Update from scikit-bio/scikit-bio@68371f2

Author: qiyunzhu

docs/dev/generated/skbio.alignment.TabularMSA.html

@@ -772,8 +772,8 @@ <h1>skbio.alignment.TabularMSA<a class="headerlink" href="#skbio-alignment-tabul
 <dt><a class="reference internal" href="skbio.sequence.DNA.html#skbio.sequence.DNA" title="skbio.sequence.DNA"><code class="xref py py-obj docutils literal notranslate"><span class="pre">skbio.sequence.DNA</span></code></a></dt><dd></dd>
 <dt><a class="reference internal" href="skbio.sequence.RNA.html#skbio.sequence.RNA" title="skbio.sequence.RNA"><code class="xref py py-obj docutils literal notranslate"><span class="pre">skbio.sequence.RNA</span></code></a></dt><dd></dd>
 <dt><a class="reference internal" href="skbio.sequence.Protein.html#skbio.sequence.Protein" title="skbio.sequence.Protein"><code class="xref py py-obj docutils literal notranslate"><span class="pre">skbio.sequence.Protein</span></code></a></dt><dd></dd>
-<dt><a class="reference external" href="https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v2.2.2)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code></a></dt><dd></dd>
-<dt><a class="reference external" href="https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.Index.html#pandas.Index" title="(in pandas v2.2.2)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pandas.Index</span></code></a></dt><dd></dd>
+<dt><a class="reference external" href="https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v2.2.3)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code></a></dt><dd></dd>
+<dt><a class="reference external" href="https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.Index.html#pandas.Index" title="(in pandas v2.2.3)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pandas.Index</span></code></a></dt><dd></dd>
 <dt><a class="reference internal" href="skbio.alignment.TabularMSA.reassign_index.html#skbio.alignment.TabularMSA.reassign_index" title="skbio.alignment.TabularMSA.reassign_index"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reassign_index</span></code></a></dt><dd></dd>
 </dl>
 </div>

docs/dev/generated/skbio.alignment.TabularMSA.sort.html

@@ -738,7 +738,7 @@ <h1>skbio.alignment.TabularMSA.sort<a class="headerlink" href="#skbio-alignment-
 <dl class="simple">
 <dt><a class="reference internal" href="skbio.alignment.TabularMSA.html#skbio.alignment.TabularMSA.index" title="skbio.alignment.TabularMSA.index"><code class="xref py py-obj docutils literal notranslate"><span class="pre">index</span></code></a></dt><dd></dd>
 <dt><a class="reference internal" href="skbio.alignment.TabularMSA.reassign_index.html#skbio.alignment.TabularMSA.reassign_index" title="skbio.alignment.TabularMSA.reassign_index"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reassign_index</span></code></a></dt><dd></dd>
-<dt><a class="reference external" href="https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.Series.sort_index.html#pandas.Series.sort_index" title="(in pandas v2.2.2)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pandas.Series.sort_index</span></code></a></dt><dd></dd>
+<dt><a class="reference external" href="https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.Series.sort_index.html#pandas.Series.sort_index" title="(in pandas v2.2.3)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pandas.Series.sort_index</span></code></a></dt><dd></dd>
 </dl>
 </div>
 <p class="rubric">Notes</p>

docs/dev/generated/skbio.diversity.alpha.lladser_ci.html

@@ -740,7 +740,7 @@
 <h1>skbio.diversity.alpha.lladser_ci<a class="headerlink" href="#skbio-diversity-alpha-lladser-ci" title="Link to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="skbio.diversity.alpha.lladser_ci">
-<span class="sig-prename descclassname"><span class="pre">skbio.diversity.alpha.</span></span><span class="sig-name descname"><span class="pre">lladser_ci</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">counts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">r</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alpha</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.95</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">f</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ci_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'ULCL'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/diversity/alpha/_lladser.py#L66"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.diversity.alpha.lladser_ci" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">skbio.diversity.alpha.</span></span><span class="sig-name descname"><span class="pre">lladser_ci</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">counts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">r</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alpha</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.95</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">f</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ci_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'ULCL'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/diversity/alpha/_lladser.py#L67"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.diversity.alpha.lladser_ci" title="Link to this definition">#</a></dt>
 <dd><p>Calculate single CI of the conditional uncovered probability.</p>
 <dl class="field-list">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
@@ -758,7 +758,8 @@ <h1>skbio.diversity.alpha.lladser_ci<a class="headerlink" href="#skbio-diversity
 conservative upper bound. If <code class="docutils literal notranslate"><span class="pre">'U'</span></code>, upper bound only, lower bound
 fixed to 0.0. If <code class="docutils literal notranslate"><span class="pre">'L'</span></code>, lower bound only, upper bound fixed to 1.0.</p>
 </dd>
-<dt><strong>seed</strong><span class="classifier">int or np.random.Generator, optional</span></dt><dd><p>A user-provided random seed or random generator instance.</p>
+<dt><strong>seed</strong><span class="classifier">int, Generator or RandomState, optional</span></dt><dd><p>A user-provided random seed or random generator instance. See
+<code class="xref py py-func docutils literal notranslate"><span class="pre">details</span></code>.</p>
 <div class="versionadded">
 <p><span class="versionmodified added">Added in version 0.6.3.</span></p>
 </div>

docs/dev/generated/skbio.diversity.alpha.lladser_pe.html

@@ -749,7 +749,8 @@ <h1>skbio.diversity.alpha.lladser_pe<a class="headerlink" href="#skbio-diversity
 </dd>
 <dt><strong>r</strong><span class="classifier">int, optional</span></dt><dd><p>Number of new colors that are required for the next prediction.</p>
 </dd>
-<dt><strong>seed</strong><span class="classifier">int or np.random.Generator, optional</span></dt><dd><p>A user-provided random seed or random generator instance.</p>
+<dt><strong>seed</strong><span class="classifier">int, Generator or RandomState, optional</span></dt><dd><p>A user-provided random seed or random generator instance. See
+<code class="xref py py-func docutils literal notranslate"><span class="pre">details</span></code>.</p>
 <div class="versionadded">
 <p><span class="versionmodified added">Added in version 0.6.3.</span></p>
 </div>

docs/dev/generated/skbio.stats.composition.dirmult_lme.html

@@ -772,8 +772,8 @@ <h1>skbio.stats.composition.dirmult_lme<a class="headerlink" href="#skbio-stats-
 <a class="reference external" href="https://www.statsmodels.org/stable/generated/statsmodels.stats.multitest.multipletests.html#statsmodels.stats.multitest.multipletests" title="(in statsmodels 0.14.3 v0.14.3)"><code class="xref py py-func docutils literal notranslate"><span class="pre">multipletests</span></code></a> function.
 Case-insensitive. If None, no correction will be performed.</p>
 </dd>
-<dt><strong>seed</strong><span class="classifier">int or np.random.Generator, optional</span></dt><dd><p>A user-provided random seed or random generator instance for drawing from the
-Dirichlet distribution.</p>
+<dt><strong>seed</strong><span class="classifier">int, Generator or RandomState, optional</span></dt><dd><p>A user-provided random seed or random generator instance for drawing from the
+Dirichlet distribution. See <code class="xref py py-func docutils literal notranslate"><span class="pre">details</span></code>.</p>
 </dd>
 <dt><strong>re_formula</strong><span class="classifier">str, optional</span></dt><dd><p>Random coefficient formula. See <a class="reference external" href="https://www.statsmodels.org/stable/generated/statsmodels.regression.mixed_linear_model.MixedLM.from_formula.html#statsmodels.regression.mixed_linear_model.MixedLM.from_formula" title="(in statsmodels 0.14.3 v0.14.3)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">MixedLM.from_formula</span></code></a>.</p>
 </dd>

docs/dev/generated/skbio.stats.composition.dirmult_ttest.html

@@ -768,8 +768,8 @@ <h1>skbio.stats.composition.dirmult_ttest<a class="headerlink" href="#skbio-stat
 <a class="reference external" href="https://www.statsmodels.org/stable/generated/statsmodels.stats.multitest.multipletests.html#statsmodels.stats.multitest.multipletests" title="(in statsmodels 0.14.3 v0.14.3)"><code class="xref py py-func docutils literal notranslate"><span class="pre">multipletests</span></code></a> function.
 Case-insensitive. If None, no correction will be performed.</p>
 </dd>
-<dt><strong>seed</strong><span class="classifier">int or np.random.Generator, optional</span></dt><dd><p>A user-provided random seed or random generator instance for drawing from the
-Dirichlet distribution.</p>
+<dt><strong>seed</strong><span class="classifier">int, Generator or RandomState, optional</span></dt><dd><p>A user-provided random seed or random generator instance for drawing from the
+Dirichlet distribution. See <code class="xref py py-func docutils literal notranslate"><span class="pre">details</span></code>.</p>
 </dd>
 </dl>
 </dd>

docs/dev/generated/skbio.stats.isubsample.html

@@ -726,7 +726,8 @@ <h1>skbio.stats.isubsample<a class="headerlink" href="#skbio-stats-isubsample" t
 return a hashable value indicating the bin that that entry should be
 placed in.</p>
 </dd>
-<dt><strong>seed</strong><span class="classifier">int or np.random.Generator, optional</span></dt><dd><p>A user-provided random seed or random generator instance.</p>
+<dt><strong>seed</strong><span class="classifier">int, Generator or RandomState, optional</span></dt><dd><p>A user-provided random seed or random generator instance. See
+<code class="xref py py-func docutils literal notranslate"><span class="pre">details</span></code>.</p>
 <div class="versionadded">
 <p><span class="versionmodified added">Added in version 0.6.3.</span></p>
 </div>

docs/dev/generated/skbio.stats.power.confidence_bound.html

@@ -707,7 +707,7 @@
 <h1>skbio.stats.power.confidence_bound<a class="headerlink" href="#skbio-stats-power-confidence-bound" title="Link to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="skbio.stats.power.confidence_bound">
-<span class="sig-prename descclassname"><span class="pre">skbio.stats.power.</span></span><span class="sig-name descname"><span class="pre">confidence_bound</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vec</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alpha</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.05</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">df</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axis</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/stats/power.py#L574"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.power.confidence_bound" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">skbio.stats.power.</span></span><span class="sig-name descname"><span class="pre">confidence_bound</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vec</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alpha</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.05</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">df</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axis</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/stats/power.py#L576"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.power.confidence_bound" title="Link to this definition">#</a></dt>
 <dd><p>Calculate a confidence bound assuming a normal distribution.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>

docs/dev/generated/skbio.stats.power.paired_subsamples.html

@@ -707,7 +707,7 @@
 <h1>skbio.stats.power.paired_subsamples<a class="headerlink" href="#skbio-stats-power-paired-subsamples" title="Link to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="skbio.stats.power.paired_subsamples">
-<span class="sig-prename descclassname"><span class="pre">skbio.stats.power.</span></span><span class="sig-name descname"><span class="pre">paired_subsamples</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">meta</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cat</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">control_cats</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">order</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">strict_match</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/stats/power.py#L626"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.power.paired_subsamples" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">skbio.stats.power.</span></span><span class="sig-name descname"><span class="pre">paired_subsamples</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">meta</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cat</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">control_cats</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">order</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">strict_match</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/stats/power.py#L628"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.power.paired_subsamples" title="Link to this definition">#</a></dt>
 <dd><p>Draw a list of samples varied by <cite>cat</cite> and matched for <cite>control_cats</cite>.</p>
 <p>This function is designed to provide controlled samples, based on a
 metadata category. For example, one could control for age, sex, education
@@ -735,7 +735,8 @@ <h1>skbio.stats.power.paired_subsamples<a class="headerlink" href="#skbio-stats-
 False, missing values (NaN) in the <cite>control_cats</cite> can be considered
 matches.</p>
 </dd>
-<dt><strong>seed</strong><span class="classifier">int or np.random.Generator, optional</span></dt><dd><p>A user-provided random seed or random generator instance.</p>
+<dt><strong>seed</strong><span class="classifier">int, Generator or RandomState, optional</span></dt><dd><p>A user-provided random seed or random generator instance. See
+<code class="xref py py-func docutils literal notranslate"><span class="pre">details</span></code>.</p>
 <div class="versionadded">
 <p><span class="versionmodified added">Added in version 0.6.3.</span></p>
 </div>