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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-skbio">Debian Med / python-skbio</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-skbio/-/commit/06332c2319e66514c9f1da5c5a1266e5704d9c57">06332c23</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-02-01T11:49:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/control: add depends on various python doc packages to fix intersphinx linking
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-skbio/-/commit/0104ce78238d8183ed49bc0a1c2bbe695549eacb">0104ce78</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-02-01T11:54:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-skbio/-/commit/91bfe6681fb4221c5a9fba8d5c6057119533da98">91bfe668</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-02-01T11:54:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update renamed lintian tag names in lintian overrides.
Changes-By: lintian-brush
Fixes: lintian: renamed-tag
See-also: https://lintian.debian.org/tags/renamed-tag.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-skbio/-/commit/8a782ffcd7c75d50b38abcd3a7dc54a074c315ab">8a782ffc</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-02-01T12:13:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Silence some lintian false-positives
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-skbio/-/commit/2828703b6d69641cadc1bbec546f8a72a2cd70bf">2828703b</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-02-01T12:13:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
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</ul>
<h4>13 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>
</li>
<li class="file-stats">
<a href="#90561facadd139a89c75324083bbe697c79487e9">
debian/patches/0002-use-libsww-as-library-not-embedded-src.patch
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</li>
<li class="file-stats">
<a href="#90247e00947007a45af599d14271a09e2a983f9f">
<span class="deleted-file">
−
debian/patches/ignore_failing_patches.patch
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</a>
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<li class="file-stats">
<a href="#bed33211feee1f443bc744266386c2389e9a8cb5">
<span class="new-file">
+
debian/patches/local_inventory
</span>
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<li class="file-stats">
<a href="#f797e72de3d411c0371db1a40d6c21941fd29f7a">
debian/patches/mathjax-path
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<li class="file-stats">
<a href="#93b6380d5716c97079e78b7dec432a3fbc5226ff">
debian/patches/no_privacy_breach_logo.patch
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<li class="file-stats">
<a href="#e49ab5c8d6d83df0e7379ba931a0f7cf21d9fbe9">
debian/patches/pandas1.1-ordination-fix.patch
</a>
</li>
<li class="file-stats">
<a href="#268dbd2a1f59e155e6ac017942dbf60abafa8960">
debian/patches/pandas1.1-valueerror.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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</li>
<li class="file-stats">
<a href="#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2">
debian/patches/simde
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<li class="file-stats">
<a href="#a14ad1d123d1f66610c61d9334c9d6e6acf57d7d">
debian/patches/soften_test
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<li class="file-stats">
<a href="#19169317775fd0def86a25ecb1aa2c551b77d8da">
debian/python3-skbio.lintian-overrides
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</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/python-skbio/-/compare/6bac95552858d04adab82b132fe4be243dc2d1fc...2828703b6d69641cadc1bbec546f8a72a2cd70bf#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-skbio (0.5.6-4) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * debian/control: add depends on various python doc packages to fix</span>
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<td class="diff-line-num new new_line" 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="plaintext"> intersphinx linking</span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext"> * debian/patches/ignore_failing_patches.patch: drop unneeded patch</span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="plaintext"> * Standards-Version: 4.5.1 (routine-update)</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="plaintext"> * Update renamed lintian tag names in lintian overrides.</span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> * Silence some lintian false-positives</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> -- Michael R. Crusoe <crusoe@debian.org> Mon, 01 Feb 2021 11:54:35 +0100</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">python-skbio (0.5.6-3.1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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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"> * Non-maintainer upload.</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/python-skbio/-/compare/6bac95552858d04adab82b132fe4be243dc2d1fc...2828703b6d69641cadc1bbec546f8a72a2cd70bf#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="25" 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="25" 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">@@ -25,8 +25,14 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Build-Depends-arch: python3-lockfile <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> python3-pytest <!nocheck></span>
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">Build-Depends-Indep: python3-sphinx <!nodoc>,</span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> python3-sphinx-bootstrap-theme <!nodoc></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> python3-sphinx-bootstrap-theme <!nodoc>,</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> python-numpy-doc <!nodoc>,</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> python3-doc <!nodoc>,</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> python-matplotlib-doc <!nodoc>,</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> python-scipy-doc <!nodoc>,</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> python-biom-format-doc <!nodoc>,</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> python-pandas-doc <!nodoc></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">Standards-Version: 4.5.1</span>
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30
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/python-skbio</span>
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31
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/python-skbio.git</span>
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32
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">Homepage: https://github.com/biocore/scikit-bio</span>
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<li id="90561facadd139a89c75324083bbe697c79487e9">
<a href="https://salsa.debian.org/med-team/python-skbio/-/compare/6bac95552858d04adab82b132fe4be243dc2d1fc...2828703b6d69641cadc1bbec546f8a72a2cd70bf#90561facadd139a89c75324083bbe697c79487e9"><strong>debian/patches/0002-use-libsww-as-library-not-embedded-src.patch</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="diff"><span class="p">From: Kevin Murray <spam@kdmurray.id.au></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="diff"><span class="p">Date: Tue, 15 Nov 2016 19:21:24 +1100</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Subject: use libsww as library, not embedded src</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">---</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> setup.py | 22 +++-------------------</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> 1 file changed, 3 insertions(+), 19 deletions(-)</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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8
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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9
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff">--- a/setup.py</span>
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10
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7
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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/setup.py</span></span>
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<li id="90247e00947007a45af599d14271a09e2a983f9f">
<a href="https://salsa.debian.org/med-team/python-skbio/-/compare/6bac95552858d04adab82b132fe4be243dc2d1fc...2828703b6d69641cadc1bbec546f8a72a2cd70bf#90247e00947007a45af599d14271a09e2a983f9f"><strong>debian/patches/ignore_failing_patches.patch</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Wed, 18 Dec 2019 09:44:59 +0100</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">FIXME: This patch should be revised and the tests should be fixed upstream</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> see: https://github.com/biocore/scikit-bio/issues/1681</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">Description: Ignore 4 tests to not block Python3 migration</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff">--- python-skbio.orig/skbio/stats/ordination/tests/test_principal_coordinate_analysis.py</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-skbio/skbio/stats/ordination/tests/test_principal_coordinate_analysis.py</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="p">@@ -10,7 +10,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> import numpy.testing as npt</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> import pandas as pd</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> from copy import deepcopy</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;">-from unittest import TestCase, main</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;">+from unittest import TestCase, main, skip</span></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"> from skbio import DistanceMatrix, OrdinationResults</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> from skbio.stats.distance import DissimilarityMatrixError</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="p">@@ -194,6 +194,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> pcoa([[1, 2], [3, 4]])</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> </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;">+@skip("FIXME: Skip failing test. See https://github.com/biocore/scikit-bio/issues/1681")</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"> class TestPCoABiplot(TestCase):</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> def setUp(self):</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> # Crawford dataset for unweighted UniFrac</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-skbio.orig/skbio/sequence/tests/test_sequence.py</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-skbio/skbio/sequence/tests/test_sequence.py</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="p">@@ -12,7 +12,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> import re</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> from types import GeneratorType</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"> from collections import Hashable</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from unittest import TestCase, main</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from unittest import TestCase, main, skip</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"> import numpy as np</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"> import numpy.testing as npt</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="p">@@ -448,6 +448,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"> with self.assertRaises(ValueError):</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"> bytes[1] = 42</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"> </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;">+ @skip("FIXME: Skip failing test. See https://github.com/biocore/scikit-bio/issues/1681")</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"> def test_init_invalid_sequence(self):</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"> # invalid dtype (numpy.ndarray input)</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"> with self.assertRaises(TypeError):</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"><span class="p">@@ -2364,6 +2365,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"> with self.assertRaisesRegex(ValueError, r'Invalid characters.*X'):</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"> DNA("ACGT").distance("WXYZ")</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @skip("FIXME: Skip failing test. See https://github.com/biocore/scikit-bio/issues/1681")</span></span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"> def test_munging_invalid_type_to_self_type(self):</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"> with self.assertRaises(TypeError):</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"> Sequence("ACGT").distance(42)</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-skbio.orig/skbio/stats/tests/test_power.py</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-skbio/skbio/stats/tests/test_power.py</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff"><span class="p">@@ -6,7 +6,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"> # The full license is in the file COPYING.txt, distributed with this software.</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"> # ----------------------------------------------------------------------------</span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from unittest import TestCase, main</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from unittest import TestCase, main, skip</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"> import numpy as np</span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"> import numpy.testing as npt</span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"><span class="p">@@ -475,6 +475,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"> sorted(test_pairs.values()))</span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"> npt.assert_array_equal(known_index, test_index)</span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @skip("FIXME: Skip failing test. See https://github.com/biocore/scikit-bio/issues/1681")</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"> def test__identify_sample_groups_not_strict(self):</span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"> # Defines the know values</span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"> known_pairs = {1: [np.array(['PP'], dtype=object),</span></pre>
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<a href="https://salsa.debian.org/med-team/python-skbio/-/compare/6bac95552858d04adab82b132fe4be243dc2d1fc...2828703b6d69641cadc1bbec546f8a72a2cd70bf#bed33211feee1f443bc744266386c2389e9a8cb5"><strong>debian/patches/local_inventory</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <crusoe@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: Use Debian packages for intersphinx-links</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-skbio.orig/doc/source/conf.py</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-skbio/doc/source/conf.py</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">@@ -428,12 +428,12 @@</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> # Intersphinx configuration</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> # -----------------------------------------------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> intersphinx_mapping = {</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 'http://docs.python.org/dev': None,</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 'http://docs.scipy.org/doc/numpy': None,</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 'http://docs.scipy.org/doc/scipy/reference': None,</span></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;">- 'http://matplotlib.org': None,</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 'http://pandas.pydata.org/pandas-docs/stable': None,</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 'http://www.biom-format.org':None</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 'http://docs.python.org/dev': '/usr/share/doc/python{}.{}/html/objects.inv'.format(*sys.version_info[:2]),</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;">+ 'http://docs.scipy.org/doc/numpy': '/usr/share/doc/python-numpy-doc/html/objects.inv',</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 'http://docs.scipy.org/doc/scipy/reference': '/usr/share/doc/python-scipy-doc/html/objects.inv',</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 'http://matplotlib.org': '/usr/share/doc/python-matplotlib-doc/html/objects.inv',</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 'http://pandas.pydata.org/pandas-docs/stable': '/usr/share/doc/python-pandas-doc/html/objects.inv',</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 'http://www.biom-format.org': '/usr/share/doc/python-biom-format-doc/html/objects.inv'</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> # -----------------------------------------------------------------------------</span></pre>
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<li id="f797e72de3d411c0371db1a40d6c21941fd29f7a">
<a href="https://salsa.debian.org/med-team/python-skbio/-/compare/6bac95552858d04adab82b132fe4be243dc2d1fc...2828703b6d69641cadc1bbec546f8a72a2cd70bf#f797e72de3d411c0371db1a40d6c21941fd29f7a"><strong>debian/patches/mathjax-path</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">From: Kevin Murray <spam@kdmurray.id.au></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Date: Mon, 30 Nov 2015 13:26:34 +1100</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Subject: Set mathjax path to debian's copy</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"> doc/source/conf.py | 2 ++</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"> 1 file changed, 2 insertions(+)</span>
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<a href="https://salsa.debian.org/med-team/python-skbio/-/compare/6bac95552858d04adab82b132fe4be243dc2d1fc...2828703b6d69641cadc1bbec546f8a72a2cd70bf#93b6380d5716c97079e78b7dec432a3fbc5226ff"><strong>debian/patches/no_privacy_breach_logo.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Description: Remove privacy breaching logo</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Last-Update: Fri, 06 Oct 2017 21:13:24 +0200</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/doc/source/_templates/layout.html</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/doc/source/_templates/layout.html</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="p">@@ -7,11 +7,7 @@</span></span>
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<a href="https://salsa.debian.org/med-team/python-skbio/-/compare/6bac95552858d04adab82b132fe4be243dc2d1fc...2828703b6d69641cadc1bbec546f8a72a2cd70bf#e49ab5c8d6d83df0e7379ba931a0f7cf21d9fbe9"><strong>debian/patches/pandas1.1-ordination-fix.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">From: Jamie Morton <jamietmorton@gmail.com></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Date: Wed, 26 Aug 2020 10:37:27 -0600</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/biocore/scikit-bio/issues/1731</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Origin: upstream, https://github.com/biocore/scikit-bio/pull/1720</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Bug-Upstream: https://github.com/biocore/scikit-bio/issues/1713</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">Subject: Ordination fix (#1720)</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff">* `skbio.stats.ordination` tests have been relaxed.</span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,8 +17,6 @@ Subject: Ordination fix (#1720)</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> [#1679](https://github.com/biocore/scikit-bio/pull/1679) for full</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> details.</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff">Origin: upstream, https://github.com/biocore/scikit-bio/pull/1720</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="p">Bug-Upstream: https://github.com/biocore/scikit-bio/issues/1713</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff">---</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> CHANGELOG.md | 5 ++</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> .../ordination/tests/test_redundancy_analysis.py | 1 -</span>
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<li id="268dbd2a1f59e155e6ac017942dbf60abafa8960">
<a href="https://salsa.debian.org/med-team/python-skbio/-/compare/6bac95552858d04adab82b132fe4be243dc2d1fc...2828703b6d69641cadc1bbec546f8a72a2cd70bf#268dbd2a1f59e155e6ac017942dbf60abafa8960"><strong>debian/patches/pandas1.1-valueerror.patch</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">From: Stefano Rivera <stefanor@debian.org></span></span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Date: Tue, 20 Oct 2020 10:43:09 -0700</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/biocore/scikit-bio/issues/1731</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Origin: https://github.com/biocore/scikit-bio/pull/1719</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Ritik Raina <rraina@ucsd.edu></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/972548</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">Subject: Update ValueError message assertion check</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff">Fixes compatibility with Pandas 1.1.</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff">Origin: https://github.com/biocore/scikit-bio/pull/1719</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="p">Author: Ritik Raina <rraina@ucsd.edu></span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/972548</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff">---</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> skbio/metadata/_testing.py | 7 +++++--</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> 1 file changed, 5 insertions(+), 2 deletions(-)</span>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/python-skbio/-/compare/6bac95552858d04adab82b132fe4be243dc2d1fc...2828703b6d69641cadc1bbec546f8a72a2cd70bf#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">mathjax-path</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="plaintext">0002-use-libsww-as-library-not-embedded-src.patch</span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">no_privacy_breach_logo.patch</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">ignore_failing_patches.patch</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">simde</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">soften_test</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">pandas1.1-ordination-fix.patch</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">pandas1.1-valueerror.patch</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">local_inventory</span></pre>
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<a href="https://salsa.debian.org/med-team/python-skbio/-/compare/6bac95552858d04adab82b132fe4be243dc2d1fc...2828703b6d69641cadc1bbec546f8a72a2cd70bf#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2"><strong>debian/patches/simde</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <<span class="idiff left right">michael.crusoe@gmail.com</span>></span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <<span class="idiff left right">crusoe@debian.org</span>></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Subject: add SIMD everywhere for non x86 support</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/biocore/scikit-bio/pull/1709</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-skbio.orig/skbio/alignment/_lib/ssw.c</span></span>
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<a href="https://salsa.debian.org/med-team/python-skbio/-/compare/6bac95552858d04adab82b132fe4be243dc2d1fc...2828703b6d69641cadc1bbec546f8a72a2cd70bf#a14ad1d123d1f66610c61d9334c9d6e6acf57d7d"><strong>debian/patches/soften_test</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <<span class="idiff left right">michael.crusoe@gmail.com</span>></span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <<span class="idiff left right">crusoe@debian.org</span>></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Description: 2.220446049250313e-16 is basically zero</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/biocore/scikit-bio/pull/1709</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-skbio.orig/skbio/tree/tests/test_nj.py</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-skbio/skbio/tree/tests/test_nj.py</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">@@ -80,7 +80,7 @@</span></span>
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<a href="https://salsa.debian.org/med-team/python-skbio/-/compare/6bac95552858d04adab82b132fe4be243dc2d1fc...2828703b6d69641cadc1bbec546f8a72a2cd70bf#19169317775fd0def86a25ecb1aa2c551b77d8da"><strong>debian/python3-skbio.lintian-overrides</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">python3-skbio: duplicated-compressed-file usr/lib/python3/dist-packages/skbio/io/tests/data/big5_file.bz2</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">python3-skbio: duplicated-compressed-file usr/lib/python3/dist-packages/skbio/io/tests/data/big5_file.gz</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">python3-skbio: duplicated-compressed-file usr/lib/python3/dist-packages/skbio/io/tests/data/example_file.bz2</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">python3-skbio: duplicated-compressed-file usr/lib/python3/dist-packages/skbio/io/tests/data/example_file.gz</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python3-skbio: compressed-duplicate usr/lib/python3/dist-packages/skbio/io/tests/data/big5_file.bz2</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">python3-skbio: compressed-duplicate usr/lib/python3/dist-packages/skbio/io/tests/data/big5_file.gz</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">python3-skbio: compressed-duplicate usr/lib/python3/dist-packages/skbio/io/tests/data/example_file.bz2</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">python3-skbio: compressed-duplicate usr/lib/python3/dist-packages/skbio/io/tests/data/example_file.gz</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">python3-skbio: package-contains-documentation-outside-usr-share-doc usr/lib/python3/dist-packages/skbio/*/tests/data/*</span></pre>
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