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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/63cd45772bb2f6a898f501980edc5863c285e8e4">63cd4577</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-07-05T23:51:41+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/watch: bring back dversionmangle
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/7ce0ba9b974c98f369a54257327f480f3ef46c09">7ce0ba9b</a></strong>
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<span>by Étienne Mollier</span>
<i>at 2021-07-10T00:03:37+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d{,/tests}/control: add full_suite autopkgtest
The full_suite autopkgtest is an additional test which executes
run-unit-test in an environment with most tools available in Debian
for use by Biopython. The idea is to be able to run as much tests as
possible, to identify missing components.
Closes: #986410
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/82d5c84e8466581b296c043c07b8aab7f7dc4212">82d5c84e</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-07-10T00:05:12+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update changelog
</pre>
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<h4>4 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="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
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<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/56e40231d7f272aacac012e04ba9d28afb90450b...82d5c84e8466581b296c043c07b8aab7f7dc4212#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,8 +2,9 @@ python-biopython (1.78+dfsg-5) UNRELEASED; urgency=medium</td>
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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;">d</span><span class="p">/</span><span class="n" style="color: #333;">control</span><span class="p">:</span> <span class="n" style="color: #333;">update</span> <span class="n" style="color: #333;">uploader</span> <span class="n" style="color: #333;">address</span></span>
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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;">d</span><span class="p">/</span><span class="n" style="color: #333;">watch</span><span class="p">:</span> <span class="n" style="color: #333;">fix</span> <span class="n" style="color: #333;">broken</span> <span class="n" style="color: #333;">url</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">github</span></span>
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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">d</span><span class="p">{,/</span><span class="n" style="color: #333;">tests</span><span class="p">}/</span><span class="n" style="color: #333;">control</span><span class="p">:</span> <span class="n" style="color: #333;">add</span> <span class="n" style="color: #333;">full_suite</span> <span class="n" style="color: #333;">autopkgtest</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;">986410</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="mosel"></span>
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<td class="new_line diff-line-num old" data-linenumber="7" 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="LC6" 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;">emollier</span><span class="p">@</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">></span> <span class="n" style="color: #333;"><span class="idiff left">Mon</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="n" style="color: #333;">Jul</span> <span class="m" style="color: #099;">2021</span> <span class="m" style="color: #099;"><span class="idiff">23</span></span><span class="p"><span class="idiff">:</span></span><span class="m" style="color: #099;"><span class="idiff">14</span></span><span class="p"><span class="idiff">:</span></span><span class="m" style="color: #099;"><span class="idiff right">47</span></span> <span class="p">+</span><span class="m" style="color: #099;">0200</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="mosel"> <span class="p">--</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">É</span><span class="n" style="color: #333;">tienne</span> <span class="n" style="color: #333;">Mollier</span> <span class="p"><</span><span class="n" style="color: #333;">emollier</span><span class="p">@</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">></span> <span class="n" style="color: #333;"><span class="idiff left">Sat</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">10</span></span> <span class="n" style="color: #333;">Jul</span> <span class="m" style="color: #099;">2021</span> <span class="m" style="color: #099;"><span class="idiff">00</span></span><span class="p"><span class="idiff">:</span></span><span class="m" style="color: #099;"><span class="idiff">04</span></span><span class="p"><span class="idiff">:</span></span><span class="m" style="color: #099;"><span class="idiff right">06</span></span> <span class="p">+</span><span class="m" style="color: #099;">0200</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC9" 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;">1.78</span><span class="p">+</span><span class="n" style="color: #333;">dfsg</span><span class="p">-</span><span class="m" style="color: #099;">4</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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<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/56e40231d7f272aacac012e04ba9d28afb90450b...82d5c84e8466581b296c043c07b8aab7f7dc4212#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">@@ -5,6 +5,8 @@ Uploaders: Charles Plessy <plessy@debian.org>,</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> Étienne Mollier <emollier@debian.org></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Section: python</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"># note: all build-dependencies marked <!nocheck>, should be tested against in</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"># the full_suite autopkgtest as well.</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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9
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> dh-python,</span>
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10
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> python3-all-dev,</span>
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<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/56e40231d7f272aacac012e04ba9d28afb90450b...82d5c84e8466581b296c043c07b8aab7f7dc4212#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># autopkgtest checking dependencies are fulfilled</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Features: test-name=dependencies</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Test-Command: sh debian/tests/run-unit-test</span>
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2
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Depends: @, python3-setuptools, python3-all</span>
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3
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Restrictions: allow-stderr</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"># autopkgtest checking every test runs fine; dependencies list should match the</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"># list of build-dependencies from d/control; see #986410 for a rationale.</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Features: test-name=full_suite</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Test-Command: sh debian/tests/run-unit-test</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Depends: @, python3-setuptools, python3-all,</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> python3-numpy,</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> python3-reportlab,</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> hevea,</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> bwa,</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> clustalo,</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> clustalw,</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> dialign,</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> dssp (>= 4.0.0),</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> emboss,</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> fasttree,</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> mafft,</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> muscle,</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> ncbi-blast+ (>= 2.10.1-3),</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> phylip,</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> phyml [any-amd64 any-i386],</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> prank,</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> probcons,</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> python3-networkx,</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> python3-mysqldb,</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> python3-matplotlib,</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> python3-mmtf,</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> python3-pil,</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> python3-rdflib,</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> python3-renderpm,</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> python3-psycopg2,</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> python3-pygments,</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> python3-scipy,</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> python3-unittest2,</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> raxml [any-amd64 any-i386],</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> samtools,</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> t-coffee,</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> wise</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">Restrictions: allow-stderr, skip-not-installable</span></pre>
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<li id="68ef9f98c01c7eecd4c605cc26048a06f3304b79">
<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/56e40231d7f272aacac012e04ba9d28afb90450b...82d5c84e8466581b296c043c07b8aab7f7dc4212#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=4</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE@-$1.tar.gz%" \</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE@-$1.tar.gz%,\</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">dversionmangle=s/\+dfsg//" \</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> https://github.com/biopython/biopython/tags \</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> (?:.*?/)?v?(\d[\d.]*)\.tar\.gz debian uupdate</span></pre>
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