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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/3435db52b892726bee725e945fdb2b74665bcc65">3435db52</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-10-08T07:04:21Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop Python2 support
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-dendropy/commit/2cab606a75cb1618bf068dc8a46568b7f6ba7d92">2cab606a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-10-08T07:05:10Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper-compat 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-dendropy/commit/e365eea5bb129fa1feef2d3f2110f77e05fd96e1">e365eea5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-10-08T07:05:20Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.4.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-dendropy/commit/2de08e84e5352458bd57bfdaf3494233b1848f2a">2de08e84</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-10-08T07:05:20Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Secure URI in copyright format
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-dendropy/commit/c8bc1e305b5fd766ca2e08b61016dacdce27c4e2">c8bc1e30</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-10-08T07:06:13Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-dendropy/commit/802d879c89b0c71f1d77df86d85e732485d63a4d">802d879c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-10-08T07:06:17Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use secure URI in Homepage field.
Fixes lintian: homepage-field-uses-insecure-uri
See https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html for more details.
</pre>
</li>
</ul>
<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="deleted-file">
−
debian/compat
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/python-dendropy/compare/aa25f419d0c544f6db4563e0344b204528b276bc...802d879c89b0c71f1d77df86d85e732485d63a4d#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-dendropy (4.4.0-2) UNRELEASED; urgency=medium</span>
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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">
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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">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Drop Python2 support</span>
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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">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> targeting bug #937698</span>
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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">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * debhelper-compat 12</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Standards-Version: 4.4.1</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Secure URI in copyright format</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target</span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> * Use secure URI in Homepage field.</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 new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 08 Oct 2019 09:01:44 +0200</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">python-dendropy (4.4.0-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> * New upstream version</span>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/python-dendropy/compare/aa25f419d0c544f6db4563e0344b204528b276bc...802d879c89b0c71f1d77df86d85e732485d63a4d#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">11</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/python-dendropy/compare/aa25f419d0c544f6db4563e0344b204528b276bc...802d879c89b0c71f1d77df86d85e732485d63a4d#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">@@ -4,36 +4,14 @@ Uploaders: Andreas Tille <tille@debian.org></td>
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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="LC7" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right"> (>= 11~</span>),</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right">-compat (= 12</span>),</span>
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8
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8
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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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11
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python3-all,</span>
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12
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> python3-setuptools</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1.4</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4.1</span></span>
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14
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/python-dendropy</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/python-dendropy.git</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">Homepage: http://dendropy.org/</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">Package: python-dendropy</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> ${python:Depends}</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">Description: DendroPy Phylogenetic Computing Library (Python 2)</span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> DendroPy is a Python library for phylogenetic computing. It provides</span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> classes and functions for the simulation, processing, and manipulation</span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> of phylogenetic trees and character matrices, and supports the reading</span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> and writing of phylogenetic data in a range of formats, such as NEXUS,</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> NEWICK, NeXML, Phylip, FASTA, etc. Application scripts for performing</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> some useful phylogenetic operations, such as data conversion and tree</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> posterior distribution summarization, are also distributed and installed</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> as part of the library. DendroPy can thus function as a stand-alone</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> library for phylogenetics, a component of more complex multi-library</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> phyloinformatic pipelines, or as a scripting “glue” that assembles and</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"> drives such pipelines.</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> This package provides python2 modules.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Homepage: https://dendropy.org/</span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Package: python3-dendropy</span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Architecture: all</span>
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<a href="https://salsa.debian.org/med-team/python-dendropy/compare/aa25f419d0c544f6db4563e0344b204528b276bc...802d879c89b0c71f1d77df86d85e732485d63a4d#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Format: http<span class="idiff left right">s</span>://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Upstream-Contact: Jeet Sukumaran <jeetsukumaran@gmail.com></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Upstream-Name: DendroPy</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Source: https://pypi.python.org/pypi/DendroPy</span>
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<a href="https://salsa.debian.org/med-team/python-dendropy/compare/aa25f419d0c544f6db4563e0344b204528b276bc...802d879c89b0c71f1d77df86d85e732485d63a4d#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">@@ -7,18 +7,19 @@ SUMTREES:=sumtrees</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">export PYBUILD_NAME=dendropy</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">%:</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> dh $@ --with python<span class="idiff left right">2,python</span>3 --buildsystem=pybuild</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> dh $@ --with python3 --buildsystem=pybuild</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> LC_ALL=en_US.utf-8 dh_auto_test || true</span>
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<td class="diff-line-num new new_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> # FIXME</span>
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14
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<td class="diff-line-num new_line" data-linenumber="16" 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">
16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> # need to add true since for Python 3.4 5 tests are failing due some</span>
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<td class="diff-line-num old_line" data-linenumber="15" 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">
15
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<td class="diff-line-num new_line" data-linenumber="17" 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">
17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> # strange encoding problem. upstream is unable to verify this and</span>
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16
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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> # there is no better idea for the moment</span>
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<td class="diff-line-num new old_line" data-linenumber="17" 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="19" 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">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">endif</span>
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17
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
18
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">override_dh_install:</span>
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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
19
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<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> dh_install</span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> ## FIXME: This needs to be clarified with python modules team</span>
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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
21
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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> mkdir -p debian/$(SUMTREES)/usr/bin</span>
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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
22
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> mv debian/python3-$(PYBUILD_NAME)/usr/bin/sumtrees.py debian/$(SUMTREES)/usr/bin/sumtrees</span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> rm -rf debian/python-$(PYBUILD_NAME)/usr/bin</span>
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24
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> rm -rf debian/python3-$(PYBUILD_NAME)/usr/bin</span></pre>
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