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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-skbio">Debian Med / python-skbio</a>
</h3>
<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/python-skbio/-/commit/4687f235e3fb4b4e26080179a8d1d76e4d17b4f4">4687f235</a></strong>
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<span>by Andreas Tille</span>
<i>at 2021-10-13T09:16:52+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">For the moment the 4 tests that are broken due to bug #992676 are excluded
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<strong><a href="https://salsa.debian.org/med-team/python-skbio/-/commit/10d0de0619787b1e5c966cc92329f4732daa1b0d">10d0de06</a></strong>
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<span>by Andreas Tille</span>
<i>at 2021-10-13T09:22:41+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
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<h4>3 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="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<a href="#7a6fc6e9c36d95cf4ac329934110581ed0e6104d">
<span class="new-file">
+
debian/patches/skip_tests_failung_due_to_scipy.patch
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/python-skbio/-/compare/38bc9129dd638cf4c819a65321bdd0329d31246d...10d0de0619787b1e5c966cc92329f4732daa1b0d#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">python-skbio (0.5.6-5) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-skbio (0.5.6-5) <span class="idiff left right">unstable</span>; 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> [ Steffen Moeller ]</span>
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Team upload.</span>
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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">@@ -11,8 +11,9 @@ python-skbio (0.5.6-5) UNRELEASED; urgency=medium</td>
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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="LC12" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> * Replace add_javascript() and add_stylesheet() in sphinx config</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> * For the moment the 4 tests that are broken due to bug #992676 are excluded</span>
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<td class="new_line diff-line-num" 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"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> -- <span class="idiff left">Steffen Moe</span>lle<span class="idiff">r</span> <<span class="idiff">moe</span>lle<span class="idiff">r</span>@debian.org> <span class="idiff">Mon, 06 Sep</span> 2021 <span class="idiff">17:2</span>7:<span class="idiff right">4</span>9 +0200</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> -- <span class="idiff left">Andreas Ti</span>lle <<span class="idiff">ti</span>lle@debian.org> <span class="idiff">Wed, 13 Oct</span> 2021 <span class="idiff">09:1</span>7:<span class="idiff right">0</span>9 +0200</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num" 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">python-skbio (0.5.6-4) unstable; urgency=medium</span>
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<td class="new_line diff-line-num" 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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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/python-skbio/-/compare/38bc9129dd638cf4c819a65321bdd0329d31246d...10d0de0619787b1e5c966cc92329f4732daa1b0d#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7" 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">@@ -7,3 +7,4 @@ pandas1.1-ordination-fix.patch</td>
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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>
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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">sphinx_add_javascript.patch</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">skip_tests_failung_due_to_scipy.patch</span></pre>
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<li id="7a6fc6e9c36d95cf4ac329934110581ed0e6104d">
<a href="https://salsa.debian.org/med-team/python-skbio/-/compare/38bc9129dd638cf4c819a65321bdd0329d31246d...10d0de0619787b1e5c966cc92329f4732daa1b0d#7a6fc6e9c36d95cf4ac329934110581ed0e6104d"><strong>debian/patches/skip_tests_failung_due_to_scipy.patch</strong></a>
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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, 13 Oct 2021 08:44:29 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/992676</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Description: For the moment the 4 tests that are broken due to bug #992676 are excluded</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/skbio/stats/distance/tests/test_permdisp.py</span>
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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/skbio/stats/distance/tests/test_permdisp.py</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -110,61 +110,6 @@</span> class testPERMDISP(TestCase):</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> check_index_type=True,</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> check_series_type=True)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </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;">- def test_centroids_eq_groups(self):</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;">- exp = [[1.2886811963240687, 1.890538910062923, 1.490527658097728],</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;">- [2.17349240061718, 2.3192679626679946, 2.028338553903792]]</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;">- exp_stat, _ = f_oneway(*exp)</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- dm = pcoa(self.eq_mat)</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- dm = dm.samples</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></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;">- obs = _compute_groups(dm, 'centroid', self.grouping_eq)</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertAlmostEqual(obs, exp_stat, places=6)</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- obs_relab = _compute_groups(dm, 'centroid', self.grouping_eq_relab)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertAlmostEqual(obs_relab, obs, places=6)</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></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;">- def test_centroids_uneq_groups(self):</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- """</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- the expected result here was calculated by hand</span></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;">- """</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- exp = [[2.5847022428144935, 2.285624595858895,</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 1.7022431146340287],</span></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;">- [1.724817266046108, 1.724817266046108],</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [2.4333280644972795, 2.389000390879655,</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 2.8547180589306036, 3.218568759338847]]</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- exp_stat, _ = f_oneway(*exp)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- dm = pcoa(self.uneq_mat)</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- dm = dm.samples</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- obs = _compute_groups(dm, 'centroid', self.grouping_uneq)</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertAlmostEqual(obs, exp_stat, places=6)</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- obs_relab = _compute_groups(dm, 'centroid', self.grouping_uneq_relab)</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertAlmostEqual(obs, obs_relab, places=6)</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def test_centroids_mixedgroups(self):</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- exp = [[2.5847022428144935, 2.285624595858895,</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 1.7022431146340287],</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [1.724817266046108, 1.724817266046108],</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [2.4333280644972795, 2.389000390879655,</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 2.8547180589306036, 3.218568759338847]]</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- dm = pcoa(self.uneq_mat)</span></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;">- dm = dm.samples</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- exp_stat, _ = f_oneway(*exp)</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- obs_mixed = _compute_groups(dm, 'centroid', self.grouping_un_mixed)</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertAlmostEqual(exp_stat, obs_mixed, places=6)</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def test_centroids_null(self):</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- dm = pcoa(self.null_mat)</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- dm = dm.samples</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- obs_null = _compute_groups(dm, 'centroid', self.grouping_eq)</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- np.isnan(obs_null)</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> def test_centroid_normal(self):</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> exp = pd.Series(index=self.exp_index,</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> data=['PERMDISP', 'F-value', 9, 2, 0.244501519876,</span></pre>
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