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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-dendropy">Debian Med / python-dendropy</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-dendropy/commit/10d0e32a2a9d9000898cadb2cf0c137a92cc0976">10d0e32a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-02-18T20:16:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 4.3.0+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-dendropy/commit/85ea7b27205bf4a450d63cdf205bee82fd26b14d">85ea7b27</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-02-18T20:17:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/4.3.0+dfsg'
Update to upstream version '4.3.0+dfsg'
with Debian dir 7b7ec3793fb71daf323ac2b70a00e448d8d11559</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-dendropy/commit/7c87916e343bc471aad1ab8ec9c7109751c9f6e7">7c87916e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-02-18T20:20:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-dendropy/commit/19c465f7162bdc27125a1a4fcb56ffe478b58ff2">19c465f7</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-02-18T20:20:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.1.3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-dendropy/commit/723cc011590cd42a60bcb0b7b34370f45ce7e096">723cc011</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-02-18T20:20:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper 11
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-dendropy/commit/368b1e320d29c5392ed258eeeb33921137fdd61b">368b1e32</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-02-19T09:29:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">do not parse d/changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-dendropy/commit/c9fd9cceabf1881c079ba3ef808833ea48f552e8">c9fd9cce</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-02-19T09:31:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Testsuite: autopkgtest-pkg-python
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-dendropy/commit/bf22906f2c356d84b5290a66349421ffec1155ef">bf22906f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-02-19T10:07:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>25 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#4990be809a537bf86e4be2fe2e8251c83d8bd129">
CHANGES.rst
</a>
</li>
<li class="file-stats">
<a href="#51d5d11207906423aac7850d39aae6511f604ff0">
DendroPy.egg-info/PKG-INFO
</a>
</li>
<li class="file-stats">
<a href="#2fa9ec55009692e0499b33faf948b0b569185991">
DendroPy.egg-info/SOURCES.txt
</a>
</li>
<li class="file-stats">
<a href="#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">
PKG-INFO
</a>
</li>
<li class="file-stats">
<a href="#01b611f94e0c55bb8374fd267be915753980c504">
<span class="new-file">
+
applications/sumlabels/sumlabels.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#5b6f5675e8179826bb0ae13324ca4b3979634f0e">
applications/sumtrees/sumtrees.py
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
debian/compat
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#33c5f920dd6e87de8413f3340f04483f01cfc9a9">
debian/patches/0001-Fix-bug-where-encoding-for-default-locale-is-None.patch
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</li>
<li class="file-stats">
<a href="#94b75511da9ff25cd971f3b79816e04bf5328cf9">
dendropy/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#b55e66c8f57b5d6320b903d5d60ec7aa2f6728ed">
dendropy/dataio/newickreader.py
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</li>
<li class="file-stats">
<a href="#225326cf9a24fd8ceba1a72f313e0744142193e1">
dendropy/dataio/nexuswriter.py
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</li>
<li class="file-stats">
<a href="#f47990668ba22c907489bd48a006f8c1a4fc24bb">
dendropy/datamodel/charmatrixmodel.py
</a>
</li>
<li class="file-stats">
<a href="#eabc6891343b2f85f7cf4519e497197f4f9f67e3">
dendropy/datamodel/taxonmodel.py
</a>
</li>
<li class="file-stats">
<a href="#58fa80fee5ac7a2b78c397754b90c48ed3d64b2a">
dendropy/datamodel/treemodel.py
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</li>
<li class="file-stats">
<a href="#02a7bb8f9dfaaf9f7b635022e9ddc59df60419df">
<span class="new-file">
+
dendropy/interop/rspr.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#d85fb2562ecc625e71ec482bd3dc5f23a264decd">
dendropy/model/birthdeath.py
</a>
</li>
<li class="file-stats">
<a href="#0bea2e6dd67ad52a51f66d3ac8ad6fc41aae90d5">
dendropy/test/test_birthdeath.py
</a>
</li>
<li class="file-stats">
<a href="#df9370d189d00eb39f19afd0657aac56f24843a4">
dendropy/test/test_dataio_newick_reader_tree.py
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</li>
<li class="file-stats">
<a href="#251a29ad9081268af6ea4c86177b85f7fa548683">
dendropy/test/test_tree_shape_kernel.py
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</li>
<li class="file-stats">
<a href="#9aba85fbb86cff51b47835c231b8f34115234f88">
dendropy/utility/textprocessing.py
</a>
</li>
<li class="file-stats">
<a href="#8c91c0296909b5ea3c496fde69e9dc44a6c6ae5f">
setup.cfg
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="4990be809a537bf86e4be2fe2e8251c83d8bd129">
<a href="https://salsa.debian.org/med-team/python-dendropy/compare/0703a46f92ffe8f38a03f3d0390cbb304ea0ab3b...bf22906f2c356d84b5290a66349421ffec1155ef#4990be809a537bf86e4be2fe2e8251c83d8bd129"><strong>CHANGES.rst</strong></a>
<hr>
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<td class="diff-line-num new new_line" data-linenumber="1" 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">
1
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Release 4.3.0</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2" 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">
2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">-------------</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" 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">
3
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4" 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">
4
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">- [SumTrees]: Important bugfix in tracking splits on consensus tree from rooted trees: previously it was possible for a split on the consensus tree to be ignored, resulting in a null (0) edge length and no (0.0) support.</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
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<td class="diff-line-num new new_line" data-linenumber="5" 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">
5
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">- Added ``sumlabels.py`` application.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">- BD tree (``dendropy.model.birth_death_tree``) now allows for preservation of extinct tips.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">- Improved performance of character subset export</span>
</pre>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Release 4.2.0</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">-------------</span>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<li id="51d5d11207906423aac7850d39aae6511f604ff0">
<a href="https://salsa.debian.org/med-team/python-dendropy/compare/0703a46f92ffe8f38a03f3d0390cbb304ea0ab3b...bf22906f2c356d84b5290a66349421ffec1155ef#51d5d11207906423aac7850d39aae6511f604ff0"><strong>DendroPy.egg-info/PKG-INFO</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Metadata-Version: 1.1</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: DendroPy</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: 4.<span class="idiff left right">2</span>.0</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 4.<span class="idiff left right">3</span>.0</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Home-page: http://packages.python.org/DendroPy/</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Author: Jeet Sukumaran and Mark T. Holder</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -115,7 +115,7 @@ Description: .. image:: https://raw.githubusercontent.com/jeetsukumaran/DendroPy</td>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="plaintext"> Current Release</span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="plaintext"> ===============</span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="plaintext"> The current release of DendroPy is version 4.<span class="idiff left right">2.0 (master-5051a46, 2016-12-28 13:25</span>:19).</span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"> The current release of DendroPy is version 4.<span class="idiff left right">3.0 (master-e251bcf, 2017-07-06 21:23</span>:19).</span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="plaintext">Keywords: phylogenetics phylogeny phylogenies phylogeography evolution evolutionary biology systematics coalescent population genetics phyloinformatics bioinformatics</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="131" 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="131" 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">@@ -131,5 +131,7 @@ Classifier: Programming Language :: Python :: 3.1</td>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="plaintext">Classifier: Programming Language :: Python :: 3.2</span>
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<td class="diff-line-num old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="plaintext">Classifier: Programming Language :: Python :: 3.3</span>
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<td class="diff-line-num old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="plaintext">Classifier: Programming Language :: Python :: 3.4</span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">Classifier: Programming Language :: Python :: 3.5</span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">Classifier: Programming Language :: Python :: 3.6</span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="plaintext">Classifier: Programming Language :: Python</span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="plaintext">Classifier: Topic :: Scientific/Engineering :: Bio-Informatics</span></pre>
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</li>
<li id="2fa9ec55009692e0499b33faf948b0b569185991">
<a href="https://salsa.debian.org/med-team/python-dendropy/compare/0703a46f92ffe8f38a03f3d0390cbb304ea0ab3b...bf22906f2c356d84b5290a66349421ffec1155ef#2fa9ec55009692e0499b33faf948b0b569185991"><strong>DendroPy.egg-info/SOURCES.txt</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">@@ -11,6 +11,7 @@ DendroPy.egg-info/entry_points.txt</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">DendroPy.egg-info/requires.txt</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">DendroPy.egg-info/top_level.txt</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">DendroPy.egg-info/zip-safe</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">applications/sumlabels/sumlabels.py</span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">applications/sumtrees/sumtrees.py</span>
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15
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">dendropy/__init__.py</span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">dendropy/__main__.py</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">@@ -63,6 +64,7 @@ dendropy/interop/genbank.py</td>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext">dendropy/interop/muscle.py</span>
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64
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext">dendropy/interop/paup.py</span>
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext">dendropy/interop/raxml.py</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">dendropy/interop/rspr.py</span>
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66
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext">dendropy/interop/rstats.py</span>
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67
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext">dendropy/interop/seqgen.py</span>
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext">dendropy/legacy/__init__.py</span>
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<a href="https://salsa.debian.org/med-team/python-dendropy/compare/0703a46f92ffe8f38a03f3d0390cbb304ea0ab3b...bf22906f2c356d84b5290a66349421ffec1155ef#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf"><strong>PKG-INFO</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Metadata-Version: 1.1</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: DendroPy</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: 4.<span class="idiff left right">2</span>.0</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 4.<span class="idiff left right">3</span>.0</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Home-page: http://packages.python.org/DendroPy/</span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Author: Jeet Sukumaran and Mark T. Holder</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -115,7 +115,7 @@ Description: .. image:: https://raw.githubusercontent.com/jeetsukumaran/DendroPy</td>
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="plaintext"> Current Release</span>
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="plaintext"> ===============</span>
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="plaintext"> </span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="plaintext"> The current release of DendroPy is version 4.<span class="idiff left right">2.0 (master-5051a46, 2016-12-28 13:25</span>:19).</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"> The current release of DendroPy is version 4.<span class="idiff left right">3.0 (master-e251bcf, 2017-07-06 21:23</span>:19).</span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="plaintext">Keywords: phylogenetics phylogeny phylogenies phylogeography evolution evolutionary biology systematics coalescent population genetics phyloinformatics bioinformatics</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">@@ -131,5 +131,7 @@ Classifier: Programming Language :: Python :: 3.1</td>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="plaintext">Classifier: Programming Language :: Python :: 3.2</span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="plaintext">Classifier: Programming Language :: Python :: 3.3</span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="plaintext">Classifier: Programming Language :: Python :: 3.4</span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">Classifier: Programming Language :: Python :: 3.5</span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">Classifier: Programming Language :: Python :: 3.6</span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="plaintext">Classifier: Programming Language :: Python</span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="plaintext">Classifier: Topic :: Scientific/Engineering :: Bio-Informatics</span></pre>
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<li id="01b611f94e0c55bb8374fd267be915753980c504">
<a href="https://salsa.debian.org/med-team/python-dendropy/compare/0703a46f92ffe8f38a03f3d0390cbb304ea0ab3b...bf22906f2c356d84b5290a66349421ffec1155ef#01b611f94e0c55bb8374fd267be915753980c504"><strong>applications/sumlabels/sumlabels.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#! /usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">##############################################################################</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">## DendroPy Phylogenetic Computing Library.</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">## Copyright 2010 Jeet Sukumaran and Mark T. Holder.</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">## All rights reserved.</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">## See "LICENSE.txt" for terms and conditions of usage.</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">## If you use this work or any portion thereof in published work,</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">## please cite it as:</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">## for phylogenetic computing. Bioinformatics 26: 1569-1571.</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">##############################################################################</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="s" style="color: #d14;">Marge labels of splits/branches from different input trees onto corresponding</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="s" style="color: #d14;">splits/branches of a single tree.</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"></span>
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24
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<pre style="margin: 0;">+<span id="LC24" 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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25
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<pre style="margin: 0;">+<span id="LC25" 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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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">argparse</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">datetime</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">time</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">socket</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">getpass</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">platform</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">dendropy</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">dendropy.utility.messaging</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ConsoleMessenger</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">dendropy.utility.cli</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">confirm_overwrite</span><span class="p">,</span> <span class="n" style="color: #333;">show_splash</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"><span class="n" style="color: #333;">_program_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"SumLabels"</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"><span class="n" style="color: #333;">_program_subtitle</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Phylogenetic Tree Label Concatenation"</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"><span class="n" style="color: #333;">_program_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Jan 20 2017"</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"><span class="n" style="color: #333;">_program_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Version 2.0.0 (</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s)"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">_program_date</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"><span class="n" style="color: #333;">_program_author</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Jeet Sukumaran"</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"><span class="n" style="color: #333;">_program_contact</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"jeetsukumaran@gmail.com"</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"><span class="n" style="color: #333;">_program_copyright</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Copyright (C) 2017 Jeet Sukumaran.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> \</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="s" style="color: #d14;">"License GPLv3+: GNU GPL version 3 or later.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> \</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="s" style="color: #d14;">"This is free software: you are free to change</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">and redistribute it. "</span> \</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="s" style="color: #d14;">"There is NO WARRANTY,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">to the extent permitted by law."</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main_cli</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">description</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">_program_name</span><span class="p">,</span> <span class="n" style="color: #333;">_program_version</span><span class="p">,</span> <span class="n" style="color: #333;">_program_subtitle</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argparse</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ArgumentParser</span><span class="p">(</span><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_program_version</span><span class="p">,</span> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">description</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="s" style="color: #d14;">"sources"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"TREEFILE"</span><span class="p">,</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"+"</span><span class="p">)</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-t"</span><span class="p">,</span><span class="s" style="color: #d14;">"--target"</span><span class="p">,</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"target_tree_filepath"</span><span class="p">,</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"path to file with tree (Newick or NEXUS format) "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="66" 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">
66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"to which labels will be written"</span><span class="p">)</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--preserve-target-labels"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="68" 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">
68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="69" 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">
69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"preserve_target_labels"</span><span class="p">,</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="71" 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">
71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"keep any existing labels on target tree (by default, these will be cleared before writing the new labels)"</span><span class="p">)</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--rooted"</span><span class="p">,</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="74" 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">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"rooted_trees"</span><span class="p">,</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="76" 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">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"treat trees as rooted"</span><span class="p">)</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--unrooted"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="78" 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">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_false"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="79" 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">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"rooted_trees"</span><span class="p">,</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="81" 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">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"treat trees as unrooted"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="82" 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">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--ignore-missing-source"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="83" 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">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="84" 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">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"ignore_missing_source"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="85" 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">
85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="86" 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">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"ignore missing source tree files (at least one must exist!)"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="87" 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">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-o"</span><span class="p">,</span><span class="s" style="color: #d14;">"--output"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="88" 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">
88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"output_filepath"</span><span class="p">,</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"path to output file (if not given, will print to standard output)"</span><span class="p">)</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-s"</span><span class="p">,</span><span class="s" style="color: #d14;">"--separator"</span><span class="p">,</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"separator"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="93" 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">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"/"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="94" 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">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"string to use to separate labels from different source trees (default='</span><span class="si" style="color: #d14;">%(default)</span><span class="s" style="color: #d14;">s')"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="95" 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">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--no-taxa-block"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="96" 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">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_false"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="97" 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">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"include_taxa_block"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="98" 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">
98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">default</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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<td class="diff-line-num new new_line" data-linenumber="99" 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">
99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"do not include a taxa block in the output treefile (otherwise will create taxa block by default)"</span><span class="p">)</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-c"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--additional-comments"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="101" 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">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="102" 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">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"additional_comments"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="103" 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">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"additional comments to be added to the summary file"</span><span class="p">)</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--to-newick"</span><span class="p">,</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="107" 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">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"to_newick_format"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="108" 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">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="109" 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">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"save results in NEWICK (PHYLIP) format (default is to save in NEXUS format)"</span><span class="p">)</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--to-phylip"</span><span class="p">,</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">,</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"to_newick_format"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="113" 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">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="114" 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">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"same as --to-newick"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="115" 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">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-r"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--replace"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="116" 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">
116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="117" 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">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"replace"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="118" 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">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="119" 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">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"replace/overwrite output file without asking if it already exists "</span><span class="p">)</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-q"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--quiet"</span><span class="p">,</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">,</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"quiet"</span><span class="p">,</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"suppress ALL logging, progress and feedback messages"</span><span class="p">)</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">()</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">quiet</span><span class="p">:</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">messaging_level</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ConsoleMessenger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ERROR_MESSAGING_LEVEL</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">messaging_level</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ConsoleMessenger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">INFO_MESSAGING_LEVEL</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">messenger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ConsoleMessenger</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"SumLabels"</span><span class="p">,</span> <span class="n" style="color: #333;">messaging_level</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">messaging_level</span><span class="p">)</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># splash</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" 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;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">quiet</span><span class="p">:</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">show_splash</span><span class="p">(</span><span class="n" style="color: #333;">prog_name</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_program_name</span><span class="p">,</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">prog_subtitle</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_program_subtitle</span><span class="p">,</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">prog_version</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_program_version</span><span class="p">,</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">prog_author</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_program_author</span><span class="p">,</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">prog_copyright</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_program_copyright</span><span class="p">,</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="p">)</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">###################################################</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Source file idiot checking</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">source_filepaths</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="147" 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">
147
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<pre style="margin: 0;">+<span id="LC147" 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;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sources</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="148" 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">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">fpath</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sources</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="149" 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">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">fpath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">expanduser</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">expandvars</span><span class="p">(</span><span class="n" style="color: #333;">fpath</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="150" 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">
150
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<pre style="margin: 0;">+<span id="LC150" 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;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">fpath</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="151" 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">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ignore_missing_source</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="152" 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">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">messenger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">send_warning</span><span class="p">(</span><span class="s" style="color: #d14;">"Source file not found: '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">fpath</span><span class="p">)</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">messenger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"Terminating due to missing source files. "</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"Use the '--ignore-missing-source' option to continue even "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="156" 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">
156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"if some files are missing."</span><span class="p">)</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="159" 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">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="n" style="color: #333;">source_filepaths</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">fpath</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="160" 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">
160
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<pre style="margin: 0;">+<span id="LC160" 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;">source_filepaths</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">messenger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"No valid sources of input trees specified. "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="162" 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">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"Please provide the path to at least one (valid and existing) file "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="163" 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">
163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"containing trees"</span><span class="p">)</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</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="n" style="color: #333;">messenger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"No sources of input trees specified. "</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"Please provide the path to at least one (valid and existing) file "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="168" 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">
168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"containing tree samples to summarize. See '--help' for other options."</span><span class="p">)</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;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">###################################################</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Lots of other idiot-checking ...</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># target tree</span></span>
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<td class="diff-line-num new new_line" data-linenumber="175" 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">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">target_tree_filepath</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="176" 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">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="n" style="color: #333;">target_tree_filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">expanduser</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">expandvars</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">target_tree_filepath</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="177" 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">
177
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<pre style="margin: 0;">+<span id="LC177" 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;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">target_tree_filepath</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="178" 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">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="n" style="color: #333;">messenger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"Target tree file not found: '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">target_tree_filepath</span><span class="p">)</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="181" 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">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">messenger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"Target tree file not specified: use the '-t' or '--target' option to provide path to target tree"</span><span class="p">)</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># output</span></span>
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<td class="diff-line-num new new_line" data-linenumber="185" 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">
185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output_filepath</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">output_dest</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdout</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">output_fpath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">expanduser</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">expandvars</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output_filepath</span><span class="p">))</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">confirm_overwrite</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">output_fpath</span><span class="p">,</span> <span class="n" style="color: #333;">replace_without_asking</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">):</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">output_dest</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">output_fpath</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</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;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># taxon set to handle target trees</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">master_taxon_namespace</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dendropy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TaxonNamespace</span><span class="p">()</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">is_rooted</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rooted_trees</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"> <span class="n" style="color: #333;">messenger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Reading target tree: '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">target_tree_filepath</span><span class="p">)</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">target_tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_rooted</span><span class="p">:</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">rooting</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"force-rooted"</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">rooting</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">tree</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">dendropy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">yield_from_files</span><span class="p">(</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="p">[</span><span class="n" style="color: #333;">target_tree_filepath</span><span class="p">,</span> <span class="s" style="color: #d14;">"rU"</span><span class="p">,],</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="n" style="color: #333;">schema</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'nexus/newick'</span><span class="p">,</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">taxon_namespace</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">master_taxon_namespace</span><span class="p">,</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">rooting</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">rooting</span><span class="p">):</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">target_tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tree</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">bipartition_labels</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">src_fpath</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">source_filepaths</span><span class="p">:</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">messenger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Reading source tree(s) from: '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">src_fpath</span><span class="p">)</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">tree</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">dendropy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">yield_from_files</span><span class="p">(</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"> <span class="p">[</span><span class="n" style="color: #333;">src_fpath</span><span class="p">,],</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"> <span class="n" style="color: #333;">schema</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'nexus/newick'</span><span class="p">,</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">taxon_namespace</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">master_taxon_namespace</span><span class="p">,</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"> <span class="n" style="color: #333;">rooting</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">rooting</span><span class="p">):</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_bipartitions</span><span class="p">()</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">bipartition</span><span class="p">,</span> <span class="n" style="color: #333;">edge</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bipartition_edge_map</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">edge</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">head_node</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">label</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" 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;">label</span><span class="p">:</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"> <span class="n" style="color: #333;">bipartition_labels</span><span class="p">[</span><span class="n" style="color: #333;">bipartition</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">label</span><span class="p">)</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">KeyError</span><span class="p">:</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"> <span class="n" style="color: #333;">bipartition_labels</span><span class="p">[</span><span class="n" style="color: #333;">bipartition</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">label</span><span class="p">]</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"> <span class="n" style="color: #333;">messenger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Mapping labels"</span><span class="p">)</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="n" style="color: #333;">target_tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_bipartitions</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="229" 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">
229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">bipartition</span><span class="p">,</span> <span class="n" style="color: #333;">edge</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">target_tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bipartition_edge_map</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"> <span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">preserve_target_labels</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">edge</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">head_node</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">label</span><span class="p">:</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="python"> <span class="n" style="color: #333;">label</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">edge</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">head_node</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">label</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">preserve_target_labels</span><span class="p">:</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"> <span class="n" style="color: #333;">edge</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">head_node</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">bipartition</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">bipartition_labels</span><span class="p">:</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"> <span class="n" style="color: #333;">label</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="n" style="color: #333;">bipartition_labels</span><span class="p">[</span><span class="n" style="color: #333;">bipartition</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC237" 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="LC238" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># messenger.send_warning("Split on target tree not found in source trees: ignoring")</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">label</span><span class="p">:</span></span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"> <span class="n" style="color: #333;">edge</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">head_node</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">separator</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">label</span><span class="p">)</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"> <span class="n" style="color: #333;">output_dataset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dendropy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DataSet</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"> <span class="n" style="color: #333;">tree_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">output_dataset</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new_tree_list</span><span class="p">(</span><span class="n" style="color: #333;">taxon_namespace</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">master_taxon_namespace</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python"> <span class="n" style="color: #333;">tree_list</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">target_tree</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">to_newick_format</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"> <span class="n" style="color: #333;">output_dataset</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">output_dest</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"> <span class="n" style="color: #333;">schema</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"newick"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"> <span class="n" style="color: #333;">suppress_rooting</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"> <span class="n" style="color: #333;">suppress_edge_lengths</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="251" 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">
251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"> <span class="n" style="color: #333;">unquoted_underscores</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="252" 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">
252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"> <span class="n" style="color: #333;">preserve_spaces</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="253" 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">
253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="n" style="color: #333;">store_tree_weights</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="254" 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">
254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="n" style="color: #333;">suppress_annotations</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="255" 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">
255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"> <span class="n" style="color: #333;">annotations_as_nhx</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="256" 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">
256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="python"> <span class="n" style="color: #333;">suppress_item_comments</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="257" 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">
257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="python"> <span class="n" style="color: #333;">suppress_leaf_taxon_labels</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="258" 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">
258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="python"> <span class="n" style="color: #333;">suppress_leaf_node_labels</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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<td class="diff-line-num new new_line" data-linenumber="259" 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">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="python"> <span class="n" style="color: #333;">suppress_internal_taxon_labels</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python"> <span class="n" style="color: #333;">suppress_internal_node_labels</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="261" 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">
261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="python"> <span class="n" style="color: #333;">node_label_element_separator</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">' '</span><span class="p">,</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="python"> <span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="263" 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">
263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="264" 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">
264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">include_taxa_block</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="265" 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">
265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="python"> <span class="n" style="color: #333;">simple</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<td class="diff-line-num new new_line" data-linenumber="266" 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">
266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="267" 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">
267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="python"> <span class="n" style="color: #333;">simple</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<td class="diff-line-num new new_line" data-linenumber="268" 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">
268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="python"> <span class="n" style="color: #333;">comment</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="269" 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">
269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="270" 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">
270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="python"> <span class="n" style="color: #333;">username</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getpass</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getuser</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="271" 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">
271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="272" 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">
272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="python"> <span class="n" style="color: #333;">username</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"a user"</span></span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="python"> <span class="n" style="color: #333;">comment</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s by </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s."</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">_program_name</span><span class="p">,</span> <span class="n" style="color: #333;">_program_version</span><span class="p">,</span> <span class="n" style="color: #333;">_program_author</span><span class="p">))</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python"> <span class="n" style="color: #333;">comment</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"Using DendroPy Version </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s by Jeet Sukumaran and Mark T. Holder."</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">dendropy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__version__</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="276" 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">
276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="python"> <span class="n" style="color: #333;">python_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"["</span><span class="p">,</span> <span class="s" style="color: #d14;">"("</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"]"</span><span class="p">,</span><span class="s" style="color: #d14;">")"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="277" 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">
277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="python"> <span class="n" style="color: #333;">comment</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"Running under Python </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s on </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s."</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">python_version</span><span class="p">,</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">platform</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="278" 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">
278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="python"> <span class="n" style="color: #333;">comment</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"Executed on </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s by </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s@</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s."</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">platform</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">node</span><span class="p">(),</span> <span class="n" style="color: #333;">username</span><span class="p">,</span> <span class="n" style="color: #333;">socket</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">gethostname</span><span class="p">()))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="279" 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">
279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">additional_comments</span><span class="p">:</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="python"> <span class="n" style="color: #333;">comment</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="python"> <span class="n" style="color: #333;">comment</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">additional_comments</span><span class="p">)</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="python"> <span class="n" style="color: #333;">output_dataset</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="python"> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">output_dest</span><span class="p">,</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="python"> <span class="n" style="color: #333;">schema</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"nexus"</span><span class="p">,</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"> <span class="n" style="color: #333;">simple</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">simple</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="286" 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">
286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python"> <span class="n" style="color: #333;">file_comments</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">comment</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="287" 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">
287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="python"> <span class="n" style="color: #333;">suppress_rooting</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="python"> <span class="n" style="color: #333;">unquoted_underscores</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="python"> <span class="n" style="color: #333;">preserve_spaces</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="python"> <span class="n" style="color: #333;">store_tree_weights</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="python"> <span class="n" style="color: #333;">suppress_annotations</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="python"> <span class="n" style="color: #333;">annotations_as_nhx</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="python"> <span class="n" style="color: #333;">suppress_item_comments</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="python"> <span class="n" style="color: #333;">suppress_leaf_taxon_labels</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="python"> <span class="n" style="color: #333;">suppress_leaf_node_labels</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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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="python"> <span class="n" style="color: #333;">suppress_internal_taxon_labels</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="python"> <span class="n" style="color: #333;">suppress_internal_node_labels</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="python"> <span class="n" style="color: #333;">node_label_element_separator</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">' '</span><span class="p">,</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="python"> <span class="p">)</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" 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;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">output_filepath</span><span class="p">:</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="python"> <span class="n" style="color: #333;">messenger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Results written to: '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'."</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">output_fpath</span><span class="p">))</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="python"></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'__main__'</span><span class="p">:</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="python"> <span class="n" style="color: #333;">main_cli</span><span class="p">()</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-dendropy/compare/0703a46f92ffe8f38a03f3d0390cbb304ea0ab3b...bf22906f2c356d84b5290a66349421ffec1155ef#5b6f5675e8179826bb0ae13324ca4b3979634f0e"><strong>applications/sumtrees/sumtrees.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">@@ -1659,6 +1659,7 @@ def main():</td>
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1659
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1659
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<pre style="margin: 0;"> <span id="LC1659" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1660
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1660
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<pre style="margin: 0;"> <span id="LC1660" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">summary_target</span><span class="p">)</span></span>
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1661
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1661
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<pre style="margin: 0;"> <span id="LC1661" class="line" lang="python"> <span class="n" style="color: #333;">_message_and_log</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">,</span> <span class="n" style="color: #333;">wrap</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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1662
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<pre style="margin: 0;">+<span id="LC1662" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encode_bipartitions</span><span class="p">()</span></span>
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1662
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1663
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<pre style="margin: 0;"> <span id="LC1663" class="line" lang="python"> <span class="n" style="color: #333;">target_trees</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1664" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1664
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<pre style="margin: 0;"> <span id="LC1665" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/python-dendropy/compare/0703a46f92ffe8f38a03f3d0390cbb304ea0ab3b...bf22906f2c356d84b5290a66349421ffec1155ef#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-dendropy (4.3.0+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Standards-Version: 4.1.3</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * debhelper 11</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * d/rules: do not parse d/changelog</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Testsuite: autopkgtest-pkg-python</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 19 Feb 2018 09:31:21 +0100</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">python-dendropy (4.2.0+dfsg-1) unstable; urgency=medium</span>
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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"> * New upstream version</span>
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<a href="https://salsa.debian.org/med-team/python-dendropy/compare/0703a46f92ffe8f38a03f3d0390cbb304ea0ab3b...bf22906f2c356d84b5290a66349421ffec1155ef#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">0</span></span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">1</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-dendropy/compare/0703a46f92ffe8f38a03f3d0390cbb304ea0ab3b...bf22906f2c356d84b5290a66349421ffec1155ef#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,14 +2,15 @@ Source: python-dendropy</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: python</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Testsuite: autopkgtest-pkg-python</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 1<span class="idiff left right">0</span>),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper (>= 1<span class="idiff left right">1~</span>),</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> dh-python,</span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python-all,</span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> python-setuptools,</span>
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10
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> python3-all,</span>
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11
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> python3-setuptools</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">Standards-Version: <span class="idiff left right">3.9.8</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Standards-Version: <span class="idiff left right">4.1.3</span></span>
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13
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/python-dendropy.git</span>
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14
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Git: https://anonscm.debian.org/git/debian-med/python-dendropy.git</span>
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15
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Homepage: http://dendropy.org/</span>
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<li id="33c5f920dd6e87de8413f3340f04483f01cfc9a9">
<a href="https://salsa.debian.org/med-team/python-dendropy/compare/0703a46f92ffe8f38a03f3d0390cbb304ea0ab3b...bf22906f2c356d84b5290a66349421ffec1155ef#33c5f920dd6e87de8413f3340f04483f01cfc9a9"><strong>debian/patches/0001-Fix-bug-where-encoding-for-default-locale-is-None.patch</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">@@ -9,7 +9,7 @@ Subject: [PATCH] Fix bug where encoding for default locale is None.</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/dendropy/utility/textprocessing.py</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/dendropy/utility/textprocessing.py</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -4<span class="idiff left right">2,6 +42,9 @@ ENCODING = locale.getdefaultlocale()[1]</span></span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -4<span class="idiff left right">5,6 +45,9 @@ except ValueError:</span></span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> if ENCODING == None:</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> ENCODING = 'UTF-8'</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> </span>
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<a href="https://salsa.debian.org/med-team/python-dendropy/compare/0703a46f92ffe8f38a03f3d0390cbb304ea0ab3b...bf22906f2c356d84b5290a66349421ffec1155ef#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,9 +2,6 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">DH_VERBOSE := 1</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">DEBPKGNAME:=$(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">docpkg:=$(DEBPKGNAME)-doc</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">SUMTREES:=sumtrees</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">export PYBUILD_NAME=dendropy</span>
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<a href="https://salsa.debian.org/med-team/python-dendropy/compare/0703a46f92ffe8f38a03f3d0390cbb304ea0ab3b...bf22906f2c356d84b5290a66349421ffec1155ef#94b75511da9ff25cd971f3b79816e04bf5328cf9"><strong>dendropy/__init__.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="104" 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">@@ -104,7 +104,7 @@ import collections</td>
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"><span class="n" style="color: #333;">version_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collections</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">namedtuple</span><span class="p">(</span><span class="s" style="color: #d14;">"dendropy_version_info"</span><span class="p">,</span></span>
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">"major"</span><span class="p">,</span> <span class="s" style="color: #d14;">"minor"</span><span class="p">,</span> <span class="s" style="color: #d14;">"micro"</span><span class="p">,</span> <span class="s" style="color: #d14;">"releaselevel"</span><span class="p">])(</span></span>
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">major</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">4</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">minor</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">minor</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;"><span class="idiff left right">3</span></span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">micro</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">releaselevel</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"> <span class="p">)</span></span>
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<li id="b55e66c8f57b5d6320b903d5d60ec7aa2f6728ed">
<a href="https://salsa.debian.org/med-team/python-dendropy/compare/0703a46f92ffe8f38a03f3d0390cbb304ea0ab3b...bf22906f2c356d84b5290a66349421ffec1155ef#b55e66c8f57b5d6320b903d5d60ec7aa2f6728ed"><strong>dendropy/dataio/newickreader.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">@@ -303,7 +303,8 @@ class NewickReader(ioservice.DataReader):</td>
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="python"> <span class="n" style="color: #333;">taxon_symbol_map_fn</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">taxon_symbol_mapper</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">require_taxon_for_symbol</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">tree</span></span>
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tree</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">StopIteration</span></span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># raise StopIteration</span></span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_read</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span></span>
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310
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="python"> <span class="n" style="color: #333;">stream</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/python-dendropy/compare/0703a46f92ffe8f38a03f3d0390cbb304ea0ab3b...bf22906f2c356d84b5290a66349421ffec1155ef#225326cf9a24fd8ceba1a72f313e0744142193e1"><strong>dendropy/dataio/nexuswriter.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">@@ -178,7 +178,7 @@ class NexusWriter(ioservice.DataWriter):</td>
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178
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># and need to be removed so as not to cause problems with our keyword</span></span>
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179
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># validation scheme</span></span>
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180
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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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">simple</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">"simple"</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">suppress_taxa_blocks</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">"suppress_taxa_block"</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">suppress_taxa_blocks</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">"suppress_taxa_block<span class="idiff left right">s</span>"</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">suppress_block_titles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">"suppress_block_titles"</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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183
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file_comments</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">"file_comments"</span><span class="p">,</span> <span class="p">[])</span></span>
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184
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file_comments</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/python-dendropy/compare/0703a46f92ffe8f38a03f3d0390cbb304ea0ab3b...bf22906f2c356d84b5290a66349421ffec1155ef#f47990668ba22c907489bd48a006f8c1a4fc24bb"><strong>dendropy/datamodel/charmatrixmodel.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">@@ -1606,7 +1606,7 @@ class CharacterMatrix(</td>
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<pre style="margin: 0;"> <span id="LC1606" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># recalculated, which will require some careful and perhaps arbitrary</span></span>
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1607
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<pre style="margin: 0;"> <span id="LC1607" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># handling of corner cases</span></span>
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1608
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<pre style="margin: 0;"> <span id="LC1608" class="line" lang="python"> <span class="n" style="color: #333;">clone</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">character_subsets</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">container</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OrderedCaselessDict</span><span class="p">()</span></span>
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1609
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<pre style="margin: 0;">-<span id="LC1609" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"><span class="idiff left right"># clone.clone_from(self</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC1609" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">indices</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">set</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">indices</span></span><span class="p">)</span></span>
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1610
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<pre style="margin: 0;"> <span id="LC1610" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">vec</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">clone</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC1611" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cell_idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">vec</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="mi" style="color: #099;">1</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC1612" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cell_idx</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">indices</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/python-dendropy/compare/0703a46f92ffe8f38a03f3d0390cbb304ea0ab3b...bf22906f2c356d84b5290a66349421ffec1155ef#eabc6891343b2f85f7cf4519e497197f4f9f67e3"><strong>dendropy/datamodel/taxonmodel.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">@@ -548,6 +548,7 @@ class TaxonNamespace(</td>
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<pre style="margin: 0;"> <span id="LC548" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">TypeError</span><span class="p">(</span><span class="s" style="color: #d14;">"TaxonNamespace() takes at most 1 non-keyword argument ({} given)"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)))</span></span>
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<pre style="margin: 0;"> <span id="LC549" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">args</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>
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># special case: construct from argument</span></span>
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="python"> <span class="n" style="color: #333;">basemodel</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DataObject</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">label</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">kwargs_set_label</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC552" class="line" lang="python"> <span class="n" style="color: #333;">other</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC553" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">other</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC554" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">Taxon</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/python-dendropy/compare/0703a46f92ffe8f38a03f3d0390cbb304ea0ab3b...bf22906f2c356d84b5290a66349421ffec1155ef#58fa80fee5ac7a2b78c397754b90c48ed3d64b2a"><strong>dendropy/datamodel/treemodel.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">@@ -772,6 +772,9 @@ class Edge(</td>
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<pre style="margin: 0;"> <span id="LC772" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__eq__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">other</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC773" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">other</span></span>
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<pre style="margin: 0;"> <span id="LC774" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__lt__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">other</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">id</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">id</span><span class="p">(</span><span class="n" style="color: #333;">other</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC778" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">###########################################################################</span></span>
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<pre style="margin: 0;"> <span id="LC779" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">### Basic Structure</span></span>
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<pre style="margin: 0;"> <span id="LC780" 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">@@ -6103,7 +6106,7 @@ class Tree(</td>
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<pre style="margin: 0;"> <span id="LC6106" class="line" lang="python"> <span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC6107" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">s</span></span>
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6108
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<pre style="margin: 0;"> <span id="LC6108" class="line" lang="python"></span>
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6106
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<pre style="margin: 0;">-<span id="LC6106" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">as_python_source</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">tree_obj_name</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">tree_args</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">oids</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC6109" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">as_python_source</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">tree_obj_name</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">tree_args</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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6107
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6110
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<pre style="margin: 0;"> <span id="LC6110" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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6108
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6111
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<pre style="margin: 0;"> <span id="LC6111" class="line" lang="python"><span class="s" style="color: #d14;"> Returns string that will rebuild this tree in Python.</span></span>
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6109
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6112
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<pre style="margin: 0;"> <span id="LC6112" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6119,10 +6122,9 @@ class Tree(</td>
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6122
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<pre style="margin: 0;"> <span id="LC6122" class="line" lang="python"> <span class="n" style="color: #333;">tree_args</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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6123
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<pre style="margin: 0;"> <span id="LC6123" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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6121
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6124
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<pre style="margin: 0;"> <span id="LC6124" class="line" lang="python"> <span class="n" style="color: #333;">tree_args</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">", "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">tree_args</span></span>
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<pre style="margin: 0;">-<span id="LC6122" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s = dendropy.Tree(label=</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="si" style="color: #d14;"><span class="idiff left">%</span></span><span class="s" style="color: #d14;"><span class="idiff right">s</span>)"</span> \</span>
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<pre style="margin: 0;">+<span id="LC6125" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s = dendropy.Tree(label=</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s)"</span> \</span>
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6126
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<pre style="margin: 0;"> <span id="LC6126" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">tree_obj_name</span><span class="p">,</span></span>
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6127
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<pre style="margin: 0;"> <span id="LC6127" class="line" lang="python"> <span class="n" style="color: #333;">label</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC6125" class="line" lang="python"> <span class="n" style="color: #333;">oid_str</span><span class="p">,</span></span>
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6128
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<pre style="margin: 0;"> <span id="LC6128" class="line" lang="python"> <span class="n" style="color: #333;">tree_args</span><span class="p">))</span></span>
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6129
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<pre style="margin: 0;"> <span id="LC6129" class="line" lang="python"></span>
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6128
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6130
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<pre style="margin: 0;"> <span id="LC6130" class="line" lang="python"> <span class="n" style="color: #333;">taxon_obj_namer</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="s" style="color: #d14;">"tax_</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="nb" style="color: #0086b3;">id</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6132" 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="6134" 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">@@ -6132,11 +6134,11 @@ class Tree(</td>
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6132
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6134
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<pre style="margin: 0;"> <span id="LC6134" class="line" lang="python"> <span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"'"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">taxon</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"'"</span></span>
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<pre style="margin: 0;"> <span id="LC6135" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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6136
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<pre style="margin: 0;"> <span id="LC6136" class="line" lang="python"> <span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"None"</span></span>
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<pre style="margin: 0;">-<span id="LC6135" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s = </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s.taxon_namespace.require_taxon(label=</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="si" style="color: #d14;"><span class="idiff left">%</span></span><span class="s" style="color: #d14;"><span class="idiff right">s</span>)"</span> \</span>
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<pre style="margin: 0;">+<span id="LC6137" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s = </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s.taxon_namespace.require_taxon(label=</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s)"</span> \</span>
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6138
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<pre style="margin: 0;"> <span id="LC6138" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">tobj_name</span><span class="p">,</span></span>
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6139
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<pre style="margin: 0;"> <span id="LC6139" class="line" lang="python"> <span class="n" style="color: #333;">tree_obj_name</span><span class="p">,</span></span>
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6140
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<pre style="margin: 0;"> <span id="LC6140" class="line" lang="python"> <span class="n" style="color: #333;">label</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC6139" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left right">oid_str</span></span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC6141" class="line" lang="python"> <span class="p">))</span></span>
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6142
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<pre style="margin: 0;"> <span id="LC6142" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC6143" class="line" lang="python"> <span class="n" style="color: #333;">node_obj_namer</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="s" style="color: #d14;">"nd_</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="nb" style="color: #0086b3;">id</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC6144" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">node</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">preorder_node_iter</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">@@ -6153,13 +6155,13 @@ class Tree(</td>
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<pre style="margin: 0;"> <span id="LC6155" class="line" lang="python"> <span class="n" style="color: #333;">ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">taxon_obj_namer</span><span class="p">(</span><span class="n" style="color: #333;">child</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">taxon</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC6156" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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6157
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<pre style="margin: 0;"> <span id="LC6157" class="line" lang="python"> <span class="n" style="color: #333;">ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"None"</span></span>
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<pre style="margin: 0;">-<span id="LC6156" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s = </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s.new_child(label=</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, taxon=</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, edge_length=</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="si" style="color: #d14;"><span class="idiff left">%</span></span><span class="s" style="color: #d14;"><span class="idiff right">s</span>)"</span> <span class="o" style="font-weight: 600;">%</span></span>
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<pre style="margin: 0;">+<span id="LC6158" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s = </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s.new_child(label=</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, taxon=</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, edge_length=</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s)"</span> <span class="o" style="font-weight: 600;">%</span></span>
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<pre style="margin: 0;"> <span id="LC6159" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">node_obj_namer</span><span class="p">(</span><span class="n" style="color: #333;">child</span><span class="p">),</span></span>
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6160
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<pre style="margin: 0;"> <span id="LC6160" class="line" lang="python"> <span class="n" style="color: #333;">nn</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC6161" class="line" lang="python"> <span class="n" style="color: #333;">label</span><span class="p">,</span></span>
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6162
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<pre style="margin: 0;"> <span id="LC6162" class="line" lang="python"> <span class="n" style="color: #333;">ct</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC6163" class="line" lang="python"> <span class="n" style="color: #333;">child</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">edge</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC6162" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left right">oid_str</span></span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC6164" class="line" lang="python"> <span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC6165" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC6166" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC6167" class="line" lang="python"></span>
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<li id="02a7bb8f9dfaaf9f7b635022e9ddc59df60419df">
<a href="https://salsa.debian.org/med-team/python-dendropy/compare/0703a46f92ffe8f38a03f3d0390cbb304ea0ab3b...bf22906f2c356d84b5290a66349421ffec1155ef#02a7bb8f9dfaaf9f7b635022e9ddc59df60419df"><strong>dendropy/interop/rspr.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#! /usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">##############################################################################</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">## DendroPy Phylogenetic Computing Library.</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">## All rights reserved.</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">## See "LICENSE.rst" for terms and conditions of usage.</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">## If you use this work or any portion thereof in published work,</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">## please cite it as:</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">## for phylogenetic computing. Bioinformatics 26: 1569-1571.</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">##############################################################################</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="s" style="color: #d14;">Wrapper for interacting with RSPR</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">subprocess</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uuid</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">tempfile</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">socket</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">random</span></span>
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<pre style="margin: 0;">+<span id="LC28" 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="LC29" 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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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">dendropy</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">dendropy.utility.messaging</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_logger</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">dendropy.utility</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">processio</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">dendropy.utility</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">textprocessing</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"><span class="n" style="color: #333;">_LOG</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_logger</span><span class="p">(</span><span class="s" style="color: #d14;">"interop.rspr"</span><span class="p">)</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"><span class="n" style="color: #333;">HOSTNAME</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">socket</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">gethostname</span><span class="p">()</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"><span class="n" style="color: #333;">PID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getpid</span><span class="p">()</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Rspr</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"><span class="s" style="color: #d14;"> This class wraps all attributes and input needed to make a call to RSPR.</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"><span class="s" style="color: #d14;"> https://github.com/cwhidden/rspr</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"><span class="s" style="color: #d14;"> RSPR:</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"><span class="s" style="color: #d14;"> Calculate approximate and exact Subtree Prune and Regraft (rSPR)</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"><span class="s" style="color: #d14;"> distances and the associated maximum agreement forests (MAFs) between pairs</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"><span class="s" style="color: #d14;"> of rooted binary trees from STDIN in newick format. Supports arbitrary labels.</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"><span class="s" style="color: #d14;"> The second tree may be multifurcating.</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"><span class="s" style="color: #d14;"> Copyright 2009-2014 Chris Whidden</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"><span class="s" style="color: #d14;"> whidden@cs.dal.ca</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"><span class="s" style="color: #d14;"> http://kiwi.cs.dal.ca/Software/RSPR</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">###</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># NOTE ON THE ``--pairwise`` FLAG</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># -------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># This determines the type of comparisons done.</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Specified without arguments, it does all distinct pairwise comparisons of</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># the input tree. Output by default is a matrix with only the upper half</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># filled. So, assuming the source has 4 trees, then:</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># $ cat 4trees.tre | rspr -pairwise</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># 0,23,24,24</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># ,0,5,7</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># ,,0,6</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Further (numerical) arguments specify the row/columns to restrict the</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># comparisons.</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># E.g., first row only: first tree to all other trees:</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># $ cat 4trees.tre | rspr -pairwise 0 1</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># 0,23,24,24</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># E.g. first two rows only: first two trees to all other trees:</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># $ cat 4trees.tre | rspr -pairwise 0 2</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># 0,23,24,24</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># ,0,5,7</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># E.g. third row only:</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># $ cat 4trees.tre | rspr -pairwise 2 3</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># ,,0,6</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># E.g. last column only: last tree to all other trees:</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># $ cat 4trees.tre | rspr -pairwise 0 4 3 4</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># 24</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># 7</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># 6</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># 0</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">algorithm</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"bb"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">optimizations</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">cc</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"><span class="s" style="color: #d14;"> Parameters</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"><span class="s" style="color: #d14;"> ----------</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"><span class="s" style="color: #d14;"> algorithm : str</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"><span class="s" style="color: #d14;"> One of "fpt", "bb", "approx".</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"><span class="s" style="color: #d14;"> optimizations: list[str] or None</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"><span class="s" style="color: #d14;"> Will be passed directly rspr (with each element prefixed by ``-``).</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"><span class="s" style="color: #d14;"> cc: bool</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"><span class="s" style="color: #d14;"> Calculate a potentially better approximation with a quadratic time</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"><span class="s" style="color: #d14;"> algorithm.</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">algorithm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">algorithm</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optimizations</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optimizations</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">compare_one_to_many</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">ref_tree</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="n" style="color: #333;">comparison_trees</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">command_args</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">newick_output_kwargs</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"><span class="s" style="color: #d14;"> Compare ``ref_tree'' to each tree in ``comparison_trees``.</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"><span class="s" style="color: #d14;"> Parameters</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"><span class="s" style="color: #d14;"> ----------</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"><span class="s" style="color: #d14;"> ref_tree : |Tree|</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"><span class="s" style="color: #d14;"> A |Tree| object to be compared to every tree in ``comparison_trees``.</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"><span class="s" style="color: #d14;"> comparison_trees : |Tree|</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"><span class="s" style="color: #d14;"> An (ordered) iterable of trees to which ``ref_tree`` should be</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"><span class="s" style="color: #d14;"> compared.</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"><span class="s" style="color: #d14;"> command_args : list or None</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"><span class="s" style="color: #d14;"> An iterable of (string) arguments to be passed to the program.</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"><span class="s" style="color: #d14;"> newick_output_kwargs : dict or None</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"><span class="s" style="color: #d14;"> A collection of keyword arguments to pass to the tree string</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"><span class="s" style="color: #d14;"> composition routines (that will generate the tree strings to be</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"><span class="s" style="color: #d14;"> used as input to rspr).</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"><span class="s" style="color: #d14;"> Returns</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"><span class="s" style="color: #d14;"> -------</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"><span class="s" style="color: #d14;"> scores : list[numeric]</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"><span class="s" style="color: #d14;"> A list of the SPR distances from ``ref_tree'' to</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"><span class="s" style="color: #d14;"> ``comparison_trees``, in order of the trees given.</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">newick_output_kwargs</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">newick_output_kwargs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># tf = tempfile.NamedTemporaryFile("w", delete=True)</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">tf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">textprocessing</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">StringIO</span><span class="p">()</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">ref_tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tf</span><span class="p">,</span> <span class="n" style="color: #333;">schema</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"newick"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">newick_output_kwargs</span><span class="p">)</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">t</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">comparison_trees</span><span class="p">:</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tf</span><span class="p">,</span> <span class="n" style="color: #333;">schema</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"newick"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">newick_output_kwargs</span><span class="p">)</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">command</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">command</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"rspr"</span><span class="p">)</span> <span class="c" style="color: #998; font-style: italic;"># TODO: command path as instance attribute</span></span>
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<td class="diff-line-num new new_line" data-linenumber="159" 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">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="n" style="color: #333;">command</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extend</span><span class="p">([</span><span class="s" style="color: #d14;">"-pairwise"</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">,</span> <span class="s" style="color: #d14;">"1"</span><span class="p">])</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">command_args</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">command</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="n" style="color: #333;">command_args</span><span class="p">)</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Popen</span><span class="p">(</span><span class="n" style="color: #333;">command</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="n" style="color: #333;">stdin</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">,</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">,</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PIPE</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="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">stderr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">processio</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">communicate</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">commands</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getvalue</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;">result_fields</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">)</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">result_fields</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">comparison_trees</span><span class="p">),</span> <span class="s" style="color: #d14;">"Expecting length {} + 1 for results, but received {}: {}"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">comparison_trees</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">result_fields</span><span class="p">),</span> <span class="n" style="color: #333;">result_fields</span><span class="p">)</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">result_fields</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:]]</span></span>
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170
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171
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<li id="d85fb2562ecc625e71ec482bd3dc5f23a264decd">
<a href="https://salsa.debian.org/med-team/python-dendropy/compare/0703a46f92ffe8f38a03f3d0390cbb304ea0ab3b...bf22906f2c356d84b5290a66349421ffec1155ef#d85fb2562ecc625e71ec482bd3dc5f23a264decd"><strong>dendropy/model/birthdeath.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,6 +28,7 @@ from dendropy.calculate import probability</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">dendropy.utility</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">GLOBAL_RNG</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">dendropy.utility.error</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TreeSimTotalExtinctionException</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">dendropy.utility</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">constants</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">dendropy.utility</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">deprecate</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">dendropy</span></span>
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<pre style="margin: 0;"> <span id="LC34" 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">@@ -37,57 +38,107 @@ def birth_death_tree(birth_rate, death_rate, birth_rate_sd=0.0, death_rate_sd=0.</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"><span class="s" style="color: #d14;"> death rate specified by ``death_rate``, with edge lengths in continuous (real)</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"><span class="s" style="color: #d14;"> units.</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"><span class="s" style="color: #d14;"> ``birth_rate_sd`` is the standard deviation of the normally-distributed mutation</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"><span class="s" style="color: #d14;"> added to the birth rate as it is inherited by daughter nodes; if 0, birth</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"><span class="s" style="color: #d14;"> rate does not evolve on the tree.</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"><span class="s" style="color: #d14;"> ``death_rate_sd`` is the standard deviation of the normally-distributed mutation</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"><span class="s" style="color: #d14;"> added to the death rate as it is inherited by daughter nodes; if 0, death</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"><span class="s" style="color: #d14;"> rate does not evolve on the tree.</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"><span class="s" style="color: #d14;"> Tree growth is controlled by one or more of the following arguments, of which</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"><span class="s" style="color: #d14;"> at least one must be specified:</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"><span class="s" style="color: #d14;"> - If ``ntax`` is given as a keyword argument, tree is grown until the number of</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"><span class="s" style="color: #d14;"> tips == ntax.</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"><span class="s" style="color: #d14;"> - If ``taxon_namespace`` is given as a keyword argument, tree is grown until the</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"><span class="s" style="color: #d14;"> number of tips == len(taxon_namespace), and the taxa are assigned randomly to the</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"><span class="s" style="color: #d14;"> tips.</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"><span class="s" style="color: #d14;"> - If ``num_extant_tips`` is given as a keyword argument, tree is grown until the</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"><span class="s" style="color: #d14;"> number of EXTANT tips equals this number.</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"><span class="s" style="color: #d14;"> - If ``num_extinct_tips`` is given as a keyword argument, tree is grown until the</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"><span class="s" style="color: #d14;"> number of EXTINCT tips equals this number.</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"><span class="s" style="color: #d14;"> - If ``num_total_tips`` is given as a keyword argument, tree is grown until the</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"><span class="s" style="color: #d14;"> number of EXTANT plus EXTINCT tips equals this number.</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"><span class="s" style="color: #d14;"> - If 'max_time' is given as a keyword argument, tree is grown for</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"><span class="s" style="color: #d14;"> a maximum of ``max_time``.</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"><span class="s" style="color: #d14;"> - If ``gsa_ntax`` is given then the tree will be simulated up to this number of</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"><span class="s" style="color: #d14;"> tips (or 0 tips), then a tree will be randomly selected from the</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"><span class="s" style="color: #d14;"> intervals which corresond to times at which the tree had exactly ``ntax``</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"><span class="s" style="color: #d14;"> leaves (or len(taxon_namespace) tips). This allows for simulations according to</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"><span class="s" style="color: #d14;"> the "General Sampling Approach" of Hartmann et al. (2010).</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"><span class="s" style="color: #d14;"> EXTANT tips (or 0 tips), then a tree will be randomly selected from the</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"><span class="s" style="color: #d14;"> intervals which corresond to times at which the tree had exactly ``num_extant_tips``</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"><span class="s" style="color: #d14;"> leaves. This allows for simulations according to the "General</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"><span class="s" style="color: #d14;"> Sampling Approach" of Hartmann et al. (2010). If this option is</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"><span class="s" style="color: #d14;"> specified, then ``num_extant_tips`` MUST be specified and</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"><span class="s" style="color: #d14;"> ``num_extinct_tips`` and ``num_total_tips`` CANNOT be specified.</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"><span class="s" style="color: #d14;"> If more than one of the above is given, then tree growth will terminate when</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"><span class="s" style="color: #d14;"> *any* of the termination conditions (i.e., number of tips == ``ntax``, or number</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"><span class="s" style="color: #d14;"> of tips == len(taxon_namespace) or maximum time = ``max_time``) are met.</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"><span class="s" style="color: #d14;"> Also accepts a Tree object (with valid branch lengths) as an argument passed</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"><span class="s" style="color: #d14;"> using the keyword ``tree``: if given, then this tree will be used; otherwise</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"><span class="s" style="color: #d14;"> a new one will be created.</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"><span class="s" style="color: #d14;"> If ``assign_taxa`` is False, then taxa will *not* be assigned to the tips;</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"><span class="s" style="color: #d14;"> otherwise (default), taxa will be assigned. If ``taxon_namespace`` is given</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"><span class="s" style="color: #d14;"> (``tree.taxon_namespace``, if ``tree`` is given), and the final number of tips on the</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"><span class="s" style="color: #d14;"> tree after the termination condition is reached is less then the number of</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"><span class="s" style="color: #d14;"> taxa in ``taxon_namespace`` (as will be the case, for example, when</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"><span class="s" style="color: #d14;"> ``ntax`` < len(``taxon_namespace``)), then a random subset of taxa in ``taxon_namespace`` will</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"><span class="s" style="color: #d14;"> be assigned to the tips of tree. If the number of tips is more than the number</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"><span class="s" style="color: #d14;"> of taxa in the ``taxon_namespace``, new Taxon objects will be created and added</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"><span class="s" style="color: #d14;"> to the ``taxon_namespace`` if the keyword argument ``create_required_taxa`` is not given as</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"><span class="s" style="color: #d14;"> False.</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"><span class="s" style="color: #d14;"> *any* one of the termination conditions are met.</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python"><span class="s" style="color: #d14;"> Under some conditions, it is possible for all lineages on a tree to go extinct.</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python"><span class="s" style="color: #d14;"> In this case, if the keyword argument ``repeat_until_success`` is |True| (the</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"><span class="s" style="color: #d14;"> default), then a new branching process is initiated.</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"><span class="s" style="color: #d14;"> If |False| (default), then a TreeSimTotalExtinctionException is raised.</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"><span class="s" style="color: #d14;"> Parameters</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"><span class="s" style="color: #d14;"> ----------</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"><span class="s" style="color: #d14;"> A Random() object or equivalent can be passed using the ``rng`` keyword;</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"><span class="s" style="color: #d14;"> otherwise GLOBAL_RNG is used.</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"><span class="s" style="color: #d14;"> birth_rate : float</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"><span class="s" style="color: #d14;"> The birth rate.</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"><span class="s" style="color: #d14;"> death_rate : float</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"><span class="s" style="color: #d14;"> The death rate.</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"><span class="s" style="color: #d14;"> birth_rate_sd : float</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"><span class="s" style="color: #d14;"> The standard deviation of the normally-distributed mutation added to</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"><span class="s" style="color: #d14;"> the birth rate as it is inherited by daughter nodes; if 0, birth rate</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"><span class="s" style="color: #d14;"> does not evolve on the tree.</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"><span class="s" style="color: #d14;"> death_rate_sd : float</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"><span class="s" style="color: #d14;"> The standard deviation of the normally-distributed mutation added to</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"><span class="s" style="color: #d14;"> the death rate as it is inherited by daughter nodes; if 0, death rate</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"><span class="s" style="color: #d14;"> does not evolve on the tree.</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"><span class="s" style="color: #d14;"> Keyword Arguments</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"><span class="s" style="color: #d14;"> -----------------</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"><span class="s" style="color: #d14;"> num_extant_tips: int</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"><span class="s" style="color: #d14;"> If specified, branching process is terminated when number of EXTANT</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"><span class="s" style="color: #d14;"> tips equals this number.</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"><span class="s" style="color: #d14;"> num_extinct_tips: int</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"><span class="s" style="color: #d14;"> If specified, branching process is terminated when number of EXTINCT</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"><span class="s" style="color: #d14;"> tips equals this number.</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"><span class="s" style="color: #d14;"> num_total_tips: int</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"><span class="s" style="color: #d14;"> If specified, branching process is terminated when number of EXTINCT</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"><span class="s" style="color: #d14;"> plus EXTANT tips equals this number.</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"><span class="s" style="color: #d14;"> max_time: float</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"><span class="s" style="color: #d14;"> If specified, branching process is terminated when time reaches or</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"><span class="s" style="color: #d14;"> exceeds this value.</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"><span class="s" style="color: #d14;"> gsa_ntax: int</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"><span class="s" style="color: #d14;"> The General Sampling Approach threshold for number of taxa. See above</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"><span class="s" style="color: #d14;"> for details.</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"><span class="s" style="color: #d14;"> tree : Tree instance</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"><span class="s" style="color: #d14;"> If given, then this tree will be used; otherwise a new one will be created.</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"><span class="s" style="color: #d14;"> taxon_namespace : TaxonNamespace instance</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"><span class="s" style="color: #d14;"> If given, then this will be assigned to the new tree, and, in addition,</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"><span class="s" style="color: #d14;"> taxa assigned to tips will be sourced from or otherwise created with</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"><span class="s" style="color: #d14;"> reference to this.</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"><span class="s" style="color: #d14;"> is_assign_extant_taxa : bool [default: True]</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"><span class="s" style="color: #d14;"> If False, then taxa will not be assigned to extant tips. If True</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"><span class="s" style="color: #d14;"> (default), then taxa will be assigned to extant tips. Taxa will be</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"><span class="s" style="color: #d14;"> assigned from the specified ``taxon_namespace`` or</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"><span class="s" style="color: #d14;"> ``tree.taxon_namespace``. If the number of taxa required exceeds the</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"><span class="s" style="color: #d14;"> number of taxa existing in the taxon namespace, new |Taxon| objects</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"><span class="s" style="color: #d14;"> will be created as needed and added to the taxon namespace.</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"><span class="s" style="color: #d14;"> is_assign_extinct_taxa : bool [default: True]</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"><span class="s" style="color: #d14;"> If False, then taxa will not be assigned to extant tips. If True</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"><span class="s" style="color: #d14;"> (default), then taxa will be assigned to extant tips. Taxa will be</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"><span class="s" style="color: #d14;"> assigned from the specified ``taxon_namespace`` or</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"><span class="s" style="color: #d14;"> ``tree.taxon_namespace``. If the number of taxa required exceeds the</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"><span class="s" style="color: #d14;"> number of taxa existing in the taxon namespace, new |Taxon| objects</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"><span class="s" style="color: #d14;"> will be created as needed and added to the taxon namespace. Note that</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"><span class="s" style="color: #d14;"> this option only makes sense if extinct tips are retained (specified via</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"><span class="s" style="color: #d14;"> 'is_retain_extinct_tips' option), and will otherwise be ignored.</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"><span class="s" style="color: #d14;"> is_add_extinct_attr: bool [default: True]</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"><span class="s" style="color: #d14;"> If True (default), add an boolean attribute indicating whether or not a</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"><span class="s" style="color: #d14;"> node is an extinct tip or not. False will skip this. Name of attribute</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"><span class="s" style="color: #d14;"> is set by 'extinct_attr_name' argument, defaulting to 'is_extinct'.</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"><span class="s" style="color: #d14;"> Note that this option only makes sense if extinct tips are retained</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"><span class="s" style="color: #d14;"> (specified via 'is_retain_extinct_tips' option), and will otherwise be</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"><span class="s" style="color: #d14;"> ignored.</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"><span class="s" style="color: #d14;"> extinct_attr_name: str [default: 'is_extinct']</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"><span class="s" style="color: #d14;"> Name of attribute to add to nodes indicating whether or not tip is extinct.</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"><span class="s" style="color: #d14;"> Note that this option only makes sense if extinct tips are retained</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"><span class="s" style="color: #d14;"> (specified via 'is_retain_extinct_tips' option), and will otherwise be</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"><span class="s" style="color: #d14;"> ignored.</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"><span class="s" style="color: #d14;"> is_retain_extinct_tips : bool [default: False]</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"><span class="s" style="color: #d14;"> If True, extinct tips will be retained on tree. Defaults to False:</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"><span class="s" style="color: #d14;"> extinct lineages removed from tree.</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"><span class="s" style="color: #d14;"> repeat_until_success: bool [default: True]</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"><span class="s" style="color: #d14;"> Under some conditions, it is possible for all lineages on a tree to go</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"><span class="s" style="color: #d14;"> extinct. In this case, if this argument is given as |True| (the</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"><span class="s" style="color: #d14;"> default), then a new branching process is initiated. If |False|</span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"><span class="s" style="color: #d14;"> (default), then a TreeSimTotalExtinctionException is raised.</span></span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"><span class="s" style="color: #d14;"> rng: random.Random() or equivalent instance</span></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"><span class="s" style="color: #d14;"> A Random() object or equivalent can be passed using the ``rng`` keyword;</span></span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"><span class="s" style="color: #d14;"> otherwise GLOBAL_RNG is used.</span></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"><span class="s" style="color: #d14;"> References</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"><span class="s" style="color: #d14;"> ----------</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -95,46 +146,116 @@ def birth_death_tree(birth_rate, death_rate, birth_rate_sd=0.0, death_rate_sd=0.</td>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"><span class="s" style="color: #d14;"> Hartmann, Wong, and Stadler "Sampling Trees from Evolutionary Models" Systematic Biology. 2010. 59(4). 465-476</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">target_num_taxa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'ntax'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">max_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'max_time'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">taxon_namespace</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'taxon_namespace'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">target_num_taxa</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">taxon_namespace</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">target_num_taxa</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">taxon_namespace</span><span class="p">)</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">taxon_namespace</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">taxon_namespace</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dendropy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TaxonNamespace</span><span class="p">()</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">gsa_ntax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'gsa_ntax'</span><span class="p">)</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"assign_taxa"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kwargs</span><span class="p">:</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">deprecate</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dendropy_deprecation_warning</span><span class="p">(</span></span>
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<td class="diff-line-num new new_line" data-linenumber="151" 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">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">message</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Deprecated: 'assign_taxa' will no longer be supported as an argument to this function. Use 'is_assign_extant_taxa' and/or 'is_assign_extinct_taxa' instead"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="152" 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">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">stacklevel</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">"assign_taxa"</span><span class="p">)</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">"is_assign_extant_taxa"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">"is_assign_extant_taxa"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a</span></span>
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<td class="diff-line-num new new_line" data-linenumber="156" 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">
156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"ntax"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kwargs</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="157" 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">
157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">deprecate</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dendropy_deprecation_warning</span><span class="p">(</span></span>
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<td class="diff-line-num new new_line" data-linenumber="158" 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">
158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">message</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Deprecated: 'ntax' is no longer supported as an argument to this function. Use one or more of the following instead: 'num_extant_tips', 'num_extinct_tips', 'num_total_tips', or 'max_time'"</span><span class="p">,</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="n" style="color: #333;">stacklevel</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="160" 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">
160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"> <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">"num_extant_tips"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">"ntax"</span><span class="p">)</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="s" style="color: #d14;">"num_extant_tips"</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="s" style="color: #d14;">"num_extinct_tips"</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kwargs</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="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="s" style="color: #d14;">"num_total_tips"</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="s" style="color: #d14;">"max_time"</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kwargs</span><span class="p">)</span> <span class="p">):</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"taxon_namespace"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kwargs</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="c" style="color: #998; font-style: italic;">### cannot support legacy approach, b/c ``taxon_namespace`` may grow during function, leading to unpredictable behavior</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># deprecate.dendropy_deprecation_warning(</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># preamble="Deprecated: The 'taxon_namespace' argument can no longer be used to specify a termination condition as a side-effect. Use one or more of the following instead with the length of the taxon namespace instance as a value: 'num_extant_tips', 'num_extinct_tips', or 'num_total_tips'",</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># old_construct="tree = birth_death_tree(\n ...\n taxon_namespace=taxon_namespace,\n ...\n)",</span></span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># new_construct="tree = birth_death_tree(\n ...\n taxon_namespace=taxon_namespace,\n num_extant_tips=len(taxon_namespace),\n ...\n)")</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># kwargs["num_extant_tips"] = len(kwargs["taxon_namespace"])</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;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"The 'taxon_namespace' argument can no longer be used to specify a termination condition as a side-effect."</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="s" style="color: #d14;">"Use one or more of the following instead with the length of the taxon namespace instance as a value: "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="174" 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">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="s" style="color: #d14;">"'num_extant_tips', 'num_extinct_tips', or 'num_total_tips'.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="175" 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">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="s" style="color: #d14;">"That is, instead of:</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="s" style="color: #d14;">" tree = birth_death_tree(</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> ...</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> taxon_namespace=taxon_namespace,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> ...</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> )</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="s" style="color: #d14;">"Use:</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="s" style="color: #d14;">" ntax = len(taxon_namespace)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> tree = birth_death_tree(</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> ...</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> taxon_namespace=taxon_namespace,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> num_extant_tips=ntax,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> ...</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> )</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Or (recommended):</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="s" style="color: #d14;">" tree = birth_death_tree(</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> ...</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> taxon_namespace=taxon_namespace,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> num_extant_tips=100,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> ...</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> )</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Note that the taxon namespace instance size may grow during any particular call of the function depending on taxon assignment/creation settings, so"</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="s" style="color: #d14;">" for stable and predictable behavor it is important to take a snapshot of the desired taxon namespace size before any call of the function, or, better yet"</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="s" style="color: #d14;">" simply pass in a constant value."</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"> <span class="p">)</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"One or more of the following must be specified: 'num_extant_tips', 'num_extinct_tips', or 'max_time'"</span><span class="p">)</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="n" style="color: #333;">target_num_extant_tips</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">"num_extant_tips"</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">target_num_extinct_tips</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">"num_extinct_tips"</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="n" style="color: #333;">target_num_total_tips</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">"num_total_tips"</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">max_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'max_time'</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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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;">gsa_ntax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'gsa_ntax'</span><span class="p">,</span> <span class="bp" style="color: #999;">None</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;">is_add_extinct_attr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'is_add_extinct_attr'</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">extinct_attr_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'extinct_attr_name'</span><span class="p">,</span> <span class="s" style="color: #d14;">'is_extinct'</span><span class="p">)</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="n" style="color: #333;">is_retain_extinct_tips</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'is_retain_extinct_tips'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">is_assign_extant_taxa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'is_assign_extant_taxa'</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">is_assign_extinct_taxa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'is_assign_extinct_taxa'</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"> <span class="n" style="color: #333;">repeat_until_success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'repeat_until_success'</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">"tree"</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">taxon_namespace</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">"taxon_namespace"</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">rng</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'rng'</span><span class="p">,</span> <span class="n" style="color: #333;">GLOBAL_RNG</span><span class="p">)</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="n" style="color: #333;">ignore_unrecognized_keyword_arguments</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'ignore_unrecognized_keyword_arguments'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">kwargs</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">ignore_unrecognized_keyword_arguments</span><span class="p">:</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Unsupported keyword arguments: {}"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format</span><span class="p">(</span><span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">()))</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"></span>
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106
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">terminate_at_full_tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">target_num_taxa</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gsa_ntax</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"When 'gsa_ntax' is used, either 'ntax' or 'taxon_namespace' must be used"</span><span class="p">)</span></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">max_time</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"At least one of the following must be specified: 'ntax', 'taxon_namespace', or 'max_time'"</span><span class="p">)</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gsa_ntax</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">terminate_at_full_tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">gsa_ntax</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">target_num_taxa</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">gsa_ntax</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">target_num_taxa</span><span class="p">:</span></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"gsa_ntax must be greater than target_num_taxa"</span><span class="p">)</span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">repeat_until_success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'repeat_until_success'</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">rng</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'rng'</span><span class="p">,</span> <span class="n" style="color: #333;">GLOBAL_RNG</span><span class="p">)</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="210" 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">
210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gsa_ntax</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="211" 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">
211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">terminate_at_full_tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># gsa_ntax = 1 + target_num_taxa</span></span>
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<td class="diff-line-num new new_line" data-linenumber="213" 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">
213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">target_num_extant_tips</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="214" 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">
214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"If 'gsa_ntax' is specified, 'num_extant_tips' must be specified"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="215" 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">
215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">target_num_extinct_tips</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="216" 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">
216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"If 'gsa_ntax' is specified, 'num_extinct_tups' cannot be specified"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">target_num_total_tips</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"If 'gsa_ntax' is specified, 'num_total_tips' cannot be specified"</span><span class="p">)</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">gsa_ntax</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">target_num_extant_tips</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"'gsa_ntax' ({}) must be greater than 'num_extant_tips' ({})"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format</span><span class="p">(</span><span class="n" style="color: #333;">gsa_ntax</span><span class="p">,</span> <span class="n" style="color: #333;">target_num_extant_tips</span><span class="p">))</span></span>
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120
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221
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="python"></span>
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121
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># initialize tree</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"tree"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kwargs</span><span class="p">:</span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">'tree'</span><span class="p">]</span></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"taxon_namespace"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kwargs</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">'taxon_namespace'</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">taxon_namespace</span><span class="p">:</span></span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Cannot specify both ``tree`` and ``taxon_namespace``"</span><span class="p">)</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tree</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">taxon_namespace</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">taxon_namespace</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">taxon_namespace</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" 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="LC227" class="line" lang="python"> <span class="n" style="color: #333;">taxon_namespace</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">taxon_namespace</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="n" style="color: #333;">extant_tips</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python"> <span class="n" style="color: #333;">extinct_tips</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tree</span><span class="p">:</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" 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;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_child_nodes</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">getattr</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">,</span> <span class="n" style="color: #333;">extinct_attr_name</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"> <span class="n" style="color: #333;">extant_tips</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">)</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_add_extinct_attr</span><span class="p">:</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"> <span class="nb" style="color: #0086b3;">setattr</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">,</span> <span class="n" style="color: #333;">extinct_attr_name</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="236" 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">
236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <span class="n" style="color: #333;">extinct_tips</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="238" 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">
238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_add_extinct_attr</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="239" 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">
239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"> <span class="nb" style="color: #0086b3;">setattr</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">,</span> <span class="n" style="color: #333;">extinct_attr_name</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="240" 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">
240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">is_add_extinct_attr</span><span class="p">:</span></span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"> <span class="nb" style="color: #0086b3;">setattr</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">,</span> <span class="n" style="color: #333;">extinct_attr_name</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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126
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242
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">taxon_namespace</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python"> <span class="n" style="color: #333;">taxon_namespace</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dendropy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TaxonNamespace</span><span class="p">()</span></span>
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127
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245
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="python"> <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dendropy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Tree</span><span class="p">(</span><span class="n" style="color: #333;">taxon_namespace</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">taxon_namespace</span><span class="p">)</span></span>
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128
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246
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_rooted</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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129
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247
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seed_node</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">edge</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span></span>
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130
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248
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seed_node</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">birth_rate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">birth_rate</span></span>
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131
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249
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seed_node</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">death_rate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">death_rate</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_add_extinct_attr</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="251" 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">
251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"> <span class="nb" style="color: #0086b3;">setattr</span><span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seed_node</span><span class="p">,</span> <span class="n" style="color: #333;">extinct_attr_name</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="252" 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">
252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"> <span class="n" style="color: #333;">extant_tips</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">([</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seed_node</span><span class="p">])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="253" 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">
253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="n" style="color: #333;">extinct_tips</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="n" style="color: #333;">initial_extant_tip_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">extant_tips</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"> <span class="n" style="color: #333;">initial_extinct_tip_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">extinct_tips</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># grow tree</span></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">leaf_nodes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">leaf_nodes</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">#_LOG.debug("Will generate a tree with no more than %s leaves to get a tree of %s leaves" % (str(gsa_ntax), str(target_num_taxa)))</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">curr_num_leaves</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">leaf_nodes</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="python"> <span class="n" style="color: #333;">total_time</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="LC258" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># for the GSA simulations targetted_time_slices is a list of tuple</span></span>
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># the first element in the tuple is the duration of the amount</span></span>
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># that the simulation spent at the (targetted) number of taxa</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">@@ -142,22 +263,26 @@ def birth_death_tree(birth_rate, death_rate, birth_rate_sd=0.0, death_rate_sd=0.</td>
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># a list of terminal edges in the tree and the length for that edge</span></span>
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># that marks the beginning of the time slice that corresponds to the</span></span>
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># targetted number of taxa.</span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="python"> <span class="n" style="color: #333;">targetted_time_slices</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">extinct_tips</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">[]</span></span></span>
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gsa_ntax</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="n" style="color: #333;">max_time</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">total_time</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">max_time</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="270" 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">
270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">target_num_extant_tips</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">extant_tips</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">target_num_extant_tips</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="271" 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">
271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<td class="diff-line-num new new_line" data-linenumber="272" 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">
272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">target_num_extinct_tips</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">extinct_tips</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">target_num_extinct_tips</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="273" 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">
273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<td class="diff-line-num new new_line" data-linenumber="274" 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">
274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">target_num_total_tips</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">extant_tips</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="n" style="color: #333;">extinct_tips</span><span class="p">))</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">target_num_total_tips</span><span class="p">:</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<td class="diff-line-num new new_line" data-linenumber="276" 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">
276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">max_time</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">total_time</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">max_time</span><span class="p">:</span></span>
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152
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277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;"><span class="idiff left right">curr_num_leaves</span></span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">gsa_ntax</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="278" 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">
278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">extant_tips</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">gsa_ntax</span><span class="p">:</span></span>
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154
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279
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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155
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280
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="python"></span>
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156
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281
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># get vector of birth/death probabilities, and</span></span>
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157
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282
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># associate with nodes/events</span></span>
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158
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283
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="python"> <span class="n" style="color: #333;">event_rates</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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159
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284
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="python"> <span class="n" style="color: #333;">event_nodes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left right">leaf_node</span>s</span><span class="p">:</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left right">extant_tip</span>s</span><span class="p">:</span></span>
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161
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286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">,</span> <span class="s" style="color: #d14;">'birth_rate'</span><span class="p">):</span></span>
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162
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287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="python"> <span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">birth_rate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">birth_rate</span></span>
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288
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">,</span> <span class="s" style="color: #d14;">'death_rate'</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">@@ -171,42 +296,38 @@ def birth_death_tree(birth_rate, death_rate, birth_rate_sd=0.0, death_rate_sd=0.</td>
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="python"> <span class="n" style="color: #333;">rate_of_any_event</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">event_rates</span><span class="p">)</span></span>
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297
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="python"></span>
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173
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298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># waiting time based on above probability</span></span>
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">#_LOG.debug("rate_of_any_event = %f" % (rate_of_any_event))</span></span>
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175
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299
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="python"> <span class="n" style="color: #333;">waiting_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rng</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">expovariate</span><span class="p">(</span><span class="n" style="color: #333;">rate_of_any_event</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="c" style="color: #998; font-style: italic;">#_LOG.debug("Drew waiting time of %f from hazard parameter of %f" % (waiting_time, rate_of_any_event))</span></span>
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177
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300
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="python"></span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gsa_ntax</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">curr_num_leaves</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">target_num_taxa</span><span class="p">):</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">gsa_ntax</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">extant_tips</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">target_num_extant_tips</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="python"> <span class="p">):</span></span>
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179
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="python"> <span class="n" style="color: #333;">edge_and_start_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left right">leaf_node</span>s</span><span class="p">:</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left right">extant_tip</span>s</span><span class="p">:</span></span>
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181
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306
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="python"> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">edge</span></span>
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182
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="python"> <span class="n" style="color: #333;">edge_and_start_length</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span><span class="p">))</span></span>
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183
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308
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="python"> <span class="n" style="color: #333;">targetted_time_slices</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">waiting_time</span><span class="p">,</span> <span class="n" style="color: #333;">edge_and_start_length</span><span class="p">))</span></span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">#_LOG.debug("Recording slice with %d edges" % len(edge_and_start_length))</span></span>
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185
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309
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">terminate_at_full_tree</span><span class="p">:</span></span>
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310
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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187
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311
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="python"></span>
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188
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312
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># add waiting time to nodes</span></span>
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left right">leaf_node</span>s</span><span class="p">:</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left right">extant_tip</span>s</span><span class="p">:</span></span>
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190
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314
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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191
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315
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="python"> <span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">edge</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">waiting_time</span></span>
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192
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316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">TypeError</span><span class="p">:</span></span>
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193
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="python"> <span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">edge</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">waiting_time</span></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">#_LOG.debug("Next waiting_time = %f" % waiting_time)</span></span>
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195
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="python"> <span class="n" style="color: #333;">total_time</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">waiting_time</span></span>
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196
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="python"></span>
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197
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320
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># if event occurs within time constraints</span></span>
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198
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">max_time</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">total_time</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">max_time</span><span class="p">:</span></span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="python"></span>
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200
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># normalize probability</span></span>
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201
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">event_rates</span><span class="p">)):</span></span>
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202
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324
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="python"> <span class="n" style="color: #333;">event_rates</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">event_rates</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">rate_of_any_event</span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="python"></span>
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204
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325
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># select node/event and process</span></span>
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205
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326
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="python"> <span class="n" style="color: #333;">nd</span><span class="p">,</span> <span class="n" style="color: #333;">birth_event</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">probability</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weighted_choice</span><span class="p">(</span><span class="n" style="color: #333;">event_nodes</span><span class="p">,</span> <span class="n" style="color: #333;">event_rates</span><span class="p">,</span> <span class="n" style="color: #333;">rng</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">rng</span><span class="p">)</span></span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">leaf_nodes</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">curr_num_leaves</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">1</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="python"> <span class="n" style="color: #333;">extant_tips</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">)</span></span>
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208
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328
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">birth_event</span><span class="p">:</span></span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">#_LOG.debug("Speciation")</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_add_extinct_attr</span><span class="p">:</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="python"> <span class="nb" style="color: #0086b3;">setattr</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">,</span> <span class="n" style="color: #333;">extinct_attr_name</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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210
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="python"> <span class="n" style="color: #333;">c1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new_child</span><span class="p">()</span></span>
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211
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332
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="python"> <span class="n" style="color: #333;">c2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new_child</span><span class="p">()</span></span>
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212
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333
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="python"> <span class="n" style="color: #333;">c1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">edge</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</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">@@ -215,93 +336,118 @@ def birth_death_tree(birth_rate, death_rate, birth_rate_sd=0.0, death_rate_sd=0.</td>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="python"> <span class="n" style="color: #333;">c1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">death_rate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">death_rate</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rng</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">gauss</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">death_rate_sd</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="python"> <span class="n" style="color: #333;">c2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">birth_rate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">birth_rate</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rng</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">gauss</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">birth_rate_sd</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="python"> <span class="n" style="color: #333;">c2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">death_rate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">death_rate</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rng</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">gauss</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">death_rate_sd</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python"> <span class="n" style="color: #333;">leaf_nodes</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">c1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="python"> <span class="n" style="color: #333;">leaf_nodes</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">c2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python"> <span class="n" style="color: #333;">curr_num_leaves</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">2</span></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="python"> <span class="n" style="color: #333;">extant_tips</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">c1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="python"> <span class="n" style="color: #333;">extant_tips</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">c2</span><span class="p">)</span></span>
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221
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<pre style="margin: 0;"> <span id="LC341" 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="LC222" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#_LOG.debug("Extinction")</span></span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">curr_num_leaves</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">:</span></span></span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#_LOG.debug("Will delete " + str(id(nd)) + " with parent = " + str(id(nd.parent_node)))</span></span></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">extinct_tips</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">append</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">nd</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">extant_tips</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">:</span></span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">extinct_tips</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">add</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">nd</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">is_add_extinct_attr</span></span><span class="p"><span class="idiff right">:</span></span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="python"> <span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">setattr</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">nd</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">extinct_attr_name</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC346" 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="LC347" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># total extinction</span></span>
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348
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gsa_ntax</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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228
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">targetted_time_slices</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">):</span></span>
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229
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;"> <span id="LC351" 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;">repeat_until_success</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">TreeSimTotalExtinctionException</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># We are going to basically restart the simulation because the tree has gone extinct (without reaching the specified ntax)</span></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="python"> <span class="n" style="color: #333;">leaf_nodes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seed_node</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="python"> <span class="n" style="color: #333;">curr_num_leaves</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seed_node</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">child_nodes</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">prune_subtree</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">,</span> <span class="n" style="color: #333;">suppress_unifurcations</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="python"> <span class="n" style="color: #333;">extinct_tips</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># We are going to basically restart the simulation because</span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># the tree has gone extinct (without reaching the specified</span></span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># ntax)</span></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="python"> <span class="n" style="color: #333;">extant_tips</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">initial_extant_tip_set</span><span class="p">)</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="python"> <span class="n" style="color: #333;">extinct_tips</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">initial_extinct_tip_set</span><span class="p">)</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">extant_tips</span><span class="p">:</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_add_extinct_attr</span><span class="p">:</span></span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="python"> <span class="nb" style="color: #0086b3;">setattr</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">,</span> <span class="n" style="color: #333;">extinct_attr_name</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="python"> <span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">clear_child_nodes</span><span class="p">()</span></span>
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238
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="python"> <span class="n" style="color: #333;">total_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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239
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">curr_num_leaves</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">leaf_nodes</span><span class="p">))</span></span>
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240
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">#_LOG.debug("Current tree \n%s" % (tree.as_ascii_plot(plot_metric='length', show_internal_node_labels=True)))</span></span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">#tree._debug_tree_is_valid()</span></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">#_LOG.debug("Terminated with %d leaves (%d, %d according to len(leaf_nodes))" % (curr_num_leaves, len(leaf_nodes), len(tree.leaf_nodes())))</span></span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gsa_ntax</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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244
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365
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="python"> <span class="n" style="color: #333;">total_duration_at_target_n_tax</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span></span>
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366
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">targetted_time_slices</span><span class="p">:</span></span>
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246
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367
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="python"> <span class="n" style="color: #333;">total_duration_at_target_n_tax</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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247
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368
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="python"> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rng</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">random</span><span class="p">()</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">total_duration_at_target_n_tax</span></span>
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248
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">#_LOG.debug("Selected rng = %f out of (0, %f)" % (r, total_duration_at_target_n_tax))</span></span>
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249
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="python"> <span class="n" style="color: #333;">selected_slice</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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250
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370
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">targetted_time_slices</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="python"> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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252
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372
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">0.0</span><span class="p">:</span></span>
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253
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="python"> <span class="n" style="color: #333;">selected_slice</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span></span>
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254
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374
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">selected_slice</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">#_LOG.debug("Selected time slice index %d" % n)</span></span>
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256
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="python"> <span class="n" style="color: #333;">edges_at_slice</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">selected_slice</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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257
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376
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="python"> <span class="n" style="color: #333;">last_waiting_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">selected_slice</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="python"></span>
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258
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">prev_length</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">edges_at_slice</span><span class="p">:</span></span>
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259
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379
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="python"> <span class="n" style="color: #333;">daughter_nd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">head_node</span></span>
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260
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380
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">daughter_nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">child_nodes</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">prune_subtree</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">,</span> <span class="n" style="color: #333;">suppress_unifurcations</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">#_LOG.debug("After pruning %s:\n%s" % (str(id(nd)), tree.as_ascii_plot(plot_metric='length', show_internal_node_labels=True)))</span></span>
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="python"> <span class="n" style="color: #333;">extinct_tips</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="python"> <span class="n" style="color: #333;">extinct_tips</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">daughter_nd</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="python"> <span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parent_node</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="python"> <span class="n" style="color: #333;">extinct_tips</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">discard</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">)</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="python"> <span class="n" style="color: #333;">extant_tips</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">discard</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">)</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">desc</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">preorder_iter</span><span class="p">():</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="python"> <span class="n" style="color: #333;">extinct_tips</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">discard</span><span class="p">(</span><span class="n" style="color: #333;">desc</span><span class="p">)</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="python"> <span class="n" style="color: #333;">extant_tips</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">discard</span><span class="p">(</span><span class="n" style="color: #333;">desc</span><span class="p">)</span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="python"> <span class="n" style="color: #333;">daughter_nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">clear_child_nodes</span><span class="p">()</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="python"> <span class="n" style="color: #333;">extinct_tips</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">discard</span><span class="p">(</span><span class="n" style="color: #333;">daughter_nd</span><span class="p">)</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="python"> <span class="n" style="color: #333;">extant_tips</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">daughter_nd</span><span class="p">)</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_add_extinct_attr</span><span class="p">:</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="python"> <span class="nb" style="color: #0086b3;">setattr</span><span class="p">(</span><span class="n" style="color: #333;">daughter_nd</span><span class="p">,</span> <span class="n" style="color: #333;">extinct_attr_name</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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271
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392
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="python"> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prev_length</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">last_waiting_time</span></span>
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272
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393
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="python"></span>
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273
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="python"></span>
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274
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="python"></span>
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275
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># tree._debug_tree_is_valid()</span></span>
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276
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># for nd in extinct_tips:</span></span>
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277
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># _LOG.debug("Will be deleting " + str(id(nd)))</span></span>
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278
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="python"></span>
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279
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">extinct_tips</span><span class="p">:</span></span>
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280
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="python"> <span class="n" style="color: #333;">bef</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">leaf_nodes</span><span class="p">())</span></span>
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281
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parent_node</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parent_node</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">child_nodes</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>
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="python"> <span class="n" style="color: #333;">nd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parent_node</span></span>
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># _LOG.debug("Deleting " + str(nd.__dict__) + '\n' + str(nd.edge.__dict__))</span></span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># for n, pnd in enumerate(tree.postorder_node_iter()):</span></span>
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285
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># _LOG.debug("%d %s" % (n, repr(pnd)))</span></span>
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286
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># _LOG.debug("Before prune of %s:\n%s" % (str(id(nd)), tree.as_ascii_plot(plot_metric='length', show_internal_node_labels=True)))</span></span>
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287
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parent_node</span><span class="p">:</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" 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;">is_retain_extinct_tips</span><span class="p">:</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="python"> <span class="n" style="color: #333;">processed_nodes</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">extinct_tips</span><span class="p">):</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">processed_nodes</span><span class="p">:</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="python"> <span class="n" style="color: #333;">processed_nodes</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">)</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="python"> <span class="n" style="color: #333;">extinct_tips</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">discard</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">)</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_child_nodes</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parent_node</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parent_node</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_child_nodes</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>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="python"> <span class="n" style="color: #333;">nd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parent_node</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="python"> <span class="n" style="color: #333;">processed_nodes</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">)</span></span>
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288
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405
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">prune_subtree</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="p">,</span> <span class="n" style="color: #333;">suppress_unifurcations</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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289
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># _LOG.debug("Deleted " + str(nd.__dict__))</span></span>
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290
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># for n, pnd in enumerate(tree.postorder_node_iter()):</span></span>
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># _LOG.debug("%d %s" % (n, repr(pnd)))</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># tree._debug_tree_is_valid()</span></span>
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">suppress_unifurcations</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># tree._debug_tree_is_valid()</span></span>
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># _LOG.debug("After deg2suppression:\n%s" % (tree.as_ascii_plot(plot_metric='length', show_internal_node_labels=True)))</span></span>
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">kwargs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"assign_taxa"</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">randomly_assign_taxa</span><span class="p">(</span><span class="n" style="color: #333;">create_required_taxa</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">rng</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">rng</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="python"></span>
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407
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># return</span></span>
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_assign_extant_taxa</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">is_assign_extinct_taxa</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="python"> <span class="n" style="color: #333;">taxon_pool</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">t</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">t</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">taxon_namespace</span><span class="p">]</span></span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="python"> <span class="n" style="color: #333;">rng</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shuffle</span><span class="p">(</span><span class="n" style="color: #333;">taxon_pool</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="python"> <span class="n" style="color: #333;">taxon_pool_labels</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">([</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">label</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">t</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">taxon_pool</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">### ONLY works if in GSA sub-section we remove ALL extant and</span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">### extinct nodes beyond time slice: expensive</span></span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">### Furthermore, main reason to use this approach is to have different</span></span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">### label prefixes for extinct vs. extant lineages, but the second time</span></span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">### this function is called with the same taxon namespace or any time</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">### this function is called with a populated taxon namespace, that</span></span>
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">### aesthetic is lost.</span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># node_pool_labels = ("T", "X")</span></span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># for node_pool_idx, node_pool in enumerate((extant_tips, extinct_tips)):</span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># for node_idx, nd in enumerate(node_pool):</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># if taxon_pool:</span></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># taxon = taxon_pool.pop()</span></span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># else:</span></span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># taxon = taxon_namespace.require_taxon("{}{}".format(node_pool_labels[node_pool_idx], node_idx+1))</span></span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># nd.taxon = taxon</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># assert not nd._child_nodes</span></span>
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="python"> <span class="n" style="color: #333;">tlabel_counter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="python"> <span class="n" style="color: #333;">leaf_nodes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">leaf_nodes</span><span class="p">()</span></span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="python"> <span class="n" style="color: #333;">rng</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shuffle</span><span class="p">(</span><span class="n" style="color: #333;">leaf_nodes</span><span class="p">)</span></span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nd_idx</span><span class="p">,</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">leaf_nodes</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC434" 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;">is_assign_extant_taxa</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">extant_tips</span><span class="p">:</span></span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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436
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<pre style="margin: 0;">+<span id="LC436" 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;">is_assign_extant_taxa</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">nd</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">extinct_tips</span><span class="p">:</span></span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">taxon_pool</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="python"> <span class="n" style="color: #333;">taxon</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">taxon_pool</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC440" 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="LC441" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="python"> <span class="n" style="color: #333;">tlabel_counter</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="python"> <span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"{}{}"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format</span><span class="p">(</span><span class="s" style="color: #d14;">"T"</span><span class="p">,</span> <span class="n" style="color: #333;">tlabel_counter</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">label</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">taxon_pool_labels</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="python"> <span class="n" style="color: #333;">taxon</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">taxon_namespace</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">require_taxon</span><span class="p">(</span><span class="n" style="color: #333;">label</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">label</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="python"> <span class="n" style="color: #333;">taxon_pool_labels</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">label</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="python"> <span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">taxon</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">taxon</span></span>
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<pre style="margin: 0;"> <span id="LC449" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tree</span></span>
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<pre style="margin: 0;"> <span id="LC450" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">discrete_birth_death_tree</span><span class="p">(</span><span class="n" style="color: #333;">birth_rate</span><span class="p">,</span> <span class="n" style="color: #333;">death_rate</span><span class="p">,</span> <span class="n" style="color: #333;">birth_rate_sd</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="n" style="color: #333;">death_rate_sd</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="python"><span class="s" style="color: #d14;"> Returns a birth-death tree with birth rate specified by ``birth_rate``, and</span></span>
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<li id="0bea2e6dd67ad52a51f66d3ac8ad6fc41aae90d5">
<a href="https://salsa.debian.org/med-team/python-dendropy/compare/0703a46f92ffe8f38a03f3d0390cbb304ea0ab3b...bf22906f2c356d84b5290a66349421ffec1155ef#0bea2e6dd67ad52a51f66d3ac8ad6fc41aae90d5"><strong>dendropy/test/test_birthdeath.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">@@ -59,7 +59,7 @@ class BirthDeathTreeTest(unittest.TestCase):</td>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"> <span class="s" style="color: #d14;">"""test that the birth-death process produces the correct number of tips with GSA."""</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">_RNG</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MockRandom</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">num_leaves</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">15</span><span class="p">):</span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">birthdeath</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">birth_death_tree</span><span class="p">(</span><span class="n" style="color: #333;">birth_rate</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="n" style="color: #333;">death_rate</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.2</span><span class="p">,</span> <span class="n" style="color: #333;">n<span class="idiff left right">tax</span></span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">num_leaves</span><span class="p">,</span> <span class="n" style="color: #333;">gsa_ntax</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">num_leaves</span><span class="p">,</span> <span class="n" style="color: #333;">rng</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_RNG</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">birthdeath</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">birth_death_tree</span><span class="p">(</span><span class="n" style="color: #333;">birth_rate</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="n" style="color: #333;">death_rate</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.2</span><span class="p">,</span> <span class="n" style="color: #333;">n<span class="idiff left right">um_extant_tips</span></span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">num_leaves</span><span class="p">,</span> <span class="n" style="color: #333;">gsa_ntax</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">num_leaves</span><span class="p">,</span> <span class="n" style="color: #333;">rng</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_RNG</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_debug_tree_is_valid</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">num_leaves</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">leaf_nodes</span><span class="p">()))</span></span>
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<pre style="margin: 0;"> <span id="LC65" 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">@@ -67,7 +67,7 @@ class BirthDeathTreeTest(unittest.TestCase):</td>
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"> <span class="s" style="color: #d14;">"""test that the pure-birth process produces the correct number of tips."""</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">_RNG</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MockRandom</span><span class="p">()</span></span>
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69
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">num_leaves</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">):</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">birthdeath</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">birth_death_tree</span><span class="p">(</span><span class="n" style="color: #333;">birth_rate</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="n" style="color: #333;">death_rate</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="n" style="color: #333;">n<span class="idiff left right">tax</span></span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">num_leaves</span><span class="p">,</span> <span class="n" style="color: #333;">rng</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_RNG</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">birthdeath</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">birth_death_tree</span><span class="p">(</span><span class="n" style="color: #333;">birth_rate</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="n" style="color: #333;">death_rate</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="n" style="color: #333;">n<span class="idiff left right">um_extant_tips</span></span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">num_leaves</span><span class="p">,</span> <span class="n" style="color: #333;">rng</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_RNG</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_debug_tree_is_valid</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">num_leaves</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">leaf_nodes</span><span class="p">()))</span></span>
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<pre style="margin: 0;"> <span id="LC73" 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">@@ -75,7 +75,7 @@ class BirthDeathTreeTest(unittest.TestCase):</td>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"> <span class="s" style="color: #d14;">"""test that the pure-birth process produces the correct number of tips with GSA."""</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">_RNG</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MockRandom</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">num_leaves</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">birthdeath</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">birth_death_tree</span><span class="p">(</span><span class="n" style="color: #333;">birth_rate</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="n" style="color: #333;">death_rate</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="n" style="color: #333;">n<span class="idiff left right">tax</span></span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">num_leaves</span><span class="p">,</span> <span class="n" style="color: #333;">gsa_ntax</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">num_leaves</span><span class="p">,</span> <span class="n" style="color: #333;">rng</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_RNG</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">birthdeath</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">birth_death_tree</span><span class="p">(</span><span class="n" style="color: #333;">birth_rate</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="n" style="color: #333;">death_rate</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="n" style="color: #333;">n<span class="idiff left right">um_extant_tips</span></span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">num_leaves</span><span class="p">,</span> <span class="n" style="color: #333;">gsa_ntax</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">num_leaves</span><span class="p">,</span> <span class="n" style="color: #333;">rng</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_RNG</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_debug_tree_is_valid</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">num_leaves</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">leaf_nodes</span><span class="p">()))</span></span>
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81
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<pre style="margin: 0;"> <span id="LC81" 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">@@ -83,7 +83,7 @@ class BirthDeathTreeTest(unittest.TestCase):</td>
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="s" style="color: #d14;">"""PureCoalescentTreeTest -- tree generation without checking [TODO: checks]"""</span></span>
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">_RNG</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MockRandom</span><span class="p">()</span></span>
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">num_leaves</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">):</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">birthdeath</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">birth_death_tree</span><span class="p">(</span><span class="n" style="color: #333;">birth_rate</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="n" style="color: #333;">death_rate</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.2</span><span class="p">,</span> <span class="n" style="color: #333;">n<span class="idiff left right">tax</span></span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">num_leaves</span><span class="p">,</span> <span class="n" style="color: #333;">rng</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_RNG</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">birthdeath</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">birth_death_tree</span><span class="p">(</span><span class="n" style="color: #333;">birth_rate</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="n" style="color: #333;">death_rate</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.2</span><span class="p">,</span> <span class="n" style="color: #333;">n<span class="idiff left right">um_extant_tips</span></span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">num_leaves</span><span class="p">,</span> <span class="n" style="color: #333;">rng</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_RNG</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_debug_tree_is_valid</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">num_leaves</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">leaf_nodes</span><span class="p">()))</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"></span>
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<li id="df9370d189d00eb39f19afd0657aac56f24843a4">
<a href="https://salsa.debian.org/med-team/python-dendropy/compare/0703a46f92ffe8f38a03f3d0390cbb304ea0ab3b...bf22906f2c356d84b5290a66349421ffec1155ef#df9370d189d00eb39f19afd0657aac56f24843a4"><strong>dendropy/test/test_dataio_newick_reader_tree.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">@@ -990,9 +990,9 @@ class NewickInternalLabelAssociationTest(unittest.TestCase):</td>
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990
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<pre style="margin: 0;"> <span id="LC990" class="line" lang="python"> <span class="n" style="color: #333;">expected_label</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">expected_labels</span><span class="p">[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bipartition</span><span class="p">)]</span></span>
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991
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<pre style="margin: 0;"> <span id="LC991" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">labels_to_edges</span><span class="p">:</span></span>
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992
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<pre style="margin: 0;"> <span id="LC992" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertIs</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">label</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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993
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<pre style="margin: 0;">-<span id="LC993" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual<span class="idiff left right">s</span></span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">edge</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">label</span><span class="p">,</span> <span class="n" style="color: #333;">expected_label</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC993" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">edge</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">label</span><span class="p">,</span> <span class="n" style="color: #333;">expected_label</span><span class="p">)</span></span>
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994
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<pre style="margin: 0;"> <span id="LC994" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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995
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<pre style="margin: 0;">-<span id="LC995" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual<span class="idiff left right">s</span></span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">label</span><span class="p">,</span> <span class="n" style="color: #333;">expected_label</span><span class="p">)</span></span>
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995
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<pre style="margin: 0;">+<span id="LC995" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">label</span><span class="p">,</span> <span class="n" style="color: #333;">expected_label</span><span class="p">)</span></span>
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996
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996
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<pre style="margin: 0;"> <span id="LC996" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertIs</span><span class="p">(</span><span class="n" style="color: #333;">nd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">edge</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">label</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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997
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997
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<pre style="margin: 0;"> <span id="LC997" class="line" lang="python"></span>
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998
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998
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<pre style="margin: 0;"> <span id="LC998" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"__main__"</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/python-dendropy/compare/0703a46f92ffe8f38a03f3d0390cbb304ea0ab3b...bf22906f2c356d84b5290a66349421ffec1155ef#251a29ad9081268af6ea4c86177b85f7fa548683"><strong>dendropy/test/test_tree_shape_kernel.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="183" 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="183" 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">@@ -183,7 +183,8 @@ class AssemblageInducedTreeManagerTestBase(unittest.TestCase):</td>
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183
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dendropy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">simulate</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">birth_death_tree</span><span class="p">(</span></span>
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184
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python"> <span class="n" style="color: #333;">birth_rate</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.1</span><span class="p">,</span></span>
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185
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">death_rate</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">taxon_namespace</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tns</span><span class="p">)</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">taxon_namespace</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tns</span><span class="p">,</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="n" style="color: #333;">num_extant_tips</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">tns</span><span class="p">))</span></span>
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187
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assemblage_leaf_sets</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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188
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assemblage_classification_regime_subtrees</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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189
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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;">for</span> <span class="n" style="color: #333;">group_id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">AssemblageInducedTreeManagerTests</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">GROUP_IDS</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/python-dendropy/compare/0703a46f92ffe8f38a03f3d0390cbb304ea0ab3b...bf22906f2c356d84b5290a66349421ffec1155ef#9aba85fbb86cff51b47835c231b8f34115234f88"><strong>dendropy/utility/textprocessing.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">@@ -37,7 +37,10 @@ except ImportError:</td>
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">###############################################################################</span></span>
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">## Unicode/String Conversions</span></span>
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39
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"><span class="n" style="color: #333;">ENCODING</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">locale</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getdefaultlocale</span><span class="p">()[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">ENCODING</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">locale</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getdefaultlocale</span><span class="p">()[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">ENCODING</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span> <span class="c" style="color: #998; font-style: italic;"># let default value be assigned below</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ENCODING</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">ENCODING</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'UTF-8'</span></span>
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<a href="https://salsa.debian.org/med-team/python-dendropy/compare/0703a46f92ffe8f38a03f3d0390cbb304ea0ab3b...bf22906f2c356d84b5290a66349421ffec1155ef#8c91c0296909b5ea3c496fde69e9dc44a6c6ae5f"><strong>setup.cfg</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">@@ -9,5 +9,4 @@ upload-dir = doc/build/html</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">[egg_info]</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">tag_build = </span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">tag_date = 0</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">tag_svn_revision = 0</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/python-dendropy/compare/0703a46f92ffe8f38a03f3d0390cbb304ea0ab3b...bf22906f2c356d84b5290a66349421ffec1155ef#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.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">@@ -91,8 +91,8 @@ ENTRY_POINTS = {}</td>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"><span class="n" style="color: #333;">SCRIPT_SUBPATHS</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'applications'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sumtrees'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sumtrees.py'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'applications'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sumlabels'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sumlabels.py'</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># ['scripts', 'sumtrees', 'cattrees.py'],</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># ['scripts', 'sumtrees', 'sumlabels.py'],</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># ['scripts', 'calculators', 'strict_consensus_merge.py'],</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># ['scripts', 'calculators', 'long_branch_symmdiff.py'],</span></span>
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98
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"><span class="p">]</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="168" 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="168" 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">@@ -168,6 +168,8 @@ setup(name='DendroPy',</td>
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168
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="python"> <span class="s" style="color: #d14;">"Programming Language :: Python :: 3.2"</span><span class="p">,</span></span>
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169
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="python"> <span class="s" style="color: #d14;">"Programming Language :: Python :: 3.3"</span><span class="p">,</span></span>
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170
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="python"> <span class="s" style="color: #d14;">"Programming Language :: Python :: 3.4"</span><span class="p">,</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="s" style="color: #d14;">"Programming Language :: Python :: 3.5"</span><span class="p">,</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="s" style="color: #d14;">"Programming Language :: Python :: 3.6"</span><span class="p">,</span></span>
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171
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="python"> <span class="s" style="color: #d14;">"Programming Language :: Python"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python"> <span class="s" style="color: #d14;">"Topic :: Scientific/Engineering :: Bio-Informatics"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python"> <span class="p">],</span></span>
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