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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/4955492de02e26ce1b39e14fa1faf23e5fc4327b">4955492d</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-09-12T19:25:03+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix typo in unversioned python patch
</pre>
</li>
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<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/15084cac1de49115c23e7e7e595da382d22b88ec">15084cac</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-09-12T21:13:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove last update date in Tutorial.tex
This went through a patch, which improves build reproducibility.
</pre>
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#b171d40a542257c0f38f5b732a05d7ff89fcf22e">
debian/patches/fix-use-of-unversionned-python.patch
→
debian/patches/fix-use-of-unversioned-python.patch
</a>
</li>
<li class="file-stats">
<a href="#e74dce535bd5702a37e2ff06371be417ecd72749">
<span class="new-file">
+
debian/patches/reproduciblebuild.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
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</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/68e959e2deccce41315988c2744262db15065ddc...15084cac1de49115c23e7e7e595da382d22b88ec#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,6 +5,7 @@ python-biopython (1.78+dfsg-1) UNRELEASED; urgency=medium</td>
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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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<pre style="margin: 0;"> <span id="LC5" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Removed</span> <span class="n" style="color: #333;">patches</span> <span class="n" style="color: #333;">applied</span> <span class="n" style="color: #333;">upstream</span><span class="p">.</span></span>
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<td class="diff-line-num 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">
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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="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">New</span> <span class="n" style="color: #333;">upstream</span> <span class="k" style="font-weight: 600;">version</span></span>
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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="n" style="color: #333;">debhelper</span><span class="p">-</span><span class="n" style="color: #333;">compat</span> <span class="m" style="color: #099;">13</span> <span class="p">(</span><span class="n" style="color: #333;">routine</span><span class="p">-</span><span class="n" style="color: #333;">update</span><span class="p">)</span></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="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Improved</span> <span class="n" style="color: #333;">build</span> <span class="n" style="color: #333;">reproducibility</span></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="mosel"></span>
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<td class="diff-line-num old_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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<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="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;">Wed</span><span class="p">,</span> <span class="m" style="color: #099;">09</span> <span class="n" style="color: #333;">Sep</span> <span class="m" style="color: #099;">2020</span> <span class="m" style="color: #099;">22</span><span class="p">:</span><span class="m" style="color: #099;">53</span><span class="p">:</span><span class="m" style="color: #099;">13</span> <span class="p">+</span><span class="m" style="color: #099;">0200</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="mosel"></span>
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<li id="b171d40a542257c0f38f5b732a05d7ff89fcf22e">
<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/68e959e2deccce41315988c2744262db15065ddc...15084cac1de49115c23e7e7e595da382d22b88ec#b171d40a542257c0f38f5b732a05d7ff89fcf22e"><strong>debian/patches/fix-use-of-unversionned-python.patch</strong>
→
<strong>debian/patches/fix-use-of-unversioned-python.patch</strong>
</a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Description: fix use of unversion<span class="idiff left right">n</span>ed 'python' interpreter</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: fix use of unversioned 'python' interpreter</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"> The Doc/Makefile uses python to evaluate the current version of the library in</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"> order to build the documentation, but the unversion<span class="idiff left right">n</span>ed "python" interpreter is</span>
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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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<li id="e74dce535bd5702a37e2ff06371be417ecd72749">
<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/68e959e2deccce41315988c2744262db15065ddc...15084cac1de49115c23e7e7e595da382d22b88ec#e74dce535bd5702a37e2ff06371be417ecd72749"><strong>debian/patches/reproduciblebuild.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: make the build reproducible</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> This patch removes the last update date, which would correspond to the moment</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> when the package was build, and wouldn't be too relevant in the document.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> Focusing on the version number would be a better approach here. This patch is</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> not needed upstream, as it would interfere with development releases, marked</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> only with the version "dev", so would benefit of the date here.</span>
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<pre style="margin: 0;">+<span id="LC7" 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="LC8" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">Last-Update: 2020-09-12</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC11" 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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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-biopython.orig/Doc/Tutorial.tex</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-biopython/Doc/Tutorial.tex</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">@@ -86,7 +86,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> \author{Jeff Chang, Brad Chapman, Iddo Friedberg, Thomas Hamelryck, \\</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> Michiel de Hoon, Peter Cock, Tiago Antao, Eric Talevich, Bartek Wilczy\'{n}ski}</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-\date{Last Update -- \today\ (Biopython \bpversion)}</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+\date{Biopython \bpversion}</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> %Hack to get the logo at the start of the HTML front page:</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> %(hopefully this isn't going to be too wide for most people)</span></pre>
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<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/68e959e2deccce41315988c2744262db15065ddc...15084cac1de49115c23e7e7e595da382d22b88ec#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -2,6 +2,7 @@ remove_mathml-qname.patch</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">privacy_breach.patch</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">privacy_breach_ie9.patch</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">blastdbv4-impl.patch</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">fix-use-of-unversion<span class="idiff left right">n</span>ed-python.patch</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">fix-use-of-unversioned-python.patch</span>
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<td class="diff-line-num 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">
6
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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="plaintext">stabilize-phyml-test.patch</span>
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<td class="diff-line-num old_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">
7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">spelling-error-in-binaries.patch</span>
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<td class="diff-line-num new old_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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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">reproduciblebuild.patch</span></pre>
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