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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/python-treetime">Debian Med / python-treetime</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-treetime/-/commit/1cd12a8d3f5353000dfe384f7f3a9ee984632181">1cd12a8d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-24T20:04:39+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.8.5</pre>
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<h4>22 changed files:</h4>
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<a href="#81ccd5c4e1f93eb3ab80c73b5532455bf4f82fe9">
.readthedocs.yml
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<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
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Makefile
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<a href="#4c23f3e77a0ef00cf8da63e8e50eef5197724f75">
changelog.md
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<a href="#22e7dfa107eaaf19f2ef7a964c85ce083c872c2e">
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docs/.dockerignore
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docs/Dockerfile
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<a href="#3f4c1daa84110ac0a1cf43167520d6d8737bc806">
docs/Makefile
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<li class="file-stats">
<a href="#ce9ae6f5204729fc4b54b97f8f3e17ffb128428c">
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docs/environment.yml
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docs/requirements.txt
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<a href="#aded7756cdea7c289134466a0d54da4f26d43abb">
docs/source/conf.py
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<a href="#41b2a620e5c90c4e7905692c175e421576881468">
docs/source/gtr.rst
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<a href="#d1ffd6c1cec13f9cfe41f6f4b27a4ad96b846682">
docs/source/treeanc.rst
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<a href="#6816bffea1e0135cbec8177205ac40891362f1a8">
docs/source/tutorials/ancestral.rst
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<a href="#55ab4c17b34670942fdad8399ccd1d321a97e95d">
docs/source/tutorials/clock.rst
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<a href="#1bd68f7b8559b0dbf5e245571cbcdc74b14fac16">
docs/source/tutorials/homoplasy.rst
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<a href="#7d1462bd4008d5703b52469948efeb2fc5640e04">
docs/source/tutorials/mugration.rst
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<a href="#9e4b18dd4973209585cacb447ee505ec303baf36">
docs/source/tutorials/timetree.rst
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<a href="#716e6f6c16580800d13452615e2c01668aacc288">
treetime/__init__.py
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<li class="file-stats">
<a href="#82a08428349f48dbbab4c8ccac6320f52b4c7a7b">
treetime/seq_utils.py
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<a href="#5233e2843fb208ffac5520b8b6d010090372931b">
treetime/sequence_data.py
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<a href="#a2e471fd9fc09543e8fd92727442680e1b76576b">
treetime/treeanc.py
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<li class="file-stats">
<a href="#0994bbb65b28bed19201420b96136d5e9f676859">
treetime/treetime.py
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<h4>Changes:</h4>
<li id="81ccd5c4e1f93eb3ab80c73b5532455bf4f82fe9">
<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/1cd12a8d3f5353000dfe384f7f3a9ee984632181#81ccd5c4e1f93eb3ab80c73b5532455bf4f82fe9"><strong>.readthedocs.yml</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># .readthedocs.yml</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;"># Read the Docs configuration file</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># See https://docs.readthedocs.io/en/stable/config-file/v2.html for details</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="c1" style="color: #998; font-style: italic;"># Required</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="nn" style="color: #555;">---</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="m" style="color: #099;">2</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># Build documentation in the docs/ directory with Sphinx</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"><span class="na" style="color: #008080;">conda</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"> <span class="na" style="color: #008080;">environment</span><span class="pi">:</span> <span class="s" style="color: #d14;">docs/environment.yml</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="yaml"><span class="na" style="color: #008080;">sphinx</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">configuration</span><span class="pi">:</span> <span class="s" style="color: #d14;">docs/source/conf.py</span></span></pre>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml"></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;"># Build documentation with MkDocs</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#mkdocs:</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># configuration: mkdocs.yml</span></span>
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<td class="old_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># Optionally build your docs in additional formats such as PDF and ePub</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="yaml"><span class="na" style="color: #008080;">formats</span><span class="pi">:</span> <span class="s" style="color: #d14;">all</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># Optionally set the version of Python and requirements required to build your docs</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="yaml"><span class="na" style="color: #008080;">python</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="yaml"> <span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="m" style="color: #099;">3.7</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="yaml"> <span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">requirements</span><span class="pi">:</span> <span class="s" style="color: #d14;">docs/requirements.txt</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">method</span><span class="pi">:</span> <span class="s" style="color: #d14;">pip</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="yaml"> <span class="na" style="color: #008080;">path</span><span class="pi">:</span> <span class="s" style="color: #d14;">.</span></span></pre>
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<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/1cd12a8d3f5353000dfe384f7f3a9ee984632181#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="make"><span class="k" style="font-weight: 600;">-include</span><span class="sx" style="color: #d14;"> .env.example</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="make"><span class="k" style="font-weight: 600;">-include</span><span class="sx" style="color: #d14;"> .env</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: #008080;">UID</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> <span class="nb" style="color: #0086b3;">id</span> <span class="nt" style="color: #000080;">-u</span><span class="nf" style="color: #900; font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: #008080;">GID</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> <span class="nb" style="color: #0086b3;">id</span> <span class="nt" style="color: #000080;">-g</span><span class="nf" style="color: #900; font-weight: 600;">)</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: #008080;">DOCS_CONTAINER_NAME</span><span class="o" style="font-weight: 600;">=</span>treetime-docs</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="make"><span class="nv" style="color: #008080;">SHELL</span> <span class="o" style="font-weight: 600;">:=</span> bash</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="make"><span class="nl">.ONESHELL</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">docs docker-docs</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="make"><span class="nl">docs</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;">$(MAKE)</span> <span class="nt" style="color: #000080;">--no-print-directory</span> <span class="nt" style="color: #000080;">-C</span> docs/ html</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="make"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="make"><span class="nl">docs-clean</span><span class="o" style="font-weight: 600;">:</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> docs/build</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="make"></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="make"><span class="nl">docker-docs</span><span class="o" style="font-weight: 600;">:</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="make"> <span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-euox</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="make"></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">docker</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">build</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-t</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$${DOCS_CONTAINER_NAME}</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="make"> <span class="nv" style="color: #008080;">--network</span><span class="o" style="font-weight: 600;">=</span>host <span class="se" style="color: #d14;">\</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="make"> <span class="nt" style="color: #000080;">--build-arg</span> <span class="nv" style="color: #008080;">UID</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> <span class="nb" style="color: #0086b3;">id</span> <span class="nt" style="color: #000080;">-u</span><span class="nf" style="color: #900; font-weight: 600;">)</span> <span class="se" style="color: #d14;">\</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="make"> <span class="nt" style="color: #000080;">--build-arg</span> <span class="nv" style="color: #008080;">GID</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> <span class="nb" style="color: #0086b3;">id</span> <span class="nt" style="color: #000080;">-g</span><span class="nf" style="color: #900; font-weight: 600;">)</span> <span class="se" style="color: #d14;">\</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="make"> docs/</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="make"></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">docker</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">run</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-it</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">--rm</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="make"> <span class="nv" style="color: #008080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="nv" style="color: #008080;">${DOCS_CONTAINER_NAME}</span>-<span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> <span class="nb" style="color: #0086b3;">date</span> +%s<span class="nf" style="color: #900; font-weight: 600;">)</span> <span class="se" style="color: #d14;">\</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="make"> <span class="nt" style="color: #000080;">--init</span> <span class="se" style="color: #d14;">\</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="make"> <span class="nt" style="color: #000080;">--user</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> <span class="nb" style="color: #0086b3;">id</span> <span class="nt" style="color: #000080;">-u</span><span class="nf" style="color: #900; font-weight: 600;">)</span>:<span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> <span class="nb" style="color: #0086b3;">id</span> <span class="nt" style="color: #000080;">-g</span><span class="nf" style="color: #900; font-weight: 600;">)</span> <span class="se" style="color: #d14;">\</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="make"> <span class="nt" style="color: #000080;">--volume</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> <span class="nb" style="color: #0086b3;">pwd</span><span class="nf" style="color: #900; font-weight: 600;">)</span>:/home/user/src <span class="se" style="color: #d14;">\</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="make"> <span class="nt" style="color: #000080;">--publish</span><span class="o" style="font-weight: 600;">=</span>8000:8000 <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="make"> <span class="nt" style="color: #000080;">--workdir</span><span class="o" style="font-weight: 600;">=</span>/home/user/src <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="make"> <span class="nt" style="color: #000080;">--env</span> <span class="s1" style="color: #d14;">'TERM=xterm-256colors'</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="nv" style="color: #008080;">${DOCS_CONTAINER_NAME}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/1cd12a8d3f5353000dfe384f7f3a9ee984632181#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">@@ -47,7 +47,7 @@ Have a look at our repository with [example data](https://github.com/neherlab/tr</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Installation and prerequisites</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="markdown">TreeTime is compatible with Python 3.<span class="idiff left">5</span> upwards and is tested on <span class="idiff right">3.5, </span>3.6, 3.7, and 3.8. It depends on several Python libraries:</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown">TreeTime is compatible with Python 3.<span class="idiff left right">6</span> upwards and is tested on 3.6, 3.7, and 3.8. It depends on several Python libraries:</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="markdown"><span class="p">*</span> numpy, scipy, pandas: for all kind of mathematical operations as matrix</span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="markdown"> operations, numerical integration, interpolation, minimization, etc.</span>
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<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/1cd12a8d3f5353000dfe384f7f3a9ee984632181#4c23f3e77a0ef00cf8da63e8e50eef5197724f75"><strong>changelog.md</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># 0.8.5</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"><span class="p"> *</span> bug fixes related to edge cases were sequences consist only of missing data</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="p"> *</span> bug fix when the CLI command <span class="sb" style="color: #d14;">`treetime`</span> is run without alignment</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="p"> *</span> more robust behavior when parsing biopython alignments (id vs name of sequence records)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p"> *</span> drop python 3.5 support</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># 0.8.4 -- re-release of 0.8.3.1</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># 0.8.3.1 -- bug fix related to Bio.Seq.Seq now bytearray</span></span>
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<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/1cd12a8d3f5353000dfe384f7f3a9ee984632181#22e7dfa107eaaf19f2ef7a964c85ce083c872c2e"><strong>docs/.dockerignore</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">*</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">!environment.yml</span></pre>
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<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/1cd12a8d3f5353000dfe384f7f3a9ee984632181#5c847cb469b962520e9fff34906a6edc6bf0852c"><strong>docs/Dockerfile</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="docker"><span class="k" style="font-weight: 600;">FROM</span><span class="s" style="color: #d14;"> continuumio/miniconda3:4.10.3</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="docker"><span class="k" style="font-weight: 600;">ARG</span><span class="s" style="color: #d14;"> DEBIAN_FRONTEND=noninteractive</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="docker"><span class="k" style="font-weight: 600;">ARG</span><span class="s" style="color: #d14;"> USER=user</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="docker"><span class="k" style="font-weight: 600;">ARG</span><span class="s" style="color: #d14;"> GROUP=user</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="docker"><span class="k" style="font-weight: 600;">ARG</span><span class="s" style="color: #d14;"> UID</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="docker"><span class="k" style="font-weight: 600;">ARG</span><span class="s" style="color: #d14;"> GID</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="docker"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="docker"><span class="k" style="font-weight: 600;">ENV</span><span class="s" style="color: #d14;"> TERM="xterm-256color"</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="docker"><span class="k" style="font-weight: 600;">ENV</span><span class="s" style="color: #d14;"> HOME="/home/user"</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="docker"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-x</span> <span class="se" style="color: #d14;">\</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">HOME</span><span class="k" style="font-weight: 600;">}</span>/src <span class="se" style="color: #d14;">\</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="docker"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span>getent group <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">GID</span><span class="k" style="font-weight: 600;">}</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span> <span class="se" style="color: #d14;">\</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="docker"> addgroup <span class="nt" style="color: #000080;">--system</span> <span class="nt" style="color: #000080;">--gid</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">GID</span><span class="k" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">GROUP</span><span class="k" style="font-weight: 600;">}</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="docker"> <span class="k" style="font-weight: 600;">else</span> <span class="se" style="color: #d14;">\</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="docker"> groupmod <span class="nt" style="color: #000080;">-n</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">GROUP</span><span class="k" style="font-weight: 600;">}</span> <span class="si" style="color: #d14;">$(</span>getent group <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">GID</span><span class="k" style="font-weight: 600;">}</span> | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-d</span>: <span class="nt" style="color: #000080;">-f1</span><span class="si" style="color: #d14;">)</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="docker"> <span class="k" style="font-weight: 600;">fi</span> <span class="se" style="color: #d14;">\</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="docker"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span>getent passwd <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">UID</span><span class="k" style="font-weight: 600;">}</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="docker"> useradd <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="docker"> <span class="nt" style="color: #000080;">--system</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="docker"> <span class="nt" style="color: #000080;">--create-home</span> <span class="nt" style="color: #000080;">--home-dir</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">HOME</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="docker"> <span class="nt" style="color: #000080;">--shell</span> /bin/bash <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="docker"> <span class="nt" style="color: #000080;">--gid</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">GROUP</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="docker"> <span class="nt" style="color: #000080;">--groups</span> <span class="nb" style="color: #0086b3;">sudo</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="docker"> <span class="nt" style="color: #000080;">--uid</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">UID</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="docker"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">USER</span><span class="k" style="font-weight: 600;">}</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="docker"> <span class="k" style="font-weight: 600;">fi</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">touch</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">HOME</span><span class="k" style="font-weight: 600;">}</span>/.hushlogin</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-x</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">chown</span> <span class="nt" style="color: #000080;">-R</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">USER</span><span class="k" style="font-weight: 600;">}</span>:<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">GROUP</span><span class="k" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">HOME</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="docker"><span class="k" style="font-weight: 600;">COPY</span><span class="s" style="color: #d14;"> environment.yml ${HOME}/src/</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="docker"><span class="k" style="font-weight: 600;">WORKDIR</span><span class="s" style="color: #d14;"> ${HOME}/src</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-x</span> <span class="se" style="color: #d14;">\</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> conda <span class="nb" style="color: #0086b3;">env </span>create docs</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="docker"><span class="k" style="font-weight: 600;">USER</span><span class="s" style="color: #d14;"> ${USER}</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-x</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> conda init bash <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"conda activate docs"</span> <span class="o" style="font-weight: 600;">>></span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">HOME</span><span class="k" style="font-weight: 600;">}</span>/.bashrc</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="docker"><span class="k" style="font-weight: 600;">CMD</span><span class="s" style="color: #d14;"> bash -c "set -x \</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="docker"> && source ${HOME}/.bashrc \</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="docker"> && cd ${HOME}/src/docs \</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="docker"> && rm -rf build \</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="docker"> && make autobuild \</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="docker"> "</span></pre>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Makefile for Sphinx documentation</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># M<span class="idiff left right">inimal m</span>akefile for Sphinx documentation</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># You can set these variables from the command line.</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="make"><span class="nv" style="color: #008080;">SPHINXOPTS</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="make"><span class="nv" style="color: #008080;">SPHINXBUILD</span> <span class="o" style="font-weight: 600;">=</span> sphinx-build</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="make"><span class="nv" style="color: #008080;">PAPER</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># You can set these variables from the command line, and also</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># from the environment for the first two.</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="make"><span class="nv" style="color: #008080;">SPHINXOPTS</span> <span class="o" style="font-weight: 600;">?=</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="make"><span class="nv" style="color: #008080;">SPHINXBUILD</span> <span class="o" style="font-weight: 600;">?=</span> sphinx-build</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="make"><span class="nv" style="color: #008080;">SOURCEDIR</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">source</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="make"><span class="nv" style="color: #008080;">BUILDDIR</span> <span class="o" style="font-weight: 600;">=</span> build</span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># User-friendly check for sphinx-build</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="make"> <span class="nl">$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don\'t have Sphinx installed, grab it from http</span><span class="o" style="font-weight: 600;">:</span><span class="nf" style="color: #900; font-weight: 600;">//sphinx-doc.org/)</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="make"></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Internal variables.</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="make"><span class="nv" style="color: #008080;">PAPEROPT_a4</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-D</span> <span class="nv" style="color: #008080;">latex_paper_size</span><span class="o" style="font-weight: 600;">=</span>a4</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="make"><span class="nv" style="color: #008080;">PAPEROPT_letter</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-D</span> <span class="nv" style="color: #008080;">latex_paper_size</span><span class="o" style="font-weight: 600;">=</span>letter</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="make"><span class="nv" style="color: #008080;">ALLSPHINXOPTS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-d</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/doctrees <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>PAPEROPT_<span class="nv" style="color: #008080;">$(PAPER)</span><span class="o" style="font-weight: 600;">)</span> <span class="nv" style="color: #008080;">$(SPHINXOPTS)</span> <span class="nb" style="color: #0086b3;">source</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># the i18n builder cannot share the environment and doctrees with the others</span></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="make"><span class="nv" style="color: #008080;">I18NSPHINXOPTS</span> <span class="o" style="font-weight: 600;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>PAPEROPT_<span class="nv" style="color: #008080;">$(PAPER)</span><span class="o" style="font-weight: 600;">)</span> <span class="nv" style="color: #008080;">$(SPHINXOPTS)</span> <span class="nb" style="color: #0086b3;">source</span></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="make"></span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">help</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Put it first so that "make" without argument is like "make help".</span></span>
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23
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="make"><span class="nl">help</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="24" 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">
24
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Please use </span><span class="se" style="color: #d14;">\`</span><span class="s2" style="color: #d14;">make <target>' where <target> is one of"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="25" 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">
25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" html to make standalone HTML files"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="26" 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">
26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" dirhtml to make HTML files named index.html in directories"</span></span>
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<td class="old_line diff-line-num 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">
27
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" singlehtml to make a single large HTML file"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="28" 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">
28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" pickle to make pickle files"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="29" 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">
29
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" json to make JSON files"</span></span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" htmlhelp to make HTML files and a HTML help project"</span></span>
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31
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" qthelp to make HTML files and a qthelp project"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="32" 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">
32
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" applehelp to make an Apple Help Book"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="33" 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">
33
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" devhelp to make HTML files and a Devhelp project"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="34" 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">
34
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" epub to make an epub"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="35" 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">
35
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" epub3 to make an epub3"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="36" 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">
36
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="37" 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">
37
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" latexpdf to make LaTeX files and run them through pdflatex"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="38" 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">
38
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" latexpdfja to make LaTeX files and run them through platex/dvipdfmx"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="39" 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">
39
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" text to make text files"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="40" 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">
40
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" man to make manual pages"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="41" 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">
41
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" texinfo to make Texinfo files"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="42" 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">
42
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" info to make Texinfo files and run them through makeinfo"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="43" 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">
43
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" gettext to make PO message catalogs"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="44" 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">
44
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" changes to make an overview of all changed/added/deprecated items"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="45" 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">
45
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" xml to make Docutils-native XML files"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="46" 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">
46
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" pseudoxml to make pseudoxml-XML files for display purposes"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="47" 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">
47
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" linkcheck to check all external links for integrity"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="48" 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">
48
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" doctest to run all doctests embedded in the documentation (if enabled)"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="49" 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">
49
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" coverage to run coverage check of the documentation (if enabled)"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="50" 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">
50
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" dummy to check syntax errors of document sources"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
51
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="make"></span>
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<td class="old_line diff-line-num old" data-linenumber="52" 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">
52
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">clean</span></span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="make"><span class="nl">clean</span><span class="o" style="font-weight: 600;">:</span></span>
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54
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/<span class="k" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="make"></span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">html</span></span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="make"><span class="nl">html</span><span class="o" style="font-weight: 600;">:</span></span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="make"> <span class="nv" style="color: #008080;">$(SPHINXBUILD)</span> <span class="nt" style="color: #000080;">-b</span> html <span class="nv" style="color: #008080;">$(ALLSPHINXOPTS)</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/html</span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span></span>
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60
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Build finished. The HTML pages are in </span><span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="s2" style="color: #d14;">/html."</span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="make"></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">dirhtml</span></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="make"><span class="nl">dirhtml</span><span class="o" style="font-weight: 600;">:</span></span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="make"> <span class="nv" style="color: #008080;">$(SPHINXBUILD)</span> <span class="nt" style="color: #000080;">-b</span> dirhtml <span class="nv" style="color: #008080;">$(ALLSPHINXOPTS)</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/dirhtml</span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span></span>
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66
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Build finished. The HTML pages are in </span><span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="s2" style="color: #d14;">/dirhtml."</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="make"></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">singlehtml</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="make"><span class="nl">singlehtml</span><span class="o" style="font-weight: 600;">:</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="make"> <span class="nv" style="color: #008080;">$(SPHINXBUILD)</span> <span class="nt" style="color: #000080;">-b</span> singlehtml <span class="nv" style="color: #008080;">$(ALLSPHINXOPTS)</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/singlehtml</span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span></span>
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72
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Build finished. The HTML page is in </span><span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="s2" style="color: #d14;">/singlehtml."</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="make"></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">pickle</span></span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="make"><span class="nl">pickle</span><span class="o" style="font-weight: 600;">:</span></span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="make"> <span class="nv" style="color: #008080;">$(SPHINXBUILD)</span> <span class="nt" style="color: #000080;">-b</span> pickle <span class="nv" style="color: #008080;">$(ALLSPHINXOPTS)</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/pickle</span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Build finished; now you can process the pickle files."</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="make"></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">json</span></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="make"><span class="nl">json</span><span class="o" style="font-weight: 600;">:</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="make"> <span class="nv" style="color: #008080;">$(SPHINXBUILD)</span> <span class="nt" style="color: #000080;">-b</span> json <span class="nv" style="color: #008080;">$(ALLSPHINXOPTS)</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/json</span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span></span>
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84
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Build finished; now you can process the JSON files."</span></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="make"></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">htmlhelp</span></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="make"><span class="nl">htmlhelp</span><span class="o" style="font-weight: 600;">:</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="make"> <span class="nv" style="color: #008080;">$(SPHINXBUILD)</span> <span class="nt" style="color: #000080;">-b</span> htmlhelp <span class="nv" style="color: #008080;">$(ALLSPHINXOPTS)</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/htmlhelp</span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span></span>
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90
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Build finished; now you can run HTML Help Workshop with the"</span> <span class="se" style="color: #d14;">\</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="make"> <span class="s2" style="color: #d14;">".hhp project file in </span><span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="s2" style="color: #d14;">/htmlhelp."</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="make"></span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">qthelp</span></span>
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<td class="old_line diff-line-num old" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="make"><span class="nl">qthelp</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="make"> <span class="nv" style="color: #008080;">$(SPHINXBUILD)</span> <span class="nt" style="color: #000080;">-b</span> qthelp <span class="nv" style="color: #008080;">$(ALLSPHINXOPTS)</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/qthelp</span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span></span>
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<td class="old_line diff-line-num old" data-linenumber="97" 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">
97
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Build finished; now you can run "</span>qcollectiongenerator<span class="s2" style="color: #d14;">" with the"</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="old_line diff-line-num old" data-linenumber="98" 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">
98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="make"> <span class="s2" style="color: #d14;">".qhcp project file in </span><span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="s2" style="color: #d14;">/qthelp, like this:"</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"# qcollectiongenerator </span><span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="s2" style="color: #d14;">/qthelp/TreeTime.qhcp"</span></span>
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100
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"To view the help file:"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="101" 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">
101
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"# assistant -collectionFile </span><span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="s2" style="color: #d14;">/qthelp/TreeTime.qhc"</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="make"></span>
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<td class="old_line diff-line-num old" data-linenumber="103" 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">
103
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">applehelp</span></span>
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<td class="old_line diff-line-num old" data-linenumber="104" 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">
104
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="make"><span class="nl">applehelp</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="105" 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">
105
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="make"> <span class="nv" style="color: #008080;">$(SPHINXBUILD)</span> <span class="nt" style="color: #000080;">-b</span> applehelp <span class="nv" style="color: #008080;">$(ALLSPHINXOPTS)</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/applehelp</span>
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<td class="old_line diff-line-num old" data-linenumber="106" 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">
106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span></span>
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<td class="old_line diff-line-num old" data-linenumber="107" 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">
107
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Build finished. The help book is in </span><span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="s2" style="color: #d14;">/applehelp."</span></span>
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<td class="old_line diff-line-num old" data-linenumber="108" 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">
108
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"N.B. You won't be able to view it unless you put it in"</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="old_line diff-line-num old" data-linenumber="109" 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">
109
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="make"> <span class="s2" style="color: #d14;">"~/Library/Documentation/Help or install it in your application"</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="old_line diff-line-num old" data-linenumber="110" 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">
110
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="make"> <span class="s2" style="color: #d14;">"bundle."</span></span>
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<td class="old_line diff-line-num old" data-linenumber="111" 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">
111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="make"></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">devhelp</span></span>
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<td class="old_line diff-line-num old" data-linenumber="113" 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">
113
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="make"><span class="nl">devhelp</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="114" 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">
114
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="make"> <span class="nv" style="color: #008080;">$(SPHINXBUILD)</span> <span class="nt" style="color: #000080;">-b</span> devhelp <span class="nv" style="color: #008080;">$(ALLSPHINXOPTS)</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/devhelp</span>
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<td class="old_line diff-line-num old" data-linenumber="115" 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">
115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span></span>
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<td class="old_line diff-line-num old" data-linenumber="116" 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">
116
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Build finished."</span></span>
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<td class="old_line diff-line-num old" data-linenumber="117" 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">
117
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"To view the help file:"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="118" 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">
118
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"# mkdir -p </span><span class="nv" style="color: #008080;">$$</span><span class="s2" style="color: #d14;">HOME/.local/share/devhelp/TreeTime"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
119
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"# ln -s </span><span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="s2" style="color: #d14;">/devhelp </span><span class="nv" style="color: #008080;">$$</span><span class="s2" style="color: #d14;">HOME/.local/share/devhelp/TreeTime"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="120" 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">
120
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"# devhelp"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="121" 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">
121
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="make"></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">epub</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="make"><span class="nl">epub</span><span class="o" style="font-weight: 600;">:</span></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="make"> <span class="nv" style="color: #008080;">$(SPHINXBUILD)</span> <span class="nt" style="color: #000080;">-b</span> epub <span class="nv" style="color: #008080;">$(ALLSPHINXOPTS)</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/epub</span>
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<td class="old_line diff-line-num old" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span></span>
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126
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Build finished. The epub file is in </span><span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="s2" style="color: #d14;">/epub."</span></span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="make"></span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">epub3</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="make"><span class="nl">epub3</span><span class="o" style="font-weight: 600;">:</span></span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="make"> <span class="nv" style="color: #008080;">$(SPHINXBUILD)</span> <span class="nt" style="color: #000080;">-b</span> epub3 <span class="nv" style="color: #008080;">$(ALLSPHINXOPTS)</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/epub3</span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span></span>
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132
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Build finished. The epub3 file is in </span><span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="s2" style="color: #d14;">/epub3."</span></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="make"></span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">latex</span></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="make"><span class="nl">latex</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="136" 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">
136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="make"> <span class="nv" style="color: #008080;">$(SPHINXBUILD)</span> <span class="nt" style="color: #000080;">-b</span> latex <span class="nv" style="color: #008080;">$(ALLSPHINXOPTS)</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/latex</span>
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<td class="old_line diff-line-num old" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span></span>
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<td class="old_line diff-line-num old" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
138
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Build finished; the LaTeX files are in </span><span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="s2" style="color: #d14;">/latex."</span></span>
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<td class="old_line diff-line-num old" data-linenumber="139" 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">
139
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Run </span><span class="se" style="color: #d14;">\`</span><span class="s2" style="color: #d14;">make' in that directory to run these through (pdf)latex"</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="old_line diff-line-num old" data-linenumber="140" 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">
140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="make"> <span class="s2" style="color: #d14;">"(use </span><span class="se" style="color: #d14;">\`</span><span class="s2" style="color: #d14;">make latexpdf' here to do that automatically)."</span></span>
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<td class="old_line diff-line-num old" data-linenumber="141" 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">
141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="make"></span>
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<td class="old_line diff-line-num old" data-linenumber="142" 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">
142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">latexpdf</span></span>
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<td class="old_line diff-line-num old" data-linenumber="143" 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">
143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="make"><span class="nl">latexpdf</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="144" 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">
144
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="make"> <span class="nv" style="color: #008080;">$(SPHINXBUILD)</span> <span class="nt" style="color: #000080;">-b</span> latex <span class="nv" style="color: #008080;">$(ALLSPHINXOPTS)</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/latex</span>
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<td class="old_line diff-line-num old" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Running LaTeX files through pdflatex..."</span></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="make"> <span class="nv" style="color: #008080;">$(MAKE)</span> <span class="nt" style="color: #000080;">-C</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/latex all-pdf</span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"pdflatex finished; the PDF files are in </span><span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="s2" style="color: #d14;">/latex."</span></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="make"></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">latexpdfja</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="make"><span class="nl">latexpdfja</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="151" 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">
151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="make"> <span class="nv" style="color: #008080;">$(SPHINXBUILD)</span> <span class="nt" style="color: #000080;">-b</span> latex <span class="nv" style="color: #008080;">$(ALLSPHINXOPTS)</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/latex</span>
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<td class="old_line diff-line-num old" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Running LaTeX files through platex and dvipdfmx..."</span></span>
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<td class="old_line diff-line-num old" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="make"> <span class="nv" style="color: #008080;">$(MAKE)</span> <span class="nt" style="color: #000080;">-C</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/latex all-pdf-ja</span>
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<td class="old_line diff-line-num old" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"pdflatex finished; the PDF files are in </span><span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="s2" style="color: #d14;">/latex."</span></span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="make"></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">text</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="make"><span class="nl">text</span><span class="o" style="font-weight: 600;">:</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="make"> <span class="nv" style="color: #008080;">$(SPHINXBUILD)</span> <span class="nt" style="color: #000080;">-b</span> text <span class="nv" style="color: #008080;">$(ALLSPHINXOPTS)</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/text</span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Build finished. The text files are in </span><span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="s2" style="color: #d14;">/text."</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="make"></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">man</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="make"><span class="nl">man</span><span class="o" style="font-weight: 600;">:</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="make"> <span class="nv" style="color: #008080;">$(SPHINXBUILD)</span> <span class="nt" style="color: #000080;">-b</span> man <span class="nv" style="color: #008080;">$(ALLSPHINXOPTS)</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/man</span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Build finished. The manual pages are in </span><span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="s2" style="color: #d14;">/man."</span></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="make"></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">texinfo</span></span>
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<td class="old_line diff-line-num old" data-linenumber="169" 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">
169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="make"><span class="nl">texinfo</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="170" 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">
170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="make"> <span class="nv" style="color: #008080;">$(SPHINXBUILD)</span> <span class="nt" style="color: #000080;">-b</span> texinfo <span class="nv" style="color: #008080;">$(ALLSPHINXOPTS)</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/texinfo</span>
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<td class="old_line diff-line-num old" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span></span>
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<td class="old_line diff-line-num old" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
172
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Build finished. The Texinfo files are in </span><span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="s2" style="color: #d14;">/texinfo."</span></span>
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<td class="old_line diff-line-num old" data-linenumber="173" 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">
173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Run </span><span class="se" style="color: #d14;">\`</span><span class="s2" style="color: #d14;">make' in that directory to run these through makeinfo"</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="old_line diff-line-num old" data-linenumber="174" 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">
174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="make"> <span class="s2" style="color: #d14;">"(use </span><span class="se" style="color: #d14;">\`</span><span class="s2" style="color: #d14;">make info' here to do that automatically)."</span></span>
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<td class="old_line diff-line-num old" data-linenumber="175" 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">
175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="make"></span>
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<td class="old_line diff-line-num old" data-linenumber="176" 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">
176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">info</span></span>
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<td class="old_line diff-line-num old" data-linenumber="177" 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">
177
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="make"><span class="nl">info</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="178" 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">
178
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="make"> <span class="nv" style="color: #008080;">$(SPHINXBUILD)</span> <span class="nt" style="color: #000080;">-b</span> texinfo <span class="nv" style="color: #008080;">$(ALLSPHINXOPTS)</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/texinfo</span>
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<td class="old_line diff-line-num old" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Running Texinfo files through makeinfo..."</span></span>
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<td class="old_line diff-line-num old" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="make"> make <span class="nt" style="color: #000080;">-C</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/texinfo info</span>
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<td class="old_line diff-line-num old" data-linenumber="181" 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">
181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"makeinfo finished; the Info files are in </span><span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="s2" style="color: #d14;">/texinfo."</span></span>
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<td class="old_line diff-line-num old" data-linenumber="182" 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">
182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="make"></span>
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<td class="old_line diff-line-num old" data-linenumber="183" 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">
183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">gettext</span></span>
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<td class="old_line diff-line-num old" data-linenumber="184" 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">
184
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="make"><span class="nl">gettext</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="185" 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">
185
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="make"> <span class="nv" style="color: #008080;">$(SPHINXBUILD)</span> <span class="nt" style="color: #000080;">-b</span> gettext <span class="nv" style="color: #008080;">$(I18NSPHINXOPTS)</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/locale</span>
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<td class="old_line diff-line-num old" data-linenumber="186" 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">
186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span></span>
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<td class="old_line diff-line-num old" data-linenumber="187" 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">
187
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Build finished. The message catalogs are in </span><span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="s2" style="color: #d14;">/locale."</span></span>
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<td class="old_line diff-line-num old" data-linenumber="188" 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">
188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="make"></span>
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<td class="old_line diff-line-num old" data-linenumber="189" 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">
189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">changes</span></span>
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<td class="old_line diff-line-num old" data-linenumber="190" 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">
190
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="make"><span class="nl">changes</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="191" 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">
191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="make"> <span class="nv" style="color: #008080;">$(SPHINXBUILD)</span> <span class="nt" style="color: #000080;">-b</span> changes <span class="nv" style="color: #008080;">$(ALLSPHINXOPTS)</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/changes</span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"The overview file is in </span><span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="s2" style="color: #d14;">/changes."</span></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="make"></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">linkcheck</span></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="make"><span class="nl">linkcheck</span><span class="o" style="font-weight: 600;">:</span></span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="make"> <span class="nv" style="color: #008080;">$(SPHINXBUILD)</span> <span class="nt" style="color: #000080;">-b</span> linkcheck <span class="nv" style="color: #008080;">$(ALLSPHINXOPTS)</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/linkcheck</span>
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<td class="old_line diff-line-num old" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span></span>
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<td class="old_line diff-line-num old" data-linenumber="199" 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">
199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Link check complete; look for any errors in the above output "</span> <span class="se" style="color: #d14;">\</span></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="make"> <span class="s2" style="color: #d14;">"or in </span><span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="s2" style="color: #d14;">/linkcheck/output.txt."</span></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="make"></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">doctest</span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="make"><span class="nl">doctest</span><span class="o" style="font-weight: 600;">:</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="make"> <span class="nv" style="color: #008080;">$(SPHINXBUILD)</span> <span class="nt" style="color: #000080;">-b</span> doctest <span class="nv" style="color: #008080;">$(ALLSPHINXOPTS)</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/doctest</span>
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205
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Testing of doctests in the sources finished, look at the "</span> <span class="se" style="color: #d14;">\</span></span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="make"> <span class="s2" style="color: #d14;">"results in </span><span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="s2" style="color: #d14;">/doctest/output.txt."</span></span>
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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="make"></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">coverage</span></span>
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<td class="old_line diff-line-num old" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="make"><span class="nl">coverage</span><span class="o" style="font-weight: 600;">:</span></span>
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210
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="make"> <span class="nv" style="color: #008080;">$(SPHINXBUILD)</span> <span class="nt" style="color: #000080;">-b</span> coverage <span class="nv" style="color: #008080;">$(ALLSPHINXOPTS)</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/coverage</span>
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211
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Testing of coverage in the sources finished, look at the "</span> <span class="se" style="color: #d14;">\</span></span>
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212
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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="make"> <span class="s2" style="color: #d14;">"results in </span><span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="s2" style="color: #d14;">/coverage/python.txt."</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;">$(SPHINXBUILD)</span> <span class="nt" style="color: #000080;">-M</span> <span class="nb" style="color: #0086b3;">help</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(SOURCEDIR)</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="s2" style="color: #d14;">"</span> <span class="nv" style="color: #008080;">$(SPHINXOPTS)</span> <span class="nv" style="color: #008080;">$(O)</span></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="make"></span>
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214
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">xml</span></span>
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215
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="make"><span class="nl">xml</span><span class="o" style="font-weight: 600;">:</span></span>
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216
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="make"> <span class="nv" style="color: #008080;">$(SPHINXBUILD)</span> <span class="nt" style="color: #000080;">-b</span> xml <span class="nv" style="color: #008080;">$(ALLSPHINXOPTS)</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/xml</span>
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217
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span></span>
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218
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Build finished. The XML files are in </span><span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="s2" style="color: #d14;">/xml."</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">help Makefile</span></span>
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219
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="make"></span>
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220
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">pseudoxml</span></span>
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221
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="make"><span class="nl">pseudoxml</span><span class="o" style="font-weight: 600;">:</span></span>
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222
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="make"> <span class="nv" style="color: #008080;">$(SPHINXBUILD)</span> <span class="nt" style="color: #000080;">-b</span> pseudoxml <span class="nv" style="color: #008080;">$(ALLSPHINXOPTS)</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/pseudoxml</span>
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223
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span></span>
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<td class="old_line diff-line-num old" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
224
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Build finished. The pseudo-XML files are in </span><span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="s2" style="color: #d14;">/pseudoxml."</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Catch-all target: route all unknown targets to Sphinx using the new</span></span>
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<td class="new_line diff-line-num new" data-linenumber="18" 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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="make"><span class="nl">%</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">Makefile</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;">$(SPHINXBUILD)</span> <span class="nt" style="color: #000080;">-M</span> <span class="nv" style="color: #008080;">$@</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(SOURCEDIR)</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="s2" style="color: #d14;">"</span> <span class="nv" style="color: #008080;">$(SPHINXOPTS)</span> <span class="nv" style="color: #008080;">$(O)</span></span>
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225
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="make"></span>
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226
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">dummy</span></span>
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227
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="make"><span class="nl">dummy</span><span class="o" style="font-weight: 600;">:</span></span>
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228
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="make"> <span class="nv" style="color: #008080;">$(SPHINXBUILD)</span> <span class="nt" style="color: #000080;">-b</span> dummy <span class="nv" style="color: #008080;">$(ALLSPHINXOPTS)</span> <span class="nv" style="color: #008080;">$(BUILDDIR)</span>/dummy</span>
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229
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span></span>
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230
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Build finished. Dummy builder generates no files."</span></span></pre>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="make"><span class="nl">autobuild</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="make"> sphinx-autobuild <span class="nt" style="color: #000080;">--host</span><span class="o" style="font-weight: 600;">=</span>0.0.0.0 <span class="nt" style="color: #000080;">--port</span><span class="o" style="font-weight: 600;">=</span>8000 <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(SOURCEDIR)</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="s2" style="color: #d14;">/html"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/1cd12a8d3f5353000dfe384f7f3a9ee984632181#ce9ae6f5204729fc4b54b97f8f3e17ffb128428c"><strong>docs/environment.yml</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">docs</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">channels</span><span class="pi">:</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">defaults</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"><span class="na" style="color: #008080;">dependencies</span><span class="pi">:</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">sphinx</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pip</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">pip</span><span class="pi">:</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">biopython>=1.67,!=1.77,!=1.78</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">numpy>=1.10.4</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pandas>=0.17.1</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">scipy>=0.16.1</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">recommonmark>=0.5.0</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">sphinx-argparse>=0.2.5</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">sphinx-autobuild</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">sphinx-markdown-tables</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">sphinx-rtd-theme</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">sphinx-tabs</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/1cd12a8d3f5353000dfe384f7f3a9ee984632181#271b54d579b58b0097c7c56b8ab060c6e3a67b4f"><strong>docs/requirements.txt</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">recommonmark>=0.5.0</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">sphinx-argparse>=0.2.5</span></pre>
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<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/1cd12a8d3f5353000dfe384f7f3a9ee984632181#aded7756cdea7c289134466a0d54da4f26d43abb"><strong>docs/source/conf.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">@@ -14,11 +14,13 @@</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;"><span class="idiff left">from</span></span><span class="idiff"> </span><span class="nn" style="color: #555;"><span class="idiff">treetime</span></span><span class="idiff"> </span><span class="kn" style="font-weight: 600;"><span class="idiff">import</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">version</span></span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># If extensions (or modules to document with autodoc) are in another directory,</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># add these directories to sys.path here. If the directory is relative to the</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># documentation root, use os.path.abspath to make it absolute, like shown here.</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#sys.path.insert(0, os.path.abspath('.'))</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">abspath</span><span class="p">(</span><span class="s" style="color: #d14;">'../..'</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">treetime</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">version</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># -- General configuration ------------------------------------------------</span></span>
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<pre style="margin: 0;"> <span id="LC26" 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">@@ -70,7 +72,7 @@ master_doc = 'index'</td>
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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="c1" style="color: #998; font-style: italic;"># General information about the project.</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"><span class="n" style="color: #333;">project</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">u</span><span class="s" style="color: #d14;">'TreeTime'</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"><span class="n" style="color: #333;">copyright</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">u</span><span class="s" style="color: #d14;">'2017-201<span class="idiff left right">9</span>, Pavel Sagulenko and Richard Neher'</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"><span class="n" style="color: #333;">copyright</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">u</span><span class="s" style="color: #d14;">'2017-20<span class="idiff left right">2</span>1, Pavel Sagulenko and Richard Neher'</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"><span class="n" style="color: #333;">author</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">u</span><span class="s" style="color: #d14;">'Pavel Sagulenko and Richard Neher'</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The version info for the project you're documenting, acts as replacement for</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">@@ -130,7 +132,7 @@ todo_include_todos = True</td>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The theme to use for HTML and HTML Help pages. See the documentation for</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># a list of builtin themes.</span></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#html_theme = 'alabaster'</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>html_theme = 'alabaster'</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"><span class="n" style="color: #333;">html_theme</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'sphinx_rtd_theme'</span></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/1cd12a8d3f5353000dfe384f7f3a9ee984632181#41b2a620e5c90c4e7905692c175e421576881468"><strong>docs/source/gtr.rst</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,7 +23,7 @@ GTR class documentation</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Sequence manipulation</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">---------------------</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">.. automethod:: treetime.GTR.<span class="idiff left right">compress_sequenc</span>e_pair</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.. automethod:: treetime.GTR.<span class="idiff left right">stat</span>e_pair</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">Distance and probability computations</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">-------------------------------------</span>
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<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/1cd12a8d3f5353000dfe384f7f3a9ee984632181#d1ffd6c1cec13f9cfe41f6f4b27a4ad96b846682"><strong>docs/source/treeanc.rst</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">@@ -42,20 +42,6 @@ Basic functions, utilities, properties</td>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">.. automethod:: treetime.TreeAnc.leaves_lookup()</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext">Sequence and profile manipulation</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext">---------------------------------</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext">.. automethod:: treetime.TreeAnc.get_mutations</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext">.. automethod:: treetime.TreeAnc.get_reconstructed_alignment</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext">.. automethod:: treetime.TreeAnc.make_reduced_alignment</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext">.. automethod:: treetime.TreeAnc.expanded_sequence</span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext">.. automethod:: treetime.TreeAnc.dict_sequence</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">Ancestral reconstruction and tree optimization</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">----------------------------------------------</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"></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">@@ -67,8 +53,6 @@ Ancestral reconstruction and tree optimization</td>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext">.. automethod:: treetime.TreeAnc.infer_gtr</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext">.. automethod:: treetime.TreeAnc.get_reconstructed_alignment</span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext">.. automethod:: treetime.TreeAnc.get_tree_dict</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/1cd12a8d3f5353000dfe384f7f3a9ee984632181#6816bffea1e0135cbec8177205ac40891362f1a8"><strong>docs/source/tutorials/ancestral.rst</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">@@ -12,7 +12,7 @@ On the command-line, ancestral reconstruction can be done via the command</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">This command will save a number of files into the directory `ancestral_results` and generate the output</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">.. code-block::</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.. code-block::<span class="idiff left right"> bash</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> Inferred GTR model:</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> Substitution rate (mu): 1.0</span>
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<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/1cd12a8d3f5353000dfe384f7f3a9ee984632181#55ab4c17b34670942fdad8399ccd1d321a97e95d"><strong>docs/source/tutorials/clock.rst</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11" 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="11" 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">@@ -11,7 +11,7 @@ This functionality is implemented as subcommand ``clock``\ :</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">This command will print the following output:</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">.. code-block::</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">.. code-block::<span class="idiff left right"> bash</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> Root-Tip-Regression:</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> --rate: 2.826e-03</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">@@ -63,7 +63,7 @@ However, these root-to-tip distances are correlated due to shared ancestry no va</td>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext">This covariation can be efficiently accounted if the sequence data set is consistent with a simple strict molecular clock model, but can give misleading results when the molecular clock model is violated.</span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext">This feature is hence off by default and can be switched on using the flag</span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext">.. code-block::</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">.. code-block::<span class="idiff left right"> bash</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext"> --covariation</span>
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<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/1cd12a8d3f5353000dfe384f7f3a9ee984632181#1bd68f7b8559b0dbf5e245571cbcdc74b14fac16"><strong>docs/source/tutorials/homoplasy.rst</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">@@ -18,7 +18,7 @@ This command will reconstruct ancestral sequences and count how many time a part</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">The basic output looks like this:</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">.. code-block::</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.. code-block::<span class="idiff left right"> bash</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> The TOTAL tree length is 6.617e-02 and 674 mutations were observed.</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> Of these 674 mutations,</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,7 +31,7 @@ This block reports how many times specific mutations, e.g. ``G27A``\ , were obse</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">The next output block summarizes how often sites in the sequence are hit by mutations.</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">This can be compared to a null expectation that mutations are uniformly and independently distributed along the sequence according to a Poisson distribution with the same number of mutations.</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext">.. code-block::</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">.. code-block::<span class="idiff left right"> bash</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> Of the 10807 positions in the genome,</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> - 10175 were hit 0 times (expected 10153.59)</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">@@ -46,7 +46,7 @@ Nonetheless, this can be a useful comparison.</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">Lastly, there is a block that highlights mutations that are most homoplasic.</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">By default, ``treetime homoplasy`` will list the first 10 mutations -- this behavior can be adjusted using the option ``-n``.</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext">.. code-block::</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">.. code-block::<span class="idiff left right"> bash</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"> The ten most homoplasic mutations are:</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"> mut multiplicity</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">@@ -67,7 +67,7 @@ Additional output</td>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext">``treetime homoplasy`` can be run with the flag ``--detailed`` which will print additional statistics, mostly concerning terminal branches.</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext">The first extra outputs are on the mutation statistics on terminal branch in analogy to the statistics for the total tree above.</span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext">.. code-block::</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">.. code-block::<span class="idiff left right"> bash</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext"> The TERMINAL branch length is 3.962e-02 and 408 mutations were observed.</span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="plaintext"> Of these 408 mutations,</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">@@ -86,7 +86,7 @@ The first extra outputs are on the mutation statistics on terminal branch in ana</td>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="plaintext">Lastly, the script outputs a list of sequences that have many mutations on the terminal branches leading up to them that also occur elsewhere in the tree.</span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="plaintext">This is can often be a sign of contamination or other problematic sequence.</span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="plaintext">.. code-block::</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">.. code-block::<span class="idiff left right"> bash</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext"> Taxons that carry positions that mutated elsewhere in the tree:</span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="plaintext"> taxon name #of homoplasic mutations</span>
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<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/1cd12a8d3f5353000dfe384f7f3a9ee984632181#7d1462bd4008d5703b52469948efeb2fc5640e04"><strong>docs/source/tutorials/mugration.rst</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">@@ -24,7 +24,7 @@ Marginal distributions of ancestral states</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">If the additional flag ``--confidence`` is added to the command, TreeTime will output a file with the inferred probability of finding an internal node in a particular discrete state.</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">A typical output would be</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">.. code-block::</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.. code-block::<span class="idiff left right"> bash</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> #name american_samoa brazil china colombia ...</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> NODE_00 0.0001 0.0003 0.0002 0 ...</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">@@ -41,7 +41,7 @@ This results in an underestimate of the transition rates and consequently over-c</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">To some extend, this effect can be mitigated in an ad-hoc fashion by manually increasing the transition rate.</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">The `mugration` command provides a flag to specify the factor, by which the mugration rate is expected to be underestimated:</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext">.. code-block::</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">.. code-block::<span class="idiff left right"> bash</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"> --sampling-bias-correction <float></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/1cd12a8d3f5353000dfe384f7f3a9ee984632181#9e4b18dd4973209585cacb447ee505ec303baf36"><strong>docs/source/tutorials/timetree.rst</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">@@ -14,7 +14,7 @@ TreeTime will attempt to parse dates, preferred formats are are "%Y-%m-%d" or nu</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">This command will estimate an GTR model, a molecular clock model, and a time-stamped phylogeny.</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">The results are saved to several files in the directory specified as `outdir` and printed to standard out:</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">.. code-block::</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.. code-block::<span class="idiff left right"> bash</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> Inferred GTR model:</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> Substitution rate (mu): 1.0</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">@@ -80,7 +80,7 @@ However, these root-to-tip distances are correlated due to shared ancestry.</td>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext">This can be efficiently accounted if the sequence data set is consistent with a simple strict molecular clock model, but can give misleading results when the molecular clock model is violated.</span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext">This feature is hence off by default and can be switched on using the flag</span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext">.. code-block::</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">.. code-block::<span class="idiff left right"> bash</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="plaintext"> --covariation</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">@@ -91,7 +91,7 @@ Fixed evolutionary rate</td>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext">If the temporal signal in the data is weak and the clock rate can't be estimated confidently from the data, it is advisable to specify the rate explicitly.</span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="plaintext">This can be done using the argument</span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="plaintext">.. code-block::</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">.. code-block::<span class="idiff left right"> bash</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="plaintext"> --clock-rate <rate></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext"></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 +104,7 @@ The later is parameterized by a time scale 'Tc' which can vary in time.</td>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="plaintext">This time scale is often called 'effective population size' Ne, but the appropriate Tc has very little to do with census population sizes.</span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="plaintext">To activate the Kingman Coalescent model in TreeTime, you need to add the flag</span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="plaintext">.. code-block::</span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">.. code-block::<span class="idiff left right"> bash</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="plaintext"> --coalescent <arg></span>
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<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/1cd12a8d3f5353000dfe384f7f3a9ee984632181#716e6f6c16580800d13452615e2c01668aacc288"><strong>treetime/__init__.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" 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;">print_function</span><span class="p">,</span> <span class="n" style="color: #333;">division</span><span class="p">,</span> <span class="n" style="color: #333;">absolute_import</span></span>
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<pre style="margin: 0;">-<span id="LC2" 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;">"0.8.<span class="idiff left right">4</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC2" 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;">"0.8.<span class="idiff left right">5</span>"</span></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;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TreeTimeError</span><span class="p">(</span><span class="nb" style="color: #0086b3;">Exception</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"> <span class="s" style="color: #d14;">"""TreeTimeError class"""</span></span>
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<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/1cd12a8d3f5353000dfe384f7f3a9ee984632181#82a08428349f48dbbab4c8ccac6320f52b4c7a7b"><strong>treetime/seq_utils.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">@@ -189,8 +189,11 @@ def seq2array(seq, word_length=1, convert_upper=False, fill_overhangs=False, amb</td>
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189
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># substitute overhanging unsequenced tails</span></span>
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fill_overhangs</span><span class="p">:</span></span>
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191
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">gaps</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;">where</span><span class="p">(</span><span class="n" style="color: #333;">seq_array</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'-'</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">seq_array</span><span class="p">[:</span><span class="n" style="color: #333;">gaps</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;">ambiguous</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;">seq_array</span><span class="p">[</span><span class="n" style="color: #333;">gaps</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="mi" style="color: #099;">1</span><span class="p">:]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ambiguous</span></span>
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">seq_array</span><span class="p">[:</span><span class="n" style="color: #333;">gaps</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;">ambiguous</span></span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="n" style="color: #333;">seq_array</span><span class="p">[</span><span class="n" style="color: #333;">gaps</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="mi" style="color: #099;">1</span><span class="p">:]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ambiguous</span></span>
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<pre style="margin: 0;">+<span id="LC195" 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="LC196" class="line" lang="python"> <span class="n" style="color: #333;">seq_array</span><span class="p">[:]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ambiguous</span></span>
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">seq_array</span></span>
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/1cd12a8d3f5353000dfe384f7f3a9ee984632181#5233e2843fb208ffac5520b8b6d010090372931b"><strong>treetime/sequence_data.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">@@ -161,9 +161,20 @@ class SequenceData(object):</td>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"></span>
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="n" style="color: #333;">in_aln</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">MultipleSeqAlignment</span><span class="p">:</span></span>
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># check whether the alignment is consistent with a nucleotide alignment.</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_aln</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">:</span> <span class="n" style="color: #333;">seq2array</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">convert_upper</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;">convert_upper</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">fill_overhangs</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;">fill_overhangs</span><span class="p">,</span> <span class="n" style="color: #333;">ambiguous</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;">ambiguous</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">in_aln</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_aln</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">in_aln</span><span class="p">:</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">:</span></span>
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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;">tmp_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span></span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="s" style="color: #d14;">'<unknown'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># use s.name if id is BioPython default (previous behavior)</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="n" style="color: #333;">tmp_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">name</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="s" style="color: #d14;">'<unknown'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># use s.id if s.name is BioPython default (change relative to previous, but what we want)</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="n" style="color: #333;">tmp_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="n" style="color: #333;">tmp_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="c1" style="color: #998; font-style: italic;"># otherwise use s.name (previous behavior)</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_aln</span><span class="p">[</span><span class="n" style="color: #333;">tmp_name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq2array</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">convert_upper</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;">convert_upper</span><span class="p">,</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="n" style="color: #333;">fill_overhangs</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;">fill_overhangs</span><span class="p">,</span> <span class="n" style="color: #333;">ambiguous</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;">ambiguous</span><span class="p">)</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"></span>
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167
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">check_alphabet</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_aln</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">()))</span></span>
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168
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">is_sparse</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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169
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">logger</span><span class="p">(</span><span class="s" style="color: #d14;">"SequenceData: loaded alignment."</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/1cd12a8d3f5353000dfe384f7f3a9ee984632181#a2e471fd9fc09543e8fd92727442680e1b76576b"><strong>treetime/treeanc.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">@@ -360,7 +360,7 @@ class TreeAnc(object):</td>
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="python"><span class="s" style="color: #d14;"> in the alignment and assign this sequence as a character array</span></span>
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="python"><span class="s" style="color: #d14;"> '''</span></span>
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">get_terminals</span><span class="p">())</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">aln</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">logger</span><span class="p">(</span><span class="s" style="color: #d14;">"**WARNING: Number of tips in tree differs from number of sequences in alignment<span class="idiff left right">!</span>**"</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">warn</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">logger</span><span class="p">(</span><span class="sa"><span class="idiff left">f</span></span><span class="s" style="color: #d14;">"**WARNING: Number of tips in tree <span class="idiff">(</span></span><span class="si" style="color: #d14;"><span class="idiff">{</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">len</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tree</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">get_terminals</span></span><span class="p"><span class="idiff">())</span></span><span class="si" style="color: #d14;"><span class="idiff">}</span></span><span class="s" style="color: #d14;"><span class="idiff">) </span>differs from number of sequences in alignment<span class="idiff"> (</span></span><span class="si" style="color: #d14;"><span class="idiff">{</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">len</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">data</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">aln</span></span><span class="p"><span class="idiff">)</span></span><span class="si" style="color: #d14;"><span class="idiff">}</span></span><span class="s" style="color: #d14;"><span class="idiff right">)</span>**"</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">warn</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="python"> <span class="n" style="color: #333;">failed_leaves</span><span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># loop over leaves and assign multiplicities of leaves (e.g. number of identical reads)</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">@@ -824,8 +824,8 @@ class TreeTime(ClockTree):</td>
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<pre style="margin: 0;"> <span id="LC824" class="line" lang="python"> <span class="s" style="color: #d14;">'Sample'</span> <span class="p">:</span> <span class="n" style="color: #333;">niter</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC825" class="line" lang="python"> <span class="s" style="color: #d14;">'ndiff'</span> <span class="p">:</span> <span class="n" style="color: #333;">ndiff</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC826" class="line" lang="python"> <span class="s" style="color: #d14;">'n_resolved'</span> <span class="p">:</span> <span class="n" style="color: #333;">n_resolved</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC827" class="line" lang="python"> <span class="s" style="color: #d14;">'seq_mode'</span> <span class="p">:</span> <span class="s" style="color: #d14;">'marginal'</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sequence_marginal</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">'joint'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC828" class="line" lang="python"> <span class="s" style="color: #d14;">'seq_LH'</span> <span class="p">:</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">sequence_marginal_LH</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sequence_marginal</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">sequence_joint_LH</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="python"> <span class="s" style="color: #d14;">'seq_mode'</span> <span class="p">:</span> <span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;">'marginal'</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sequence_marginal</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">'joint'</span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">aln</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'no sequences given'</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="python"> <span class="s" style="color: #d14;">'seq_LH'</span> <span class="p">:</span> <span class="p"><span class="idiff left">(</span></span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">sequence_marginal_LH</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sequence_marginal</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">sequence_joint_LH</span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">aln</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC829" class="line" lang="python"> <span class="s" style="color: #d14;">'pos_mode'</span> <span class="p">:</span> <span class="s" style="color: #d14;">'marginal'</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">time_marginal</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">'joint'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC830" class="line" lang="python"> <span class="s" style="color: #d14;">'pos_LH'</span> <span class="p">:</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">positional_marginal_LH</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">time_marginal</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">positional_joint_LH</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC831" class="line" lang="python"> <span class="s" style="color: #d14;">'coal_mode'</span> <span class="p">:</span> <span class="n" style="color: #333;">Tc</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">@@ -982,8 +982,9 @@ def plot_vs_years(tt, step = None, ax=None, confidence=None, ticks=True, **kwarg</td>
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<pre style="margin: 0;"> <span id="LC982" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">NotReadyError</span><span class="p">(</span><span class="s" style="color: #d14;">"confidence needs to be either a float (for max posterior region) or a two numbers specifying lower and upper bounds"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC983" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC984" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">n</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tt</span><span class="p">.</span><span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">find_clades</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC985" class="line" lang="python"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cfunc</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">confidence</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC986" class="line" lang="python"> <span class="n" style="color: #333;">ax</span><span class="p">.</span><span class="n" style="color: #333;">plot</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">offset</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">ones</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">))</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">n</span><span class="p">.</span><span class="n" style="color: #333;">ypos</span><span class="p">,</span> <span class="n" style="color: #333;">lw</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="mf" style="color: #099;">0.5</span><span class="p">,</span><span class="mf" style="color: #099;">0.5</span><span class="p">,</span><span class="mf" style="color: #099;">0.5</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC985" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">n</span><span class="p">.</span><span class="n" style="color: #333;">bad_branch</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC986" class="line" lang="python"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cfunc</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">confidence</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC987" class="line" lang="python"> <span class="n" style="color: #333;">ax</span><span class="p">.</span><span class="n" style="color: #333;">plot</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">offset</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">ones</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">))</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">n</span><span class="p">.</span><span class="n" style="color: #333;">ypos</span><span class="p">,</span> <span class="n" style="color: #333;">lw</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="mf" style="color: #099;">0.5</span><span class="p">,</span><span class="mf" style="color: #099;">0.5</span><span class="p">,</span><span class="mf" style="color: #099;">0.5</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC988" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fig</span><span class="p">,</span> <span class="n" style="color: #333;">ax</span></span>
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<pre style="margin: 0;"> <span id="LC989" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC990" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">treetime_to_newick</span><span class="p">(</span><span class="n" style="color: #333;">tt</span><span class="p">,</span> <span class="n" style="color: #333;">outf</span><span class="p">):</span></span>
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