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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:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/f22b5861ea0fbc97be03aad5ec69fd6c8824d46c">f22b5861</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-09-11T00:16:53+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">forward phyml test patch upstream
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/083b8a55e95877028689cc14dd82d43119e1f143">083b8a55</a></strong>
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<span>by Étienne Mollier</span>
<i>at 2020-09-11T22:49:21+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add spelling-error-in-binaries.patch
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<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/68e959e2deccce41315988c2744262db15065ddc">68e959e2</a></strong>
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<span>by Étienne Mollier</span>
<i>at 2020-09-11T23:18:30+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added privacy_breach_ie9.patch
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#312e12f531b01ef15a9d2e4d240bc931f7d36ec3">
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+
debian/patches/privacy_breach_ie9.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#cde80ecebd009f562baf24329028f4c4a34c3404">
<span class="new-file">
+
debian/patches/spelling-error-in-binaries.patch
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<li class="file-stats">
<a href="#fef0564902ac564ac66ff83866c813c84374a053">
debian/patches/stabilize-phyml-test.patch
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<h4>Changes:</h4>
<li id="312e12f531b01ef15a9d2e4d240bc931f7d36ec3">
<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/891939b0eb21c2cc0bddbc7738dbe5f7ba377221...68e959e2deccce41315988c2744262db15065ddc#312e12f531b01ef15a9d2e4d240bc931f7d36ec3"><strong>debian/patches/privacy_breach_ie9.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: fix privacy breach with html5shiv</span></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="diff"> Actually the script called is commented out, except when reading the page with</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="diff"> Internet Explorer 9. This patch makes sure the script is not called at all,</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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> even if it is very unlikely that HTML document installed in Debian will ever</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> be read with this browser.</span>
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<pre style="margin: 0;">+<span id="LC6" 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="LC7" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">Last-Update: 2020-09-11</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC10" 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="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-biopython.orig/Doc/cookbook/Restriction/Restriction.html</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-biopython/Doc/cookbook/Restriction/Restriction.html</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="p">@@ -75,9 +75,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> code span.vs { color: #4070a0; } /* VerbatimString */</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </style></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <!--[if lt IE 9]></span></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;">- <script src="//cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv-printshiv.min.js"></script></span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <![endif]--></span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </head></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> <h1 id="working-with-restriction-enzymes">Working with restriction enzymes</h1></span></pre>
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<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/891939b0eb21c2cc0bddbc7738dbe5f7ba377221...68e959e2deccce41315988c2744262db15065ddc#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">remove_mathml-qname.patch</span>
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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-unversionned-python.patch</span>
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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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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">spelling-error-in-binaries.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/891939b0eb21c2cc0bddbc7738dbe5f7ba377221...68e959e2deccce41315988c2744262db15065ddc#cde80ecebd009f562baf24329028f4c4a34c3404"><strong>debian/patches/spelling-error-in-binaries.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: fix lintian message spelling-error-in-binary</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> As a side note, lintian reports another spelling error "algorith" in another</span>
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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: no</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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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-biopython.orig/Bio/Cluster/clustermodule.c</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;">+++ python-biopython/Bio/Cluster/clustermodule.c</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="p">@@ -2132,7 +2132,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> "\n"</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> " - transpose: if equal to 0: the distances between rows are\n"</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> " calculated;\n"</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-" if equal to 1, the distances beteeen columns are calculated.\n"</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+" if equal to 1, the distances between columns are calculated.\n"</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> "\n"</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> " - dist: specifies the distance function to be used:\n"</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> "\n"</span></pre>
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<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/891939b0eb21c2cc0bddbc7738dbe5f7ba377221...68e959e2deccce41315988c2744262db15065ddc#fef0564902ac564ac66ff83866c813c84374a053"><strong>debian/patches/stabilize-phyml-test.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">@@ -5,8 +5,8 @@ Description: stabilize the test involving phyml</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"> environment variable PHYMLCPUS, allows one to avoid the message "No protocol</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"> specified" in the error output, which interferes with the version test.</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: <span class="idiff left right">no</span></span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="p">Last-Update: 2020-09-1<span class="idiff left right">0</span></span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">Forwarded: <span class="idiff left right">https://github.com/biopython/biopython/pull/3268</span></span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">Last-Update: 2020-09-1<span class="idiff left right">1</span></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/Tests/test_phyml_tool.py</span></span>
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