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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-cogent">Debian Med / python-cogent</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cogent/-/commit/b316c606bc02b9b044b600a4ff746bd5736a16ad">b316c606</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-11-30T10:24:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">numba is back in the archive
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cogent/-/commit/4f0cee7e5609145888762d0289a120606b648471">4f0cee7e</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-11-30T10:36:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Only build for Python3.8 as numba does not yet support Python 3.9. See https://bugs.debian.org/972246
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cogent/-/commit/0b322ba71a0df68e5a07d5e16aab5b10ea6fba2f">0b322ba7</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-11-30T10:37:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cogent/-/commit/29c24ea6c46f1e80ab3ce24e703170b5ebc154b7">29c24ea6</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-11-30T10:37:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update renamed lintian tag names in lintian overrides.
Changes-By: lintian-brush
Fixes: lintian: renamed-tag
See-also: https://lintian.debian.org/tags/renamed-tag.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cogent/-/commit/4ac9f833f18d9075706ca7f45bdd5e07eb3f0981">4ac9f833</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-11-30T10:39:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Mark Debian-specific patches as not needing forwarding.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cogent/-/commit/6bb41983cf65f2a4682e64e784e2a9ead7700917">6bb41983</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-11-30T10:39:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#6365abe88f3afecfc8346965bbb4822915620145">
debian/patches/fix_interpreter.patch
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<li class="file-stats">
<a href="#0325e4f25102e77f8a7e2b29dd07d7e574a1b96e">
debian/patches/sphinx.patch
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<li class="file-stats">
<a href="#c02f7fd8e133d4f074f5a7dcd397172d4de1af0d">
debian/python3-cogent3.lintian-overrides
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/python-cogent/-/compare/3c8613318add1168f258255209b49ea0692a4d8c...6bb41983cf65f2a4682e64e784e2a9ead7700917#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">python-cogent (2020.6.30a0+dfsg-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-cogent (2020.6.30a0+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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<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"> * Team upload.</span>
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<td class="diff-line-num new_line" data-linenumber="4" 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="LC4" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> [ Balint Reczey ]</span>
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<td class="diff-line-num new_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext"> * New upstream version 2020.6.30a0+dfsg</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" 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="8" 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">@@ -6,11 +8,14 @@ python-cogent (2020.6.30a0+dfsg-1) UNRELEASED; urgency=medium</td>
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<td class="diff-line-num new_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</span>
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<td class="diff-line-num new_line" data-linenumber="10" 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="LC10" class="line" lang="plaintext"> * Rules-Requires-Root: no (routine-update)</span>
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<td class="diff-line-num new_line old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> TODO: Wait until python-numba is installable again (problem with </span>
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<td class="diff-line-num new_line old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> ongoing testing transition known as auto-upperlimit-python3-llvmlite.)</span>
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<td class="diff-line-num new_line old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> Also check RFA bug #935626</span>
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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="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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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> -- Balint Reczey <rbalint@ubuntu.com> Fri, 03 Jul 2020 12:09:54 +0200</span>
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<td class="diff-line-num new old_line" data-linenumber="14" 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="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> [ Michael R. Crusoe ]</span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext"> * Only build for Python3.8 as numba does not yet support Python 3.9.</span>
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<td class="diff-line-num new new_line" data-linenumber="14" 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="LC14" class="line" lang="plaintext"> See https://bugs.debian.org/972246</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">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> * Standards-Version: 4.5.1 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> * Mark Debian-specific patches as not needing forwarding.</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"> -- Michael R. Crusoe <crusoe@debian.org> Mon, 30 Nov 2020 10:39:30 +0100</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">python-cogent (2020.2.7a+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/python-cogent/-/compare/3c8613318add1168f258255209b49ea0692a4d8c...6bb41983cf65f2a4682e64e784e2a9ead7700917#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">@@ -25,7 +25,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> python3-sphinxcontrib.bibtex,</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> cython3,</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> pandoc</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/python-cogent</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/python-cogent.git</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">Homepage: https://github.com/cogent3/cogent3</span>
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<a href="https://salsa.debian.org/med-team/python-cogent/-/compare/3c8613318add1168f258255209b49ea0692a4d8c...6bb41983cf65f2a4682e64e784e2a9ead7700917#6365abe88f3afecfc8346965bbb4822915620145"><strong>debian/patches/fix_interpreter.patch</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Tue, 07 Jan 2020 20:12:00 +0100</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Description: Fix broken interpreter lines</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff">--- a/src/cogent3/phylo/maximum_likelihood.py</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/cogent3/phylo/maximum_likelihood.py</span></span>
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<a href="https://salsa.debian.org/med-team/python-cogent/-/compare/3c8613318add1168f258255209b49ea0692a4d8c...6bb41983cf65f2a4682e64e784e2a9ead7700917#0325e4f25102e77f8a7e2b29dd07d7e574a1b96e"><strong>debian/patches/sphinx.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Tue, 07 Jan 2020 20:12:00 +0100</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Description: Work around failure in sphinx doc processing</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff">--- a/doc/conf.py</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/doc/conf.py</span></span>
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<a href="https://salsa.debian.org/med-team/python-cogent/-/compare/3c8613318add1168f258255209b49ea0692a4d8c...6bb41983cf65f2a4682e64e784e2a9ead7700917#c02f7fd8e133d4f074f5a7dcd397172d4de1af0d"><strong>debian/python3-cogent3.lintian-overrides</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"># Test suite needs all these files</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">python3-cogent3: <span class="idiff left right">duplicated-compressed-fil</span>e *</span></pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">python3-cogent3: <span class="idiff left right">compressed-duplicat</span>e *</span></pre>
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<a href="https://salsa.debian.org/med-team/python-cogent/-/compare/3c8613318add1168f258255209b49ea0692a4d8c...6bb41983cf65f2a4682e64e784e2a9ead7700917#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,6 +10,8 @@ export PYBUILD_BEFORE_TEST=cp -r {dir}/tests/data {build_dir}</td>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: #008080;">PYBUILD_NAME</span><span class="o" style="font-weight: 600;">=</span>cogent3</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: #008080;">PYBUILD_DISABLE</span><span class="o" style="font-weight: 600;">=</span>3.9</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="make"><span class="k" style="font-weight: 600;">include</span><span class="sx" style="color: #d14;"> /usr/share/dpkg/default.mk</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="make"><span class="nl">%</span><span class="o" style="font-weight: 600;">:</span></span>
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