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<h3>
Graham Inggs 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/66f48b6c18bfab51b8dc6c3a32a4d15da8da4e59">66f48b6c</a></strong>
<div>
<span>by Graham Inggs</span>
<i>at 2018-12-05T11:40:14Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Clean up some trailing whitespace in debian/* files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/commit/93ba4c4b5bc6d044a7ce280a2b16bde1747d1f33">93ba4c4b</a></strong>
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<span>by Graham Inggs</span>
<i>at 2018-12-05T11:43:25Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Prepare for upload to unstable
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<h4>3 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="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/python-biopython/compare/a5a7c263a604ecb6004a9112954cba79749f7358...93ba4c4b5bc6d044a7ce280a2b16bde1747d1f33#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">python</span><span class="p">-</span><span class="n" style="color: #333;">biopython</span> <span class="p">(</span><span class="m" style="color: #099;">1.72</span><span class="p">+</span><span class="n" style="color: #333;">dfsg</span><span class="p">-</span><span class="m" style="color: #099;">2</span><span class="p">)</span> <span class="n" style="color: #333;"><span class="idiff left right">UNRELEASED</span></span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">python</span><span class="p">-</span><span class="n" style="color: #333;">biopython</span> <span class="p">(</span><span class="m" style="color: #099;">1.72</span><span class="p">+</span><span class="n" style="color: #333;">dfsg</span><span class="p">-</span><span class="m" style="color: #099;">2</span><span class="p">)</span> <span class="n" style="color: #333;"><span class="idiff left right">unstable</span></span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
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2
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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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<pre style="margin: 0;"> <span id="LC3" 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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<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="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Remove</span> <span class="n" style="color: #333;">unneeded</span> <span class="n" style="color: #333;">comment</span> <span class="n" style="color: #333;">about</span> <span class="n" style="color: #333;">samtools</span> <span class="p">-</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">is</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">found</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">biopython</span></span>
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5
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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="n" style="color: #333;">anyway</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="mosel"></span>
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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;">Graham</span> <span class="n" style="color: #333;">Inggs</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;">Team</span> <span class="n" style="color: #333;">upload</span></span>
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8
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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;">Fix</span> <span class="n" style="color: #333;">compatibility</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">ReportLab</span> <span class="m" style="color: #099;">3.5</span> <span class="p">(</span><span class="n" style="color: #333;">Closes</span><span class="p">:</span> <span class="p">#</span><span class="m" style="color: #099;">913064</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Clean</span> <span class="n" style="color: #333;">up</span> <span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">trailing</span> <span class="n" style="color: #333;">whitespace</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">debian</span><span class="p">/*</span> <span class="n" style="color: #333;">files</span></span>
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9
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="mosel"> <span class="p">--</span> <span class="n" style="color: #333;"><span class="idiff left">Andreas</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Tille</span></span><span class="idiff"> </span><span class="p"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">tille</span></span><span class="p"><span class="idiff">@</span></span><span class="n" style="color: #333;"><span class="idiff">debian</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">org</span></span><span class="p"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Sat</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">28</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Jul</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">2018</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">05</span></span><span class="p"><span class="idiff">:</span></span><span class="m" style="color: #099;"><span class="idiff">06</span></span><span class="p"><span class="idiff">:</span></span><span class="m" style="color: #099;"><span class="idiff">54</span></span><span class="idiff"> </span><span class="p"><span class="idiff">+</span></span><span class="m" style="color: #099;"><span class="idiff right">02</span>00</span></span>
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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;"><span class="idiff left">Graham</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Inggs</span></span><span class="idiff"> </span><span class="p"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">ginggs</span></span><span class="p"><span class="idiff">@</span></span><span class="n" style="color: #333;"><span class="idiff">debian</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">org</span></span><span class="p"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Wed</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">05</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Dec</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">2018</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">11</span></span><span class="p"><span class="idiff">:</span></span><span class="m" style="color: #099;"><span class="idiff">41</span></span><span class="p"><span class="idiff">:</span></span><span class="m" style="color: #099;"><span class="idiff">01</span></span><span class="idiff"> </span><span class="p"><span class="idiff">+</span></span><span class="m" style="color: #099;"><span class="idiff right">00</span>00</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="mosel"><span class="n" style="color: #333;">python</span><span class="p">-</span><span class="n" style="color: #333;">biopython</span> <span class="p">(</span><span class="m" style="color: #099;">1.72</span><span class="p">+</span><span class="n" style="color: #333;">dfsg</span><span class="p">-</span><span class="m" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">unstable</span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="mosel"></span>
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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">@@ -60,7 +62,7 @@ python-biopython (1.70+dfsg-2) unstable; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="mosel"><span class="s1" style="color: #d14;"> * Fixed build dependencies (added python-setuptools) (Closes: #869597).</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="mosel"><span class="s1" style="color: #d14;"> -- Steffen Moeller <moeller@debian.org> Mon, 31 Jul 2017 18:24:01 +0200</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="mosel"><span class="s1" style="color: #d14;"><span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="mosel"><span class="s1" style="color: #d14;">python-biopython (1.70+dfsg-1) unstable; urgency=medium</span></span>
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="mosel"><span class="s1" style="color: #d14;"> * Team upload</span></span>
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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">@@ -71,7 +73,7 @@ python-biopython (1.70+dfsg-1) unstable; urgency=medium</td>
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71
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="mosel"><span class="s1" style="color: #d14;"> * debian/rules: Merged two redundant clean overrides</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="mosel"><span class="s1" style="color: #d14;"> -- Steffen Moeller <moeller@debian.org> Sun, 23 Jul 2017 18:08:39 +0200</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="mosel"><span class="s1" style="color: #d14;"><span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="mosel"><span class="s1" style="color: #d14;">python-biopython (1.68+dfsg-3) unstable; urgency=medium</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="mosel"><span class="s1" style="color: #d14;"> * (Build-)Depend: phyml only on those architectures where it is available</span></span>
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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">@@ -214,7 +216,7 @@ python-biopython (1.64+dfsg-1) unstable; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="mosel"><span class="s1" style="color: #d14;">python-biopython (1.63+dfsg-5) unstable; urgency=medium</span></span>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="mosel"><span class="s1" style="color: #d14;"> * Apply upstream fix to fix cpairwise2 import issue under python3<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="mosel"><span class="s1" style="color: #d14;"> * Apply upstream fix to fix cpairwise2 import issue under python3</span></span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Closes: #747494</span></span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="mosel"><span class="s1" style="color: #d14;"> -- Andreas Tille <tille@debian.org> Sat, 10 May 2014 07:52:48 +0200</span></span>
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<a href="https://salsa.debian.org/med-team/python-biopython/compare/a5a7c263a604ecb6004a9112954cba79749f7358...93ba4c4b5bc6d044a7ce280a2b16bde1747d1f33#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">@@ -102,7 +102,7 @@ Description: Python library for bioinformatics (implemented in Python 2)</td>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext"> extremely liberal and compatible with almost every license in</span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext"> the world. The project works along with the Open Bioinformatics</span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="plaintext"> Foundation, who generously provide web and CVS space for</span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="plaintext"> the project.<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"> the project.</span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="plaintext"> This package is targeting Python version 2.</span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="plaintext"></span>
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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">@@ -153,7 +153,7 @@ Description: Python library for bioinformatics (implemented in Python 3)</td>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="plaintext"> extremely liberal and compatible with almost every license in</span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="plaintext"> the world. The project works along with the Open Bioinformatics</span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="plaintext"> Foundation, who generously provide web and CVS space for</span>
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="plaintext"> the project.<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext"> the project.</span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="plaintext"> This package is targeting Python version 3.</span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/python-biopython/compare/a5a7c263a604ecb6004a9112954cba79749f7358...93ba4c4b5bc6d044a7ce280a2b16bde1747d1f33#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">@@ -16,7 +16,7 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">BUILDARCH := $(shell dpkg-architecture -qDEB_BUILD_ARCH)</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"># If `$(CURDIR)/setup.py test` would be called these tests need to be excluded since they require to be online</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">#EXCLUDEONLINE=Entrez_online HotRand NCBI_qblast SCOP_online SeqIO_online TogoWS<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">#EXCLUDEONLINE=Entrez_online HotRand NCBI_qblast SCOP_online SeqIO_online TogoWS</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"># Since `run_texts.py --online` is used the test requiring online connections are excluded by the test suite</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">EXCLUDEONLINE=</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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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">@@ -98,7 +98,7 @@ else</td>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="plaintext"> rm -f debian/tmp_tests/Tests/Quality/example.fastq.gz</span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext"> # We also keep the tests we need to avoid for later inspection</span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext"> cp -a Tests_avoid debian/tmp_tests</span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="plaintext"> # in the Debian package dialign it is not needed to set DIALIGN2_DIR but the test is verifying this dir<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"> # in the Debian package dialign it is not needed to set DIALIGN2_DIR but the test is verifying this dir</span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext"> # to run the EMBOSS test test_Emboss also requires to have the environment variable EMBOSS_ROOT set</span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext"> LC_ALL=C.UTF-8 dh_auto_test -- --test --system=custom \</span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="plaintext"> --test-args='set -e; \</span>
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