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<h3>
Graham Inggs pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-skbio">Debian Med / python-skbio</a>
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<h4>
Commits:
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<li>
<strong><a href="https://salsa.debian.org/med-team/python-skbio/-/commit/b2fce2be09077fcd328bf460386c15ee9432c2d0">b2fce2be</a></strong>
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<span>by Graham Inggs</span>
<i>at 2021-12-03T17:22:50+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cherry-pick upstream commit to fix dtypes and warnings
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<strong><a href="https://salsa.debian.org/med-team/python-skbio/-/commit/395bb024ebfd41430418fb892b7d38fa70e91bf4">395bb024</a></strong>
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<span>by Graham Inggs</span>
<i>at 2021-12-03T17:23:56+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop skip_tests_failung_due_to_scipy.patch, no longer needed
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<strong><a href="https://salsa.debian.org/med-team/python-skbio/-/commit/78913d16c1e591dd39f7bbf294861239d205a54c">78913d16</a></strong>
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<span>by Graham Inggs</span>
<i>at 2021-12-03T17:24:55+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Prepare for upload to unstable
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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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<a href="#d9b9a62748b89a1d948017b50196908da9b2c623">
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+
debian/patches/fix-dtype-precision-warnings.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<a href="#7a6fc6e9c36d95cf4ac329934110581ed0e6104d">
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−
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/2616e52a5a2d51b96c29e1bed0d524dea8adeee2...78913d16c1e591dd39f7bbf294861239d205a54c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">python-skbio (0.5.6-6) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-skbio (0.5.6-6) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Remove Tim Booth from Uploaders (Thanks to Tim for all his work)</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" 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="8" 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">@@ -6,8 +8,11 @@ python-skbio (0.5.6-6) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> [ Graham Inggs ]</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * Regenerate the .c files at build time by cython3</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> Closes: #1000864</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * Cherry-pick upstream commit to fix dtypes and warnings</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> Closes: #992676, #999523</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * Drop skip_tests_failung_due_to_scipy.patch, no longer needed</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> -- <span class="idiff left">Andreas Tille <tille</span>@debian.org> <span class="idiff">Tue, 30 Nov</span> 2021 1<span class="idiff">4:0</span>4:1<span class="idiff">6</span> +0<span class="idiff right">1</span>00</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> -- <span class="idiff left">Graham Inggs <ginggs</span>@debian.org> <span class="idiff">Fri, 03 Dec</span> 2021 1<span class="idiff">5:2</span>4:1<span class="idiff">8</span> +0<span class="idiff right">0</span>00</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">python-skbio (0.5.6-5) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<li id="d9b9a62748b89a1d948017b50196908da9b2c623">
<a href="https://salsa.debian.org/med-team/python-skbio/-/compare/2616e52a5a2d51b96c29e1bed0d524dea8adeee2...78913d16c1e591dd39f7bbf294861239d205a54c#d9b9a62748b89a1d948017b50196908da9b2c623"><strong>debian/patches/fix-dtype-precision-warnings.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: fix dtype, precision, warnings, and more</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Origin: upstream, https://github.com/biocore/scikit-bio/commit/357c7fe847187bc540c4914c3ffd607d9432857d</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Evan Bolyen <ebolyen@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2021-10-26</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/doc/source/_templates/autosummary/class.rst</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/doc/source/_templates/autosummary/class.rst</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -16,7 +16,9 @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> '__repr__',</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> '__setattr__',</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> '__sizeof__',</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;">- '__subclasshook__'] and item.startswith('__')) %}</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ '__subclasshook__',</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;">+ '__init_subclass__',</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ '__class_getitem__'] and item.startswith('__')) %}</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> {{ built_in_methods.append(item) or '' }}</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> {% endif %}</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> {% endfor %}</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;">--- a/doc/source/conf.py</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;">+++ b/doc/source/conf.py</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="p">@@ -69,16 +69,13 @@</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> return specials[display_name], '', summary, real_name</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> return display_name, sig, summary, real_name</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </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;">- skip = ['__init_subclass__']</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> items = []</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> for item in super(NewAuto, self).get_items(names):</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if item[0] not in skip:</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;">- temp_item = fix_item(*item)</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;">- # Drop slot_wrappers (see above)</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;">- if temp_item is not None:</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;">- items.append(temp_item)</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;">-</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ temp_item = fix_item(*item)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # Drop slot_wrappers (see above)</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if temp_item is not None:</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ items.append(temp_item)</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> return items</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"> autosummary.Autosummary = NewAuto</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/skbio/alignment/_indexing.py</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/skbio/alignment/_indexing.py</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="p">@@ -7,7 +7,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> # ----------------------------------------------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> from abc import ABCMeta, abstractmethod</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;">-import collections</span></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;">+import collections.abc</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> import numpy as np</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> import pandas as pd</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="p">@@ -160,7 +160,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> complete_key = False</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> partial_key = False</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> duplicated_key = False</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;">- if not isinstance(indexable, collections.Hashable):</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if not isinstance(indexable, collections.abc.Hashable):</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> return False</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> if axis == 0 and self._has_fancy_index():</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> try:</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;">--- a/skbio/alignment/_pairwise.py</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/skbio/alignment/_pairwise.py</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="p">@@ -793,7 +793,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> def _init_matrices_sw(aln1, aln2, gap_open_penalty, gap_extend_penalty):</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> shape = (aln2.shape.position+1, aln1.shape.position+1)</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> score_matrix = np.zeros(shape)</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- traceback_matrix = np.zeros(shape, dtype=np.int)</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ traceback_matrix = np.zeros(shape, dtype=int)</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> traceback_matrix += _traceback_encoding['uninitialized']</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> traceback_matrix[0, :] = _traceback_encoding['alignment-end']</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> traceback_matrix[:, 0] = _traceback_encoding['alignment-end']</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="p">@@ -803,7 +803,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> def _init_matrices_nw(aln1, aln2, gap_open_penalty, gap_extend_penalty):</span>
</pre>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> shape = (aln2.shape.position+1, aln1.shape.position+1)</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> score_matrix = np.zeros(shape)</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- traceback_matrix = np.zeros(shape, dtype=np.int)</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ traceback_matrix = np.zeros(shape, dtype=int)</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> traceback_matrix += _traceback_encoding['uninitialized']</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> traceback_matrix[0, 0] = _traceback_encoding['alignment-end']</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="p">@@ -826,7 +826,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> aln1, aln2, gap_open_penalty, gap_extend_penalty):</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> shape = (aln2.shape.position+1, aln1.shape.position+1)</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> score_matrix = np.zeros(shape)</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- traceback_matrix = np.zeros(shape, dtype=np.int)</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ traceback_matrix = np.zeros(shape, dtype=int)</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> traceback_matrix += _traceback_encoding['uninitialized']</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> traceback_matrix[0, 0] = _traceback_encoding['alignment-end']</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/skbio/alignment/_tabular_msa.py</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/skbio/alignment/_tabular_msa.py</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="p">@@ -781,7 +781,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> if minter is not None and index is not None:</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> raise ValueError(</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> "Cannot use both `minter` and `index` at the same time.")</span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self._seqs = pd.Series([])</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self._seqs = pd.Series([], dtype=object)</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> self.extend(sequences, minter=minter, index=index,</span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> reset_index=minter is None and index is None)</span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="p">@@ -1983,12 +1983,13 @@</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> step=1)</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> if len(self):</span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self._seqs = self._seqs.append(pd.Series(sequences, index=index))</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self._seqs = self._seqs.append(pd.Series(sequences, index=index,</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ dtype=object))</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> # Not using Series.append to avoid turning a RangeIndex supplied</span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> # via `index` parameter into an Int64Index (this happens in pandas</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> # 0.18.0).</span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self._seqs = pd.Series(sequences, index=index)</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self._seqs = pd.Series(sequences, index=index, dtype=object)</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> # When extending a TabularMSA without sequences, the number of</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> # positions in the TabularMSA may change from zero to non-zero. If</span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/skbio/alignment/tests/test_tabular_msa.py</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/skbio/alignment/tests/test_tabular_msa.py</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="p">@@ -6,7 +6,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC121" 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="LC122" class="line" lang="diff"> # ----------------------------------------------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> </span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import collections</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import collections.abc</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"> import copy</span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> import unittest</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> import functools</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="p">@@ -1377,6 +1377,8 @@</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> 'd']},</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> index=[('b', 'x', 0)]))</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> </span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @unittest.skipIf(tuple(map(int, pd.__version__.split('.'))) < (1, 2, 5),</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "Old pandas will return empty frame")</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> def test_multiindex_complicated_axis_empty_selection(self):</span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> a = RNA("UUAG", metadata={0: 0}, positional_metadata={0: [1, 2, 3, 4]})</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> b = RNA("UAAG", metadata={1: 0}, positional_metadata={1: [1, 2, 3, 4]})</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="p">@@ -1386,13 +1388,12 @@</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> positional_metadata={'c': ['a', 'b', 'c', 'd']},</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> index=[('a', 'x', 0), ('a', 'x', 1), ('a', 'y', 2),</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> ('b', 'x', 0)])</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(self.get(msa, (([False, True, False, True],</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 'x', 2), Ellipsis)),</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- TabularMSA([], metadata={'x': 'y'},</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # TODO: Change for #1198</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- positional_metadata=None,</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- index=[]))</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # Pandas will KeyError when the intersection is empty</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # change appears to have happened in:</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # https://github.com/pandas-dev/pandas/pull/42245</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # but this was not bisected to confirm</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ with self.assertRaises(KeyError):</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.get(msa, (([False, True, False, True], 'x', 2), Ellipsis))</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"> </span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> def test_bool_index_scalar_bool_label(self):</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> a = DNA("ACGA", metadata={0: 0}, positional_metadata={0: [1, 2, 3, 4]})</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="p">@@ -3642,7 +3643,7 @@</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"> </span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> class TestHashable(unittest.TestCase):</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> def test_unhashable_type(self):</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertNotIsInstance(TabularMSA([]), collections.Hashable)</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertNotIsInstance(TabularMSA([]), collections.abc.Hashable)</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"> </span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> def test_unhashable_object(self):</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> with self.assertRaisesRegex(TypeError, r'unhashable'):</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/skbio/diversity/_util.py</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/skbio/diversity/_util.py</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="p">@@ -6,7 +6,7 @@</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"> # The full license is in the file COPYING.txt, distributed with this software.</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"> # ----------------------------------------------------------------------------</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"> </span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import collections</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import collections.abc</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"> </span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> import numpy as np</span>
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<td class="new_line diff-line-num new" data-linenumber="177" 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">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> import pandas as pd</span>
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<td class="new_line diff-line-num new" data-linenumber="178" 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">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"><span class="p">@@ -22,7 +22,10 @@</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"> </span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"> """</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"> counts = np.asarray(counts)</span>
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<td class="new_line diff-line-num new" data-linenumber="182" 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">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not np.all(np.isreal(counts)):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="183" 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">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ try:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="184" 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">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if not np.all(np.isreal(counts)):</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ raise Exception</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except Exception:</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> raise ValueError("Counts vector must contain real-valued entries.")</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> if counts.ndim != 1:</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"> raise ValueError("Only 1-D vectors are supported.")</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"><span class="p">@@ -47,7 +50,8 @@</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"> return np.asarray(counts)</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"> else:</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"> </span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if len(counts) == 0 or not isinstance(counts[0], collections.Iterable):</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if len(counts) == 0 or not isinstance(counts[0],</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ collections.abc.Iterable):</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"> counts = [counts]</span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"> counts = np.asarray(counts)</span>
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<td class="new_line diff-line-num new" data-linenumber="199" 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">
199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"> if counts.ndim > 2:</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/skbio/io/format/fasta.py</span></span>
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<td class="new_line diff-line-num new" data-linenumber="201" 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">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/skbio/io/format/fasta.py</span></span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"><span class="p">@@ -778,7 +778,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"> fh.write('>%s\n%s\n' % (header, seq_str))</span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"> if qual is not None:</span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- qual_str = ' '.join(np.asarray(qual_scores, dtype=np.str))</span></span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ qual_str = ' '.join(np.asarray(qual_scores, dtype=str))</span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"> if max_width is not None:</span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"> qual_str = qual_wrapper.fill(qual_str)</span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"> qual.write('>%s\n%s\n' % (header, qual_str))</span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/skbio/io/format/gff3.py</span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/skbio/io/format/gff3.py</span></span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"><span class="p">@@ -214,7 +214,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"> # ----------------------------------------------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"> import re</span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from collections import Iterable</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from collections.abc import Iterable</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"> from skbio.sequence import DNA, Sequence</span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"> from skbio.io import create_format, GFF3FormatError</span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/skbio/io/format/lsmat.py</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/skbio/io/format/lsmat.py</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"><span class="p">@@ -225,7 +225,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"> for id_, vals in zip(ids, obj.data):</span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"> fh.write("%s" % id_)</span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"> fh.write(delimiter)</span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fh.write(delimiter.join(np.asarray(vals, dtype=np.str)))</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fh.write(delimiter.join(np.asarray(vals, dtype=str)))</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"> fh.write('\n')</span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"> </span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"> </span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/skbio/io/format/ordination.py</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/skbio/io/format/ordination.py</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"><span class="p">@@ -411,7 +411,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"> def _format_vector(vector, id_=None):</span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- formatted_vector = '\t'.join(np.asarray(vector, dtype=np.str))</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ formatted_vector = '\t'.join(np.asarray(vector, dtype=str))</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"> if id_ is None:</span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"> return "%s\n" % formatted_vector</span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/skbio/sequence/_grammared_sequence.py</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/skbio/sequence/_grammared_sequence.py</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"><span class="p">@@ -345,7 +345,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"> "Note: Use `lowercase` if your sequence contains lowercase "</span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"> "characters not in the sequence's alphabet."</span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"> % ('s' if len(bad) > 1 else '',</span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [str(b.tostring().decode("ascii")) for b in bad] if</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ [str(b.tobytes().decode("ascii")) for b in bad] if</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"> len(bad) > 1 else bad[0],</span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"> list(self.alphabet)))</span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/skbio/sequence/_sequence.py</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/skbio/sequence/_sequence.py</span></span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"><span class="p">@@ -25,7 +25,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"> class Sequence(MetadataMixin, PositionalMetadataMixin, IntervalMetadataMixin,</span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- collections.Sequence, SkbioObject):</span></span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ collections.abc.Sequence, SkbioObject):</span></span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"> """Store generic sequence data and optional associated metadata.</span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"> ``Sequence`` objects do not enforce an alphabet or grammar and are thus the</span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"><span class="p">@@ -424,7 +424,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"> @property</span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"> def _string(self):</span>
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return self._bytes.tostring()</span></span>
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return self._bytes.tobytes()</span></span>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"> @classonlymethod</span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"> @experimental(as_of="0.4.1")</span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"><span class="p">@@ -1305,7 +1305,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"> index = self._munge_to_index_array(lowercase)</span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"> outbytes = self._bytes.copy()</span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"> outbytes[index] ^= self._ascii_invert_case_bit_offset</span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return str(outbytes.tostring().decode('ascii'))</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return str(outbytes.tobytes().decode('ascii'))</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"> </span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"> @stable(as_of="0.4.0")</span>
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"> def count(self, subsequence, start=None, end=None):</span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"><span class="p">@@ -1812,7 +1812,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"> # Downcast from int64 to uint8 then convert to str. This is safe</span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"> # because we are guaranteed to have indices in the range 0 to 255</span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"> # inclusive.</span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- chars = indices.astype(np.uint8).tostring().decode('ascii')</span></span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ chars = indices.astype(np.uint8).tobytes().decode('ascii')</span></span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"> obs_counts = freqs[indices]</span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"> if relative:</span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"><span class="p">@@ -2102,7 +2102,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"> """</span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"> if isinstance(sliceable, str):</span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"> if sliceable in self.positional_metadata:</span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if self.positional_metadata[sliceable].dtype == np.bool:</span></span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if self.positional_metadata[sliceable].dtype == bool:</span></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"> sliceable = self.positional_metadata[sliceable]</span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"> raise TypeError("Column '%s' in positional metadata does "</span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"><span class="p">@@ -2121,7 +2121,7 @@</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"> if isinstance(s, (bool, np.bool_)):</span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"> bool_mode = True</span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"> elif isinstance(s, (slice, int, np.signedinteger)) or (</span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- hasattr(s, 'dtype') and s.dtype != np.bool):</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ hasattr(s, 'dtype') and s.dtype != bool):</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"> int_mode = True</span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"> else:</span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"> raise TypeError("Invalid type in iterable: %s, must be one"</span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"><span class="p">@@ -2132,7 +2132,7 @@</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"> " int.")</span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"> sliceable = np.r_[sliceable]</span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"> </span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if sliceable.dtype == np.bool:</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if sliceable.dtype == bool:</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"> if sliceable.size != len(self):</span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"> raise ValueError("Boolean array (%d) does not match length of"</span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"> " sequence (%d)."</span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/skbio/sequence/tests/test_sequence.py</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/skbio/sequence/tests/test_sequence.py</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"><span class="p">@@ -11,7 +11,7 @@</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"> import itertools</span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"> import re</span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"> from types import GeneratorType</span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from collections import Hashable</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from collections.abc import Hashable</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"> from unittest import TestCase, main</span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"> import numpy as np</span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/skbio/stats/distance/_base.py</span></span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/skbio/stats/distance/_base.py</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"><span class="p">@@ -547,8 +547,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"> subset = self._data[i_idx, j_indices]</span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"> values.append(subset)</span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- i = pd.Series(i, name='i')</span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- j = pd.Series(j, name='j')</span></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ i = pd.Series(i, name='i', dtype=str)</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ j = pd.Series(j, name='j', dtype=str)</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"> values = pd.Series(np.hstack(values), name='value')</span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"> return pd.concat([i, j, values], axis=1)</span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/skbio/stats/distance/_mantel.py</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/skbio/stats/distance/_mantel.py</span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"><span class="p">@@ -282,7 +282,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"> perm_gen = (corr_func(x.permute(condensed=True), y_flat)[0]</span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"> for _ in range(permutations))</span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- permuted_stats = np.fromiter(perm_gen, np.float, count=permutations)</span></span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ permuted_stats = np.fromiter(perm_gen, float, count=permutations)</span></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"> if alternative == 'two-sided':</span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"> count_better = (np.absolute(permuted_stats) >=</span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/skbio/stats/distance/_permdisp.py</span></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/skbio/stats/distance/_permdisp.py</span></span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"><span class="p">@@ -139,8 +139,8 @@</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"> test statistic name F-value</span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"> sample size 6</span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"> number of groups 2</span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- test statistic 1.03296</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- p-value 0.35</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ test statistic ... 1.03...</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ p-value ...</span></span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"> number of permutations 99</span>
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"> Name: PERMDISP results, dtype: object</span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"> </span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"><span class="p">@@ -155,7 +155,7 @@</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff"> test statistic name F-value</span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"> sample size 6</span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"> number of groups 2</span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- test statistic 1.03296</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ test statistic ... 1.03...</span></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"> p-value NaN</span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"> number of permutations 0</span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"> Name: PERMDISP results, dtype: object</span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"><span class="p">@@ -175,8 +175,8 @@</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"> test statistic name F-value</span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"> sample size 6</span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"> number of groups 2</span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- test statistic 3.67082</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- p-value 0.428571</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ test statistic ... 3.67...</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ p-value ... 0.42...</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff"> number of permutations 6</span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="diff"> Name: PERMDISP results, dtype: object</span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="diff"> </span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"><span class="p">@@ -194,8 +194,8 @@</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="diff"> test statistic name F-value</span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff"> sample size 6</span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"> number of groups 2</span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- test statistic 3.67082</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- p-value 0.428571</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ test statistic ... 3.67...</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ p-value ... 0.42...</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff"> number of permutations 6</span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="diff"> Name: PERMDISP results, dtype: object</span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="diff"> </span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="diff"><span class="p">@@ -248,7 +248,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="diff"> centroids = samples.groupby('grouping').apply(_config_med)</span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="diff"> </span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="diff"> for label, df in samples.groupby('grouping'):</span>
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- groups.append(cdist(df.values[:, :-1], [centroids.loc[label].values],</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ groups.append(cdist(df.values[:, :-1].astype('float64'),</span></span>
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ [centroids.loc[label].values],</span></span>
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"> metric='euclidean'))</span>
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="diff"> stat, _ = f_oneway(*groups)</span>
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/skbio/stats/distance/tests/test_base.py</span></span>
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/skbio/stats/distance/tests/test_base.py</span></span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="diff"><span class="p">@@ -935,7 +935,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"> def test_to_series_1x1(self):</span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff"> series = self.dm_1x1.to_series()</span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- exp = pd.Series([], index=[])</span></span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ exp = pd.Series([], index=[], dtype='float64')</span></span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff"> assert_series_almost_equal(series, exp)</span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="diff"> def test_to_series_2x2(self):</span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/skbio/stats/distance/tests/test_bioenv.py</span></span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/skbio/stats/distance/tests/test_bioenv.py</span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="diff"><span class="p">@@ -146,7 +146,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="diff"> # same distances yields *very* similar results. Thus, the discrepancy</span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="diff"> # seems to stem from differences when computing ranks/ties.</span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff"> obs = bioenv(self.dm_vegan, self.df_vegan)</span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- assert_data_frame_almost_equal(obs, self.exp_results_vegan)</span></span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ assert_data_frame_almost_equal(obs, self.exp_results_vegan, rtol=1e-3)</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="diff"> def test_bioenv_no_distance_matrix(self):</span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="diff"> with self.assertRaises(TypeError):</span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/skbio/stats/distance/tests/test_permanova.py</span></span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/skbio/stats/distance/tests/test_permanova.py</span></span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="diff"><span class="p">@@ -12,7 +12,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="diff"> import numpy as np</span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="diff"> import pandas as pd</span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from pandas.util.testing import assert_series_equal</span></span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from pandas.testing import assert_series_equal</span></span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="diff"> from skbio import DistanceMatrix</span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="diff"> from skbio.stats.distance import permanova</span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/skbio/stats/distance/tests/test_permdisp.py</span></span>
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<pre style="margin: 0;">+<span id="LC443" 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="LC444" class="line" lang="diff"><span class="p">@@ -12,7 +12,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="diff"> import numpy as np</span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="diff"> import numpy.testing as npt</span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="diff"> import pandas as pd</span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from pandas.util.testing import assert_series_equal</span></span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from pandas.testing import assert_series_equal</span></span>
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450
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="diff"> from scipy.stats import f_oneway</span>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="diff"> import hdmedians as hd</span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/skbio/stats/gradient.py</span></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/skbio/stats/gradient.py</span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="diff"><span class="p">@@ -168,7 +168,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="diff"> np.abs((w_vector[i] - w_vector[i-1]))</span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="diff"> )</span>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return trajectories</span></span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return trajectories.astype('float64')</span></span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="diff"> def _ANOVA_trajectories(category, res_by_group):</span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/skbio/stats/ordination/_utils.py</span></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/skbio/stats/ordination/_utils.py</span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="diff"><span class="p">@@ -237,7 +237,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="diff"> distance_matrix : 2D array_like</span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="diff"> Distance matrix.</span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- distance_matrix = distance_matrix.astype(np.float)</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ distance_matrix = distance_matrix.astype(float)</span></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="diff"> for i in np.arange(len(distance_matrix)):</span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="diff"> distance_matrix[i] = (distance_matrix[i] * distance_matrix[i]) / -2</span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="diff"><span class="p">@@ -259,7 +259,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="diff"> e_matrix : 2D array_like</span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="diff"> A matrix representing the "E matrix" as described above.</span>
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- e_matrix = e_matrix.astype(np.float)</span></span>
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ e_matrix = e_matrix.astype(float)</span></span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="diff"> row_means = np.zeros(len(e_matrix), dtype=float)</span>
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="diff"> col_means = np.zeros(len(e_matrix), dtype=float)</span>
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/skbio/stats/ordination/tests/test_principal_coordinate_analysis.py</span></span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/skbio/stats/ordination/tests/test_principal_coordinate_analysis.py</span></span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="diff"><span class="p">@@ -15,7 +15,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="diff"> from skbio import DistanceMatrix, OrdinationResults</span>
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="diff"> from skbio.stats.distance import DissimilarityMatrixError</span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="diff"> from skbio.stats.ordination import pcoa, pcoa_biplot</span>
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from skbio.util import get_data_path, assert_ordination_results_equal</span></span>
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from skbio.util import (get_data_path, assert_ordination_results_equal,</span></span>
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ assert_data_frame_almost_equal)</span></span>
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="diff"> class TestPCoA(TestCase):</span>
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="diff"><span class="p">@@ -262,7 +263,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="diff"> full = pcoa_biplot(self.ordination, self.descriptors).features</span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="diff"> # the biplot should be identical regardless of the number of axes used</span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- pd.util.testing.assert_almost_equal(subset, full.iloc[:, :2])</span></span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ assert_data_frame_almost_equal(subset, full.iloc[:, :2])</span></span>
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="diff"> def test_mismatching_samples(self):</span>
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="diff"> new_index = self.descriptors.index.tolist()</span>
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/skbio/stats/tests/test_composition.py</span></span>
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/skbio/stats/tests/test_composition.py</span></span>
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="diff"><span class="p">@@ -10,7 +10,7 @@</span></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="diff"> from unittest import TestCase, main</span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="diff"> import numpy as np</span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="diff"> import numpy.testing as npt</span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import pandas.util.testing as pdt</span></span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import pandas.testing as pdt</span></span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="diff"> from numpy.random import normal</span>
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="diff"> import pandas as pd</span>
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="diff"> import scipy</span>
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="diff"><span class="p">@@ -256,7 +256,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="diff"> def test_clr_inv(self):</span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="diff"> npt.assert_allclose(clr_inv(self.rdata1), self.ortho1)</span>
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- npt.assert_allclose(clr(clr_inv(self.rdata1)), self.rdata1)</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ npt.assert_allclose(clr(clr_inv(self.rdata1)), self.rdata1,</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rtol=1e-4, atol=1e-5)</span></span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="diff"> </span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="diff"> # make sure that inplace modification is not occurring</span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="diff"> clr_inv(self.rdata1)</span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="diff"><span class="p">@@ -521,7 +522,7 @@</span></span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="diff"> normal(10, 1, L),</span>
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="diff"> normal(10, 1, L)))</span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="diff"> self.table2 = np.absolute(self.table2)</span>
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.table2 = pd.DataFrame(self.table2.astype(np.int).T)</span></span>
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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.table2 = pd.DataFrame(self.table2.astype(int).T)</span></span>
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="diff"> self.cats2 = pd.Series([0]*D + [1]*D)</span>
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="diff"> # Real valued data with 2 groupings and no significant difference</span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="diff"><span class="p">@@ -554,7 +555,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="diff"> normal(10, 1, L),</span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="diff"> normal(10, 1, L)))</span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="diff"> self.table4 = np.absolute(self.table4)</span>
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.table4 = pd.DataFrame(self.table4.astype(np.int).T)</span></span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.table4 = pd.DataFrame(self.table4.astype(int).T)</span></span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="diff"> self.cats4 = pd.Series([0]*D + [1]*D + [2]*D)</span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="diff"> </span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="diff"> # Noncontiguous case</span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="diff"><span class="p">@@ -635,7 +636,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="diff"> normal(10, 10, L),</span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="diff"> normal(10, 10, L)))</span>
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="diff"> self.table9 = np.absolute(self.table9)+1</span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.table9 = pd.DataFrame(self.table9.astype(np.int).T)</span></span>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.table9 = pd.DataFrame(self.table9.astype(int).T)</span></span>
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="diff"> self.cats9 = pd.Series([0]*D + [1]*D + [2]*D)</span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="diff"> </span>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="diff"> # Real valued data with 2 groupings</span>
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="diff"><span class="p">@@ -669,7 +670,7 @@</span></span>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="diff"> normal(10, 10, L),</span>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="diff"> normal(10, 10, L)))</span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="diff"> self.table10 = np.absolute(self.table10) + 1</span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.table10 = pd.DataFrame(self.table10.astype(np.int).T)</span></span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.table10 = pd.DataFrame(self.table10.astype(int).T)</span></span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="diff"> self.cats10 = pd.Series([0]*D + [1]*D)</span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="diff"> </span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="diff"> # zero count</span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/skbio/stats/tests/test_gradient.py</span></span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/skbio/stats/tests/test_gradient.py</span></span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="diff"><span class="p">@@ -13,7 +13,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="diff"> import numpy as np</span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="diff"> import pandas as pd</span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="diff"> import numpy.testing as npt</span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import pandas.util.testing as pdt</span></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import pandas.testing as pdt</span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="diff"> </span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="diff"> from skbio.util import get_data_path, assert_data_frame_almost_equal</span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="diff"> from skbio.stats.gradient import (GradientANOVA, AverageGradientANOVA,</span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="diff"><span class="p">@@ -237,7 +237,7 @@</span></span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="diff"> 's6': np.array([2.1795918367]),</span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="diff"> 's7': np.array([17.8]),</span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="diff"> 's8': np.array([20.3428571428])},</span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- orient='index')</span></span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ orient='index').astype(np.float64)</span></span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="diff"> obs = _weight_by_vector(trajectory, w_vector)</span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="diff"> assert_data_frame_almost_equal(obs.sort_index(), exp.sort_index())</span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="diff"> </span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="diff"><span class="p">@@ -254,16 +254,16 @@</span></span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="diff"> w_vector = pd.Series(np.array([1, 2, 3, 4, 5, 6, 7, 8]),</span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="diff"> ['s1', 's2', 's3', 's4',</span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="diff"> 's5', 's6', 's7', 's8']).astype(np.float64)</span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- exp = pd.DataFrame.from_dict({'s1': np.array([1.0]),</span></span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 's2': np.array([2.0]),</span></span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 's3': np.array([3.0]),</span></span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 's4': np.array([4.0]),</span></span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 's5': np.array([5.0]),</span></span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 's6': np.array([6.0]),</span></span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 's7': np.array([7.0]),</span></span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 's8': np.array([8.0])</span></span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ exp = pd.DataFrame.from_dict({'s1': np.array([1]),</span></span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 's2': np.array([2]),</span></span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 's3': np.array([3]),</span></span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 's4': np.array([4]),</span></span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 's5': np.array([5]),</span></span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 's6': np.array([6]),</span></span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 's7': np.array([7]),</span></span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 's8': np.array([8])</span></span>
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="diff"> },</span>
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- orient='index')</span></span>
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ orient='index').astype(np.float64)</span></span>
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="diff"> obs = _weight_by_vector(trajectory, w_vector)</span>
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="diff"> assert_data_frame_almost_equal(obs.sort_index(), exp.sort_index())</span>
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="diff"><span class="p">@@ -276,11 +276,12 @@</span></span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="diff"> trajectory.sort_values(by=0, inplace=True)</span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="diff"> w_vector = pd.Series(np.array([25, 30, 35, 40, 45]),</span>
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611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="diff"> ['s2', 's3', 's4', 's5', 's6']).astype(np.float64)</span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- exp = pd.DataFrame.from_dict({'s2': np.array([2.0]),</span></span>
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613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 's3': np.array([3.0]),</span></span>
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 's4': np.array([4.0]),</span></span>
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 's5': np.array([5.0]),</span></span>
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 's6': np.array([6.0])}, orient='index')</span></span>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ exp = pd.DataFrame.from_dict({'s2': np.array([2]),</span></span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 's3': np.array([3]),</span></span>
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619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 's4': np.array([4]),</span></span>
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 's5': np.array([5]),</span></span>
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 's6': np.array([6])},</span></span>
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622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ orient='index').astype(np.float64)</span></span>
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="diff"> obs = _weight_by_vector(trajectory, w_vector)</span>
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="diff"> assert_data_frame_almost_equal(obs.sort_index(), exp.sort_index())</span>
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/skbio/tree/_tree.py</span></span>
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/skbio/tree/_tree.py</span></span>
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="diff"><span class="p">@@ -2186,7 +2186,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="diff"> (lo, hi, end) = (mids[0], mids[-1], len(result))</span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="diff"> prefixes = [PAD] * (lo + 1) + [PA + '|'] * \</span>
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="diff"> (hi - lo - 1) + [PAD] * (end - hi)</span>
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- mid = np.int(np.trunc((lo + hi) / 2))</span></span>
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mid = int(np.trunc((lo + hi) / 2))</span></span>
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="diff"> prefixes[mid] = char1 + '-' * (LEN - 2) + prefixes[mid][-1]</span>
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="diff"> result = [p + l for (p, l) in zip(prefixes, result)]</span>
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="diff"> if show_internal:</span>
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/skbio/tree/tests/test_nj.py</span></span>
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/skbio/tree/tests/test_nj.py</span></span>
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="diff"><span class="p">@@ -80,8 +80,9 @@</span></span>
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="diff"> self.expected1_str)</span>
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="diff"> # what is the correct way to compare TreeNode objects for equality?</span>
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="diff"> actual_TreeNode = nj(self.dm1)</span>
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # precision error on ARM: 1.6653345369377348e-16 != 0.0</span></span>
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="diff"> self.assertAlmostEqual(actual_TreeNode.compare_tip_distances(</span>
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.expected1_TreeNode), 0.0)</span></span>
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.expected1_TreeNode), 0.0, places=10)</span></span>
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="diff"> def test_nj_dm2(self):</span>
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="diff"> actual_TreeNode = nj(self.dm2)</span>
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/skbio/util/_exception.py</span></span>
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/skbio/util/_exception.py</span></span>
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="diff"><span class="p">@@ -9,7 +9,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="diff"> class TestingUtilError(Exception):</span>
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="diff"> """Raised when an exception is needed to test exception handling."""</span>
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- pass</span></span>
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ __test__ = False # prevent py-test from collecting it</span></span>
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="diff"> class OverrideError(AssertionError):</span>
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/skbio/util/_testing.py</span></span>
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/skbio/util/_testing.py</span></span>
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="diff"><span class="p">@@ -12,7 +12,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="diff"> import numpy as np</span>
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="diff"> import numpy.testing as npt</span>
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import pandas.util.testing as pdt</span></span>
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import pandas.testing as pdt</span></span>
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="diff"> from scipy.spatial.distance import pdist</span>
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="diff"> from ._decorator import experimental</span>
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="diff"><span class="p">@@ -265,7 +265,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="diff"> @experimental(as_of="0.4.0")</span>
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-def assert_data_frame_almost_equal(left, right):</span></span>
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+def assert_data_frame_almost_equal(left, right, rtol=1e-5):</span></span>
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="diff"> """Raise AssertionError if ``pd.DataFrame`` objects are not "almost equal".</span>
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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="diff"> </span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="diff"> Wrapper of ``pd.util.testing.assert_frame_equal``. Floating point values</span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="diff"><span class="p">@@ -306,10 +306,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="diff"> check_index_type=True,</span>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="diff"> check_column_type=True,</span>
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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="diff"> check_frame_type=True,</span>
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685
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- check_less_precise=False,</span></span>
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686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="diff"> check_names=True,</span>
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687
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="diff"> by_blocks=False,</span>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- check_exact=False)</span></span>
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ check_exact=False,</span></span>
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rtol=rtol)</span></span>
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="diff"> # this check ensures that empty DataFrames with different indices do not</span>
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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="diff"> # compare equal. exact=True specifies that the type of the indices must be</span>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="diff"> # exactly the same</span>
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="diff"><span class="p">@@ -323,7 +323,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="diff"> check_dtype=True,</span>
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="diff"> check_index_type=True,</span>
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="diff"> check_series_type=True,</span>
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- check_less_precise=False,</span></span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="diff"> check_names=True,</span>
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="diff"> check_exact=False,</span>
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701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="diff"> check_datetimelike_compat=False,</span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/skbio/util/tests/test_testing.py</span></span>
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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/skbio/util/tests/test_testing.py</span></span>
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="diff"><span class="p">@@ -228,7 +228,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="diff"> def setUp(self):</span>
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="diff"> self.series = [</span>
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- pd.Series(),</span></span>
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pd.Series(dtype='float64'),</span></span>
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pd.Series(dtype=object),</span></span>
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="diff"> pd.Series(dtype='int64'),</span>
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712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="diff"> pd.Series([1, 2, 3]),</span>
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713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="diff"> pd.Series([3, 2, 1]),</span>
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/skbio/workflow.py</span></span>
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/skbio/workflow.py</span></span>
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="diff"><span class="p">@@ -204,7 +204,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="diff"> from copy import deepcopy</span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="diff"> from time import time</span>
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719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="diff"> from functools import update_wrapper</span>
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720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from collections import Iterable</span></span>
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721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from collections.abc import Iterable</span></span>
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722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="diff"> from types import MethodType</span>
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723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="diff"> </span>
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724
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="diff"> from skbio.util._decorator import experimental</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/python-skbio/-/compare/2616e52a5a2d51b96c29e1bed0d524dea8adeee2...78913d16c1e591dd39f7bbf294861239d205a54c#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">@@ -7,4 +7,4 @@ pandas1.1-ordination-fix.patch</td>
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7
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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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<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"><span class="idiff left right">skip_tests_failung_due_to_scipy</span>.patch</span></pre>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"><span class="idiff left right">fix-dtype-precision-warnings</span>.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/python-skbio/-/compare/2616e52a5a2d51b96c29e1bed0d524dea8adeee2...78913d16c1e591dd39f7bbf294861239d205a54c#7a6fc6e9c36d95cf4ac329934110581ed0e6104d"><strong>debian/patches/skip_tests_failung_due_to_scipy.patch</strong>
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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="LC5" class="line" lang="diff"></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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<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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<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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<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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<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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<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="LC63" 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="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="LC66" 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="LC67" class="line" lang="diff"> def test_centroid_normal(self):</span>
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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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<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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