-0002-1468-7697</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="markdown"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Elias Harkins</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown"> <span class="na" style="color: #008080;">affiliation</span><span class="pi">:</span> <span class="m" style="color: #099;">2</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown"> <span class="na" style="color: #008080;">orcid</span><span class="pi">:</span> <span class="s" style="color: #d14;">0000-0001-6525-9134</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="markdown"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Augur Contributors</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="markdown"> <span class="na" style="color: #008080;">affiliation</span><span class="pi">:</span> <span class="m" style="color: #099;">3</span></span>
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25
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Trevor Bedford</span></span>
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26
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown"> <span class="na" style="color: #008080;">affiliation</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">1,</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">2"</span></span>
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27
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34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="markdown"> <span class="na" style="color: #008080;">orcid</span><span class="pi">:</span> <span class="s" style="color: #d14;">0000-0002-4039-5794</span></span>
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28
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<td class="diff-line-num new_line" data-linenumber="35" 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">
35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="markdown"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Richard A. Neher</span></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="markdown"> <span class="na" style="color: #008080;">affiliation</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;"><span class="idiff left">4,</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff right">5</span>"</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown"> <span class="na" style="color: #008080;">affiliation</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;"><span class="idiff left">3,</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff right">4</span>"</span></span>
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30
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="markdown"> <span class="na" style="color: #008080;">orcid</span><span class="pi">:</span> <span class="s" style="color: #d14;">0000-0003-2525-1407</span></span>
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31
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="markdown"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Emma B. Hodcroft</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="markdown"> <span class="na" style="color: #008080;">affiliation</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;"><span class="idiff left">4,</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">5,</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff right">6</span>"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="39" 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">
39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown"> <span class="na" style="color: #008080;">affiliation</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;"><span class="idiff left">3,</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">4,</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff right">5</span>"</span></span>
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33
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40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="markdown"> <span class="na" style="color: #008080;">orcid</span><span class="pi">:</span> <span class="s" style="color: #d14;">0000-0002-0078-2212</span></span>
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34
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="markdown"><span class="na" style="color: #008080;">affiliations</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="markdown"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Molecular and Cell Biology Program, University of Washington, Seattle, WA, USA</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Molecular and Cell<span class="idiff left right">ular</span> Biology Program, University of Washington, Seattle, WA, USA</span></span>
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36
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="markdown"> <span class="na" style="color: #008080;">index</span><span class="pi">:</span> <span class="m" style="color: #099;">1</span></span>
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37
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44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="markdown"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA</span></span>
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38
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45
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="markdown"> <span class="na" style="color: #008080;">index</span><span class="pi">:</span> <span class="m" style="color: #099;">2</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="markdown"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Open Source Software community</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="markdown"> <span class="na" style="color: #008080;">index</span><span class="pi">:</span> <span class="m" style="color: #099;">3</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="markdown"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Biozentrum, University of Basel, Basel, Switzerland</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="markdown"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Swiss Institute of Bioinformatics, Basel, Switzerland</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="markdown"> <span class="na" style="color: #008080;">index</span><span class="pi">:</span> <span class="m" style="color: #099;"><span class="idiff left right">5</span></span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="markdown"> <span class="na" style="color: #008080;">index</span><span class="pi">:</span> <span class="m" style="color: #099;"><span class="idiff left right">4</span></span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="markdown"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="markdown"> <span class="na" style="color: #008080;">index</span><span class="pi">:</span> <span class="m" style="color: #099;"><span class="idiff left right">6</span></span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="markdown"><span class="na" style="color: #008080;">date</span><span class="pi">:</span> <span class="s" style="color: #d14;">5 <span class="idiff left">November </span></span><span class="m" style="color: #099;"><span class="idiff right">2020</span></span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="markdown"> <span class="na" style="color: #008080;">index</span><span class="pi">:</span> <span class="m" style="color: #099;"><span class="idiff left right">5</span></span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown"><span class="na" style="color: #008080;">date</span><span class="pi">:</span> <span class="s" style="color: #d14;">5 <span class="idiff left">January </span></span><span class="m" style="color: #099;"><span class="idiff right">2021</span></span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="markdown"><span class="na" style="color: #008080;">bibliography</span><span class="pi">:</span> <span class="s" style="color: #d14;">paper.bib</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="markdown"><span class="nn" style="color: #555;">---</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="markdown"></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">@@ -102,6 +107,7 @@ Augur can be installed from PyPI ([nextstrain-augur](https://pypi.org/project/ne</td>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="markdown"><span class="gh" style="color: #999;"># Acknowledgments</span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="markdown">Thank you to all of <span class="p">[</span><span class="nv" style="color: #008080;">the open source community members who have contributed to Augur</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/graphs/contributors</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="markdown">Specifically, we thank Eric Danielson, Eddie Lebow, Barney Potter, Ryan Grout, Sai Kiran Kollapudi, Mingye Wang, Carol Willing, Louise Moncla, Thomas Caswell, Sidney Bell, Terry Jones, Christian Clauss, Julien Bordellier, Gytis Dudas, Cameron Devine, Samuel Zhang, Akshay Subramanian, Christopher Tomkins-Tinch, Danielle Kain, Pierre Barrat-Charlaix, Rhys Kidd, Chris Woszczak, Tony Tung, Mathias Walter, and Zachary Sailer.</span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="markdown">Thank you to Dan Fornika from BCCDC Public Health Laboratory for creating the first conda recipe for Augur in Bioconda.</span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="markdown">JHu is a Graduate Research Fellow and is supported by the NIH grant NIAID F31AI140714.</span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="markdown">TB is a Pew Biomedical Scholar.</span>
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<a href="https://salsa.debian.org/med-team/augur/-/compare/bb58b81e4f3a2a198c5ddd2fa4709917a654e7c6...d80b50c3679d73a836b9dcd304426a3edf8c0238#225cc818de93cbf949f751310621362b4d1d00f3"><strong>scripts/identify_emerging_clades.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">@@ -230,9 +230,15 @@ if __name__ == '__main__':</td>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">row_df</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">distinct_subclades</span><span class="p">.</span><span class="n" style="color: #333;">iterrows</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="python"> <span class="n" style="color: #333;">parent_clade</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">row_df</span><span class="p">[</span><span class="s" style="color: #d14;">"parent_clade"</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python"> <span class="n" style="color: #333;">mutations</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">row_df</span><span class="p">[</span><span class="s" style="color: #d14;">"mutations"</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="python"> <span class="sa">f</span><span class="s" style="color: #d14;">"<li><a target='_new' href='</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">nextstrain_url</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">?c=gt-</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">mutation_region</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">_</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">mutations</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">&p=grid'></span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">parent_clade</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">: </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">mutations</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"></a></li>"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC235" 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;">oh</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">filter_attribute</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"> <span class="sa">f</span><span class="s" style="color: #d14;">"<li><a target='_new' href='</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">nextstrain_url</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">?c=gt-</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">mutation_region</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">_</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">mutations</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">&f_</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">filter_attribute</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">=</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">filter_value</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">&transmissions=hide&p=grid'></span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">parent_clade</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">: </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">mutations</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"></a></li>"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC236" 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;">oh</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"> <span class="sa">f</span><span class="s" style="color: #d14;">"<li><a target='_new' href='</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">nextstrain_url</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">?c=gt-</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">mutation_region</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">_</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">mutations</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">&transmissions=hide&p=grid'></span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">parent_clade</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">: </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">mutations</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"></a></li>"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC241" 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;">oh</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"</ul>"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">oh</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/augur/-/compare/bb58b81e4f3a2a198c5ddd2fa4709917a654e7c6...d80b50c3679d73a836b9dcd304426a3edf8c0238#081890624636fe474b1df86be458d3200baa3001"><strong>scripts/verify_meta_json.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">@@ -39,7 +39,7 @@ if __name__=="__main__":</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"author_info"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">data</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">verify_author_info</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"author_info"</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: author_info does not exist. This build needs to be updated and will soon be incompat<span class="idiff left right">a</span>ble with auspice."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: author_info does not exist. This build needs to be updated and will soon be incompat<span class="idiff left right">i</span>ble with auspice."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># set_trace()</span></span></pre>
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<a href="https://salsa.debian.org/med-team/augur/-/compare/bb58b81e4f3a2a198c5ddd2fa4709917a654e7c6...d80b50c3679d73a836b9dcd304426a3edf8c0238#9db30a8891be7b63bf8fe1f26d0ffb472e77c96b"><strong>tests/test_frequencies.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">@@ -66,19 +66,42 @@ def test_get_pivots_from_tree_only(tree):</td>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_get_pivots_from_start_and_end_date</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"><span class="s" style="color: #d14;"> Test pivot calculation from a given start and end date instead of a given tree.</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"><span class="s" style="color: #d14;"> Test pivot calculation from a given start and end date instead of a given tree</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"><span class="s" style="color: #d14;"> First pivot is the first day of the month immediately following start_date</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"><span class="s" style="color: #d14;"> Last pivot is the first day of the month immediately preceding end_date</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"><span class="s" style="color: #d14;"> Current logic converts numeric date 2015.5 to 2015-07-02, hence using 2015.49</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">pivot_frequency</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">3</span></span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">start_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">2015.<span class="idiff left right">5</span></span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">pivot_frequency</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">1</span></span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">start_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">2015.<span class="idiff left right">49</span></span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">end_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">2018.5</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">observations</span> <span class="o" style="font-weight: 600;">=</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;">pivots</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_pivots</span><span class="p">(</span><span class="n" style="color: #333;">observations</span><span class="p">,</span> <span class="n" style="color: #333;">pivot_frequency</span><span class="p">,</span> <span class="n" style="color: #333;">start_date</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">start_date</span><span class="p">,</span> <span class="n" style="color: #333;">end_date</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">end_date</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">pivots</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">ndarray</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;"><span class="idiff left">pivots</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</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">pivots</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]</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">pivot_frequency</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff right">12.0</span></span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">pivots</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left right">start_date</span></span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">pivots</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="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left right">end_date</span></span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;"><span class="idiff left">np</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">round</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">12</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">pivots</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</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">pivots</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">])</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</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 right">pivot_frequency</span></span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">pivots</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mf" style="color: #099;"><span class="idiff left right">2015.5</span></span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">pivots</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="o" style="font-weight: 600;">==</span> <span class="mf" style="color: #099;"><span class="idiff left right">2018.5</span></span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">pivots</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="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">end_date</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">pivot_frequency</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_get_pivots_by_months</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="s" style="color: #d14;">"""Get pivots where intervals are defined by months.</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">pivots</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_pivots</span><span class="p">(</span><span class="n" style="color: #333;">observations</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span> <span class="n" style="color: #333;">pivot_interval</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">start_date</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">2015.0</span><span class="p">,</span> <span class="n" style="color: #333;">end_date</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">2016.0</span><span class="p">,</span> <span class="n" style="color: #333;">pivot_interval_units</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"months"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Pivots should include all 12 months of the year plus the month represented</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># by the end date, since the pandas month interval uses "month starts". See</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># pandas date offsets documentation for more details:</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># https://pandas.pydata.org/pandas-docs/stable/user_guide/timeseries.html#offset-aliases</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">pivots</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">13</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_get_pivots_by_weeks</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="s" style="color: #d14;">"""Get pivots where intervals are defined as weeks instead of months.</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">pivots</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_pivots</span><span class="p">(</span><span class="n" style="color: #333;">observations</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span> <span class="n" style="color: #333;">pivot_interval</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">start_date</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">2015.0</span><span class="p">,</span> <span class="n" style="color: #333;">end_date</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">2016.0</span><span class="p">,</span> <span class="n" style="color: #333;">pivot_interval_units</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"weeks"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">pivots</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">52</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_get_pivots_by_invalid_unit</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="n" style="color: #333;">match</span><span class="o" style="font-weight: 600;">=</span><span class="sa">r</span><span class="s" style="color: #d14;">".*invalid_unit.*is not supported.*"</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">pivots</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_pivots</span><span class="p">(</span><span class="n" style="color: #333;">observations</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span> <span class="n" style="color: #333;">pivot_interval</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">start_date</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">2015.0</span><span class="p">,</span> <span class="n" style="color: #333;">end_date</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">2016.0</span><span class="p">,</span> <span class="n" style="color: #333;">pivot_interval_units</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"invalid_unit"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC105" 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="LC106" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Test KDE frequency estimation for trees</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="110" 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">@@ -110,7 +133,7 @@ class TestTreeKdeFrequencies(object):</td>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">frequencies</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kde_frequencies</span><span class="p">.</span><span class="n" style="color: #333;">estimate</span><span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">kde_frequencies</span><span class="p">,</span> <span class="s" style="color: #d14;">"pivots"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">kde_frequencies</span><span class="p">.</span><span class="n" style="color: #333;">pivots</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left right">start_date</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="136" 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="LC136" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">kde_frequencies</span><span class="p">.</span><span class="n" style="color: #333;">pivots</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mf" style="color: #099;"><span class="idiff left right">2015.5833</span></span></span>
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114
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">kde_frequencies</span><span class="p">,</span> <span class="s" style="color: #d14;">"frequencies"</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="115" 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">
115
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">frequencies</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">())[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">shape</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kde_frequencies</span><span class="p">.</span><span class="n" style="color: #333;">pivots</span><span class="p">.</span><span class="n" style="color: #333;">shape</span></span>
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116
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"></span>
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