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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>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/python-cogent/commit/e29c6cdbf0f3cb2cf8f6a18a79359fdbb6b76d8a">e29c6cdb</a></strong>
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<span>by Andreas Tille</span>
<i>at 2018-06-05T21:53:43+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix suite fails with latest matplotlib
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#4d4f6ef83af2877362c82311d33e4ca3543d2238">
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+
debian/patches/numpy-doctests.patch
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<li class="file-stats">
<a href="#25d9ba177293e2b5e1f5141ec899346c6ff76ec7">
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+
debian/patches/numpy_xor.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/python-cogent/commit/e29c6cdbf0f3cb2cf8f6a18a79359fdbb6b76d8a#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</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">@@ -7,8 +7,9 @@ python-cogent (1.9-12) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> * debhelper 11</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> * Point Vcs fields to salsa.debian.org</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * Standards-Version: 4.1.4</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Fix suite fails with latest matplotlib</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Wed, 28 Mar 2018 19:03:41</span> +0200</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Tue, 05 Jun 2018 21:47:29</span> +0200</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">python-cogent (1.9-11) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<li id="4d4f6ef83af2877362c82311d33e4ca3543d2238">
<a href="https://salsa.debian.org/med-team/python-cogent/commit/e29c6cdbf0f3cb2cf8f6a18a79359fdbb6b76d8a#4d4f6ef83af2877362c82311d33e4ca3543d2238"><strong>debian/patches/numpy-doctests.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Description: Ensure doctests pass with different numpy versions</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> The numpy output format changed with numpy 1.14 and this causes doctests to</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> fail if raw numerical output is compared. See</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> https://wiki.debian.org/ContinuousIntegration/TriagingTips/numpy-1.14-doctests</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">Author: Stuart Prescott <stuart@debian.org></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">Last-Update: Tue, 05 Jun 2018 15:32:46 +0000 (UTC)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">Origin: https://github.com/pycogent/pycogent/files/2072985/numpy-doctests.patch</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff">Bug-Debian: https://bugs.debian.org/899205</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"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/alltests.py</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/alltests.py</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -6,6 +6,14 @@</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> import doctest, cogent.util.unit_test as unittest, sys, os</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> from cogent.util.misc import app_path</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# Whitespace changes between numpy 1.13 and 1.14 will cause the doctests</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;">+# to fail; when doctests are updated to 1.14 format, this can be removed.</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;">+try: # CRUFT</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;">+ import numpy as np</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;">+ np.set_printoptions(legacy='1.13')</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;">+except TypeError:</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pass</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> __author__ = "Peter Maxwell and Gavin Huttley"</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> __copyright__ = "Copyright 2007-2016, The Cogent Project"</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> __credits__ = ["Peter Maxwell", "Gavin Huttley", "Rob Knight",</span></pre>
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<li id="25d9ba177293e2b5e1f5141ec899346c6ff76ec7">
<a href="https://salsa.debian.org/med-team/python-cogent/commit/e29c6cdbf0f3cb2cf8f6a18a79359fdbb6b76d8a#25d9ba177293e2b5e1f5141ec899346c6ff76ec7"><strong>debian/patches/numpy_xor.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Description: Use xor rather than subtraction on booleans</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> Numpy no longer accepts the ambiguous construction of a-b when a and b are bools.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> Normally, this can be replaced with XORs.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Author: Stuart Prescott <stuart@debian.org></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">Last-Update: Tue, 05 Jun 2018 15:32:46 +0000 (UTC)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">Origin: https://github.com/pycogent/pycogent/files/2072984/numpy_xor.patch</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">Bug-Debian: https://bugs.debian.org/899205</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"><span class="gd" style="color: #000; background-color: #fdd;">--- a/cogent/core/sequence.py</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/cogent/core/sequence.py</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1248,7 +1248,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> gap_indices = map(self.Alphabet.index, self.MolType.Gaps)</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> valid_indices = self._data < len(self.Alphabet)</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> for i in gap_indices:</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;">- valid_indices -= self._data == i</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;">+ valid_indices ^= self._data == i</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> result = compress(valid_indices, self._data)</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> return self.__class__(result, Info=self.Info)</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="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/cogent/maths/distance_transform.py</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;">+++ b/cogent/maths/distance_transform.py</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -670,9 +670,9 @@</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> return zeros((0,0),'d')</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> dists = zeros((numrows,numrows),'d')</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> for i in range(numrows):</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;">- r1 = datamtx[i] # cache here</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;">+ r1 = datamtx[i].astype(dists.dtype) # cache here</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> for j in range(i):</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- dists[i,j] = dists[j,i] = sum(abs(r1 - datamtx[j]))</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ dists[i,j] = dists[j,i] = sum(abs(r1 - datamtx[j].astype(dists.dtype)))</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> return dists</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/python-cogent/commit/e29c6cdbf0f3cb2cf8f6a18a79359fdbb6b76d8a#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,3 +9,5 @@ skip_weak_tests.patch</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">adapt_to_ncbi-data_201609.patch</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">ignore_numpy_test_issue.patch</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">usr_bin_ls.patch</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">numpy_xor.patch</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">numpy-doctests.patch</span></pre>
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