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<h3>
Michael R. Crusoe 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/5ba0c16d0f9053eb5be1d5739598d818e1d0ce0c">5ba0c16d</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-12-15T08:46:50Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">arm64 patch from upstream to fix the PairwiseAligner
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/commit/420cf81a3e48db8378215ba7ded160bac6e976ca">420cf81a</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-12-15T12:01:03Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix the Bio.Cluster._cluster doctests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/commit/361e50911aca15d399f86f5a435e92c372e539a2">361e5091</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-12-15T12:14:01Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">samtools now available everywhere
</pre>
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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</li>
<li class="file-stats">
<a href="#3bbd20c245189d0fe4c828fe3956f517955a46b7">
<span class="new-file">
+
debian/patches/arm.patch
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</li>
<li class="file-stats">
<a href="#585fcbc6ad5348da6e40e217ae8cd9cba59f4fa5">
<span class="new-file">
+
debian/patches/fix_doctests
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</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/python-biopython/compare/0a768f257b583e714af82d5a96c2de09960d703a...361e50911aca15d399f86f5a435e92c372e539a2#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,8 +9,9 @@ python-biopython (1.75+dfsg-2) UNRELEASED; urgency=medium</td>
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9
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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 class="p">*</span> <span class="n" style="color: #333;">Added</span> <span class="n" style="color: #333;">missing</span> <span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">dependencies</span><span class="p">:</span> <span class="n" style="color: #333;">python</span><span class="p">-</span><span class="n" style="color: #333;">unittest2</span><span class="p">,</span> <span class="n" style="color: #333;">python</span><span class="p">{,</span><span class="m" style="color: #099;">3</span><span class="p">}-</span><span class="n" style="color: #333;">networkx</span><span class="p">,</span></span>
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10
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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="n" style="color: #333;">samtools</span></span>
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11
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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">
11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">i386</span><span class="p">:</span> <span class="n" style="color: #333;">build</span><span class="p">-</span><span class="n" style="color: #333;">dep</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">raxml</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">testing</span> <span class="n" style="color: #333;">purposes</span></span>
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<td class="diff-line-num old old_line" data-linenumber="12" 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">
12
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<td class="diff-line-num new_line old" data-linenumber="12" 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="LC12" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Fix</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">ignoring</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">errors</span> <span class="n" style="color: #333;">so</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">python3</span> <span class="n" style="color: #333;">tests</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">still</span></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">
13
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<td class="diff-line-num new_line old" data-linenumber="12" 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="mosel"> <span class="nf" style="color: #900; font-weight: 600;">run</span><span class="p">.</span></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">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">debian</span><span class="p">/</span><span class="n" style="color: #333;">patches</span><span class="p">/</span><span class="n" style="color: #333;">arm64</span><span class="p">.</span><span class="n" style="color: #333;">patch</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">upstream</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">fix</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">PairwiseAligner</span></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">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">debian</span><span class="p">/</span><span class="n" style="color: #333;">patches</span><span class="p">/</span><span class="n" style="color: #333;">fix_doctest</span><span class="p">:</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">me</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">fix</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">Bio</span><span class="p">.</span><span class="n" style="color: #333;">Cluster</span><span class="p">.</span><span class="n" style="color: #333;">_cluster</span> <span class="n" style="color: #333;">doctests</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="mosel"> <span class="n" style="color: #333;">Now</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">tests</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">required</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">pass</span> <span class="n" style="color: #333;">again</span><span class="p">.</span></span>
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14
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<td class="diff-line-num new_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">
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="mosel"></span>
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15
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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">
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="mosel"> <span class="p">[</span> <span class="n" style="color: #333;">Andreas</span> <span class="n" style="color: #333;">Tille</span> <span class="p">]</span></span>
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16
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Drop</span> <span class="n" style="color: #333;">Python2</span> <span class="k" style="font-weight: 600;">package</span></span>
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<a href="https://salsa.debian.org/med-team/python-biopython/compare/0a768f257b583e714af82d5a96c2de09960d703a...361e50911aca15d399f86f5a435e92c372e539a2#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="39" 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">@@ -39,7 +39,7 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> python3-setuptools,</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"> python3-unittest2,</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"> raxml [any-amd64 any-i386],</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"> samtools<span class="idiff left right"> [alpha arm64 armel armhf hppa ia64 m68k mips mips64el mipsel powerpc powerpcspe ppc64 ppc64el s390x sh4 sparc64]</span>,</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> samtools,</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"> t-coffee,</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> wise,</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> python3-pygments</span>
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<a href="https://salsa.debian.org/med-team/python-biopython/compare/0a768f257b583e714af82d5a96c2de09960d703a...361e50911aca15d399f86f5a435e92c372e539a2#3bbd20c245189d0fe4c828fe3956f517955a46b7"><strong>debian/patches/arm.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Origin: https://github.com/biopython/biopython/pull/2402</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Michiel de Hoon <mjldehoon@yahoo.com></span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: use signed char for mapping</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/Bio/Align/_aligners.c b/Bio/Align/_aligners.c</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gh" style="color: #999;">index 5cce71c5f7..bd9ce01859 100644</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/Bio/Align/_aligners.c</span></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/Bio/Align/_aligners.c</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -1698,7 +1698,7 @@</span> typedef struct {</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> PyObject* query_gap_function;</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> Py_buffer substitution_matrix;</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> PyObject* alphabet;</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;">- char mapping[256];</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;">+ signed char mapping[256];</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> } Aligner;</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"> </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -2025,7 +2025,7 @@</span> Aligner_set_substitution_matrix(Aligner* self, PyObject* values, void* closure)</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> alphabet = PyObject_GetAttrString(values, "alphabet");</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> if (alphabet) {</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> int i;</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char* mapping = self->mapping;</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ signed char* mapping = self->mapping;</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> #if PY_MAJOR_VERSION > 2</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> if (PyUnicode_Check(alphabet)) {</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> const char* characters = PyUnicode_AsUTF8AndSize(alphabet, &size);</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="p">@@ -2081,7 +2081,7 @@</span> Aligner_set_alphabet(Aligner* self, PyObject* alphabet, void* closure)</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> int i, j;</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> Py_ssize_t size = -1;</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char* mapping = self->mapping;</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ signed char* mapping = self->mapping;</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> if (self->substitution_matrix.obj) {</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> PyErr_SetString(PyExc_AttributeError,</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> "can't set alphabet if a substitution matrix is used");</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="p">@@ -6283,7 +6283,8 @@</span> Aligner_watermansmithbeyer_local_align_matrix(Aligner* self,</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> static int*</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-convert_sequence_to_ints(const char mapping[], Py_ssize_t n, const char s[])</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+convert_sequence_to_ints(const signed char mapping[], Py_ssize_t n,</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ const char s[])</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> char c;</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> Py_ssize_t i;</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="p">@@ -6382,7 +6383,7 @@</span> sequence_converter(PyObject* argument, void* pointer)</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> #endif</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> const int flag = PyBUF_FORMAT | PyBUF_C_CONTIGUOUS;</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> Aligner* aligner;</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char* mapping;</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ signed char* mapping;</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> if (argument == NULL) {</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> if (view->obj) PyBuffer_Release(view);</span></pre>
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<a href="https://salsa.debian.org/med-team/python-biopython/compare/0a768f257b583e714af82d5a96c2de09960d703a...361e50911aca15d399f86f5a435e92c372e539a2#585fcbc6ad5348da6e40e217ae8cd9cba59f4fa5"><strong>debian/patches/fix_doctests</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: Fix Bio.Cluster._cluster doctests</span></span>
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<pre style="margin: 0;">+<span id="LC3" 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="LC4" 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="LC5" class="line" lang="diff"><span class="p">@@ -1438,16 +1438,17 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> "\n"</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> " Examples are:\n"</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> "\n"</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+" >>> from numpy import array\n"</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> " >>> distance = array([[0.0, 1.1, 2.3],\n"</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> " ... [1.1, 0.0, 4.5],\n"</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> " ... [2.3, 4.5, 0.0]])\n"</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-" (option #1)\n"</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+" >>> # (option #1)\n"</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> " >>> distance = array([1.1, 2.3, 4.5])\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;">-" (option #2)\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;">+" >>> # (option #2)\n"</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> " >>> distance = [array([]),\n"</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> " ... array([1.1]),\n"</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> " ... array([2.3, 4.5])]\n"</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-" (option #3)\n"</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+" >>> # (option #3)\n"</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> "\n"</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> " These three correspond to the same distance matrix.\n"</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> "\n"</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="p">@@ -1596,16 +1597,17 @@</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> "\n"</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> " Examples are:\n"</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> "\n"</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+" >>> from numpy import array\n"</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> " >>> distance = array([[0.0, 1.1, 2.3],\n"</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> " ... [1.1, 0.0, 4.5],\n"</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> " ... [2.3, 4.5, 0.0]])\n"</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-" # option 1.\n"</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+" >>> # option 1.\n"</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> " >>> distance = array([1.1, 2.3, 4.5])\n"</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-" # option 2.\n"</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+" >>> # option 2.\n"</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> " >>> distance = [array([]),\n"</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> " ... array([1.1]),\n"</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> " ... array([2.3, 4.5])]\n"</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-" # option 3.\n"</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+" >>> # option 3.\n"</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> "\n"</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> " These three correspond to the same distance matrix.\n"</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> "\n"</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="p">@@ -2318,7 +2320,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> "Adding the column means to the dot product of the coordinates and the\n"</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> "principal components, i.e.\n"</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> "\n"</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-" >>> columnmean + dot(coordinates, pc)\n"</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+" 'columnmean + dot(coordinates, pc)'\n"</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> "\n"</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> "recreates the data matrix.\n";</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/python-biopython/compare/0a768f257b583e714af82d5a96c2de09960d703a...361e50911aca15d399f86f5a435e92c372e539a2#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">@@ -4,3 +4,5 @@ reportlab3.5.patch</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">python_3.8_iteration_fix.patch</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"># 5af680b5043c9f160a19e4bb0deab0ccc271280d.patch</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">exclude_docstring_tests.patch</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">arm.patch</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">fix_doctests</span></pre>
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<a href="https://salsa.debian.org/med-team/python-biopython/compare/0a768f257b583e714af82d5a96c2de09960d703a...361e50911aca15d399f86f5a435e92c372e539a2#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">@@ -107,7 +107,7 @@ else</td>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="plaintext"> cp -a Doc/examples {build_dir}/Doc; \</span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="plaintext"> cp -a Tests {build_dir}; \</span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="plaintext"> cd {build_dir}/Tests; \</span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="plaintext"> env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter} run_tests.py --offline<span class="idiff left right"> || true</span>'</span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext"> env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter} run_tests.py --offline'</span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="plaintext"> mv Tests_avoid/* Tests</span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="plaintext"> rmdir Tests_avoid</span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="plaintext">endif</span>
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