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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-biopython">Debian Med / python-biopython</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/d186c316e96dc8846b86047a117bf9c032b23c8d">d186c316</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-09-19T14:16:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix-use-of-unversioned-python.patch not-needed
The choice of providing, or not, the "python" command as interpreter,
to either python2 or python3, if I trust PEP 394, is distribution
dependent:
https://www.python.org/dev/peps/pep-0394/
Thus this patch is Debian specific.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/1f39ebe789a087d8bc248ed8dd8776f67434eabf">1f39ebe7</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-09-19T14:29:03+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">forward spelling-error-in-binaries.patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/4f20bee2fba89c944a80d812dda7b5a048968e00">4f20bee2</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-09-19T14:30:16+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/changelog: added note about patches overhaul
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/2950963ca6dacfd19788f70440edf248b0fe0576">2950963c</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-09-19T14:37:01+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove_mathml-qname.patch is forwarded, somehow
upstream is aware of the problem and has had long term objective to
not redistribute those files.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/f4f41aebd08313023b535681e6a1a283b8f9d788">f4f41aeb</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-09-19T14:38:22+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">privacy_breach.patch set forwarded not-needed
</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="#b171d40a542257c0f38f5b732a05d7ff89fcf22e">
debian/patches/fix-use-of-unversioned-python.patch
</a>
</li>
<li class="file-stats">
<a href="#376aaf59ef82170962d12a3347ff003a46b6034c">
debian/patches/privacy_breach.patch
</a>
</li>
<li class="file-stats">
<a href="#d452dcc994db05717b376de6a706aff4a11e3a17">
debian/patches/remove_mathml-qname.patch
</a>
</li>
<li class="file-stats">
<a href="#cde80ecebd009f562baf24329028f4c4a34c3404">
debian/patches/spelling-error-in-binaries.patch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/6d43a7339ec9e5055d1ce04ba103e5cba72adf53...f4f41aebd08313023b535681e6a1a283b8f9d788#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" 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">@@ -2,6 +2,7 @@ python-biopython (1.78+dfsg-2) UNRELEASED; urgency=medium</td>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="mosel"></span>
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Added</span> <span class="n" style="color: #333;">DEP3</span> <span class="n" style="color: #333;">description</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">blastdbv4</span><span class="p">-</span><span class="n" style="color: #333;">tests</span><span class="p">-</span><span class="n" style="color: #333;">filter</span><span class="p">-</span><span class="n" style="color: #333;">archs</span><span class="p">.</span><span class="n" style="color: #333;">patch</span><span class="p">.</span></span>
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<td class="diff-line-num old_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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<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">
4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Removed</span><span class="p">,</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">last</span><span class="p">,</span> <span class="n" style="color: #333;">patch</span> <span class="n" style="color: #333;">working</span> <span class="n" style="color: #333;">around</span> <span class="n" style="color: #333;">makeblastd</span> <span class="n" style="color: #333;">bug</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">v5</span><span class="p">.</span></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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Reviewed</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">forwarded</span> <span class="n" style="color: #333;">patches</span> <span class="n" style="color: #333;">upstream</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">applicable</span><span class="p">.</span></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">
6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="mosel"></span>
</pre>
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<td class="diff-line-num new_line" data-linenumber="7" 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="LC7" class="line" lang="mosel"> <span class="p">--</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">É</span><span class="n" style="color: #333;">tienne</span> <span class="n" style="color: #333;">Mollier</span> <span class="p"><</span><span class="n" style="color: #333;">etienne</span><span class="p">.</span><span class="n" style="color: #333;">mollier</span><span class="p">@</span><span class="n" style="color: #333;">mailoo</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">></span> <span class="n" style="color: #333;">Mon</span><span class="p">,</span> <span class="m" style="color: #099;">14</span> <span class="n" style="color: #333;">Sep</span> <span class="m" style="color: #099;">2020</span> <span class="m" style="color: #099;">21</span><span class="p">:</span><span class="m" style="color: #099;">28</span><span class="p">:</span><span class="m" style="color: #099;">54</span> <span class="p">+</span><span class="m" style="color: #099;">0200</span></span>
</pre>
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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="mosel"></span>
</pre>
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<br>
</li>
<li id="b171d40a542257c0f38f5b732a05d7ff89fcf22e">
<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/6d43a7339ec9e5055d1ce04ba103e5cba72adf53...f4f41aebd08313023b535681e6a1a283b8f9d788#b171d40a542257c0f38f5b732a05d7ff89fcf22e"><strong>debian/patches/fix-use-of-unversioned-python.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">@@ -3,7 +3,7 @@ Description: fix use of unversioned 'python' interpreter</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"> order to build the documentation, but the unversioned "python" interpreter is</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"> not available anymore, at least not in the build context.</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">Author: Étienne Mollier <etienne.mollier@mailoo.org></span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Forwarded: no<span class="idiff left right">t-needed</span></span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="p">Last-Update: 2020-09-09</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span></span>
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<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/6d43a7339ec9e5055d1ce04ba103e5cba72adf53...f4f41aebd08313023b535681e6a1a283b8f9d788#376aaf59ef82170962d12a3347ff003a46b6034c"><strong>debian/patches/privacy_breach.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, 12 May 2015 11:08:43 +0200</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Description: Do not use privacy-breach-logo</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/Tests/Blast/html_msgid_29_blastx_001.html</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/Tests/Blast/html_msgid_29_blastx_001.html</span></span>
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<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/6d43a7339ec9e5055d1ce04ba103e5cba72adf53...f4f41aebd08313023b535681e6a1a283b8f9d788#d452dcc994db05717b376de6a706aff4a11e3a17"><strong>debian/patches/remove_mathml-qname.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: Wed, 30 Apr 2014 14:47:53 +0200</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Bugs-Debian: http://bugs.debian.org/746484</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Forwarded<span class="idiff left right">-Upstream: yes</span></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Forwarded<span class="idiff left right">: https://bugs.debian.org/746484#15</span></span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">Description: Remove non DFSG free DTD</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff">--- a/Bio/Entrez/DTDs/modules.ent</span>
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<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/6d43a7339ec9e5055d1ce04ba103e5cba72adf53...f4f41aebd08313023b535681e6a1a283b8f9d788#cde80ecebd009f562baf24329028f4c4a34c3404"><strong>debian/patches/spelling-error-in-binaries.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">@@ -3,7 +3,7 @@ Description: fix lintian message spelling-error-in-binary</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"> binary, but the matching source code does not show any such issue in strings,</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"> so it might have been a string sliced at a bad place by the compiler.</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">Author: Étienne Mollier <etienne.mollier@mailoo.org></span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="p">Forwarded: <span class="idiff left right">no</span></span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Forwarded: <span class="idiff left right">https://github.com/biopython/biopython/pull/3282</span></span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="p">Last-Update: 2020-09-11</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span></span>
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