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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-cogent">Debian Med / python-cogent</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cogent/commit/f9a5048cacca2cc1864fd995b5f6d7b55d7c6a01">f9a5048c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-08T14:02:10+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update dependencies and todo
</pre>
</li>
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<strong><a href="https://salsa.debian.org/med-team/python-cogent/commit/627ed619306bc8c8031f85bbc2a233f2628a7639">627ed619</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-01-08T14:02:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upstream name is cogent3
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</li>
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/python-cogent/compare/c3c8c7d0e19fb742b9a97d313ad90f3a2261adff...627ed619306bc8c8031f85bbc2a233f2628a7639#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" 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="diff-line-num unfold js-unfold new_line" data-linenumber="14" 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">@@ -14,7 +14,8 @@ python-cogent (2019.12.6a-1) UNRELEASED; urgency=medium</td>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="14" 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="LC14" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,</span>
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<td class="diff-line-num old_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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<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="plaintext"> Repository-Browse.</span>
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<td class="diff-line-num old_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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<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="plaintext"> * Fix day-of-week for changelog entry 1.5.3-1.</span>
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<td class="diff-line-num old old_line" data-linenumber="17" 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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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC17" class="line" lang="plaintext"> TODO: package scitrack (https://github.com/HuttleyLab/scitrack)</span>
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<td class="diff-line-num new old_line" data-linenumber="18" 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="17" 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="LC17" class="line" lang="plaintext"> TODO: scitrack (#948415 in new)</span>
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<td class="diff-line-num new old_line" data-linenumber="18" 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="18" 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="LC18" class="line" lang="plaintext"> tinydb (https://salsa.debian.org/python-team/modules/tinydb #819649)</span>
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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="19" 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="LC19" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="19" 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">
19
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<td class="diff-line-num new_line" data-linenumber="20" 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="LC20" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 07 Jan 2020 20:12:00 +0100</span>
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20
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<td class="diff-line-num new_line" data-linenumber="21" 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="LC21" class="line" lang="plaintext"></span>
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<br>
</li>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/python-cogent/compare/c3c8c7d0e19fb742b9a97d313ad90f3a2261adff...627ed619306bc8c8031f85bbc2a233f2628a7639#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,12 +11,14 @@ Build-Depends: debhelper-compat (= 12),</td>
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<td class="diff-line-num old_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="plaintext"> python3-matplotlib,</span>
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<td class="diff-line-num old_line" data-linenumber="12" 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">
12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> python3-numpy,</span>
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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext"> python3-pandas,</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="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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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> python3-scitrack,</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="15" 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="LC15" class="line" lang="plaintext"> python3-tqdm,</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="16" 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="LC16" class="line" lang="plaintext"> python3-tinydb,</span>
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<td class="diff-line-num old_line" data-linenumber="14" 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">
14
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<td class="diff-line-num new_line" data-linenumber="17" 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="LC17" class="line" lang="plaintext"> python3-setuptools,</span>
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<td class="diff-line-num old_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">
15
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<td class="diff-line-num new_line" data-linenumber="18" 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="LC18" class="line" lang="plaintext"> python3-sphinx,</span>
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<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="19" 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="LC19" class="line" lang="plaintext"> python3-numpydoc,</span>
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<td class="diff-line-num old_line" data-linenumber="17" 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="LC20" class="line" lang="plaintext"> python3-nbsphinx,</span>
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<td class="diff-line-num old_line" data-linenumber="18" 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="LC21" class="line" lang="plaintext"> python3-sphinxcontrib.bibtex,</span>
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<td class="diff-line-num new_line old" data-linenumber="22" 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="LC19" class="line" lang="plaintext"> python3-tqdm,</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> cython3,</span>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> ncbi-blast+-legacy,</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> bwa [any-amd64],</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="42" 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">@@ -40,13 +42,17 @@ Vcs-Browser: https://salsa.debian.org/med-team/python-cogent</td>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/python-cogent.git</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">Homepage: https://github.com/cogent3/cogent3</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext">Package: python3-cogent</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">Package: python3-cogent<span class="idiff left right">3</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"> ${python3:Depends},</span>
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"> python3-matplotlib,</span>
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"> python3-pandas</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> python3-plotly,</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> python3-scitrack,</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> python3-tqdm,</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> python3-tinydb</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext">Recommends: ncbi-blast+-legacy,</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext"> bwa [any-amd64],</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext"> cd-hit,</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">@@ -82,8 +88,8 @@ Section: doc</td>
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82
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext"> libjs-jquery,</span>
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84
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext"> libjs-underscore</span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="plaintext">Suggests: python<span class="idiff left right">-cogent</span> (= ${binary:Version})</span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="plaintext">Description: docs for python<span class="idiff left right">-cogent</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">Suggests: python<span class="idiff left right">3-cogent3</span> (= ${binary:Version})</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">Description: docs for python<span class="idiff left right">3-cogent3</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext"> PyCogent is a software library for genomic biology.</span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext"> It is distinguished by many unique built-in capabilities (such as true codon</span>
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<a href="https://salsa.debian.org/med-team/python-cogent/compare/c3c8c7d0e19fb742b9a97d313ad90f3a2261adff...627ed619306bc8c8031f85bbc2a233f2628a7639#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">@@ -42,7 +42,7 @@ FAIL_ON_S390X_TESTS := test_maths.test_optimisers \</td>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="make"><span class="nv" style="color: #008080;">FAIL_ON_MIPS_TESTS</span> <span class="o" style="font-weight: 600;">:=</span> test_seqsim.test_sequence_generators</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: #008080;">PYBUILD_NAME</span><span class="o" style="font-weight: 600;">=</span>cogent</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: #008080;">PYBUILD_NAME</span><span class="o" style="font-weight: 600;">=</span>cogent<span class="idiff left right">3</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="make"><span class="k" style="font-weight: 600;">include</span><span class="sx" style="color: #d14;"> /usr/share/dpkg/default.mk</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="make"></span>
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