Update from scikit-bio/scikit-bio@685994b

docs/dev/generated/skbio.diversity.beta_diversity.html

@@ -734,7 +734,7 @@ <h1>skbio.diversity.beta_diversity<a class="headerlink" href="#skbio-diversity-b
 <dt><a class="reference internal" href="skbio.diversity.beta.html#module-skbio.diversity.beta" title="skbio.diversity.beta"><code class="xref py py-obj docutils literal notranslate"><span class="pre">skbio.diversity.beta</span></code></a></dt><dd></dd>
 <dt><a class="reference internal" href="skbio.diversity.get_beta_diversity_metrics.html#skbio.diversity.get_beta_diversity_metrics" title="skbio.diversity.get_beta_diversity_metrics"><code class="xref py py-obj docutils literal notranslate"><span class="pre">skbio.diversity.get_beta_diversity_metrics</span></code></a></dt><dd></dd>
 <dt><a class="reference internal" href="skbio.diversity.alpha_diversity.html#skbio.diversity.alpha_diversity" title="skbio.diversity.alpha_diversity"><code class="xref py py-obj docutils literal notranslate"><span class="pre">skbio.diversity.alpha_diversity</span></code></a></dt><dd></dd>
-<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.distance.pdist.html#scipy.spatial.distance.pdist" title="(in SciPy v1.15.0)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.spatial.distance.pdist</span></code></a></dt><dd></dd>
+<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.distance.pdist.html#scipy.spatial.distance.pdist" title="(in SciPy v1.15.1)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.spatial.distance.pdist</span></code></a></dt><dd></dd>
 <dt><a class="reference external" href="https://scikit-learn.org/stable/modules/generated/sklearn.metrics.pairwise_distances.html#sklearn.metrics.pairwise_distances" title="(in scikit-learn v1.6)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">sklearn.metrics.pairwise_distances</span></code></a></dt><dd></dd>
 </dl>
 </div>

docs/dev/generated/skbio.diversity.get_beta_diversity_metrics.html

@@ -693,7 +693,7 @@ <h1>skbio.diversity.get_beta_diversity_metrics<a class="headerlink" href="#skbio
 <dl class="simple">
 <dt><a class="reference internal" href="skbio.diversity.beta_diversity.html#skbio.diversity.beta_diversity" title="skbio.diversity.beta_diversity"><code class="xref py py-obj docutils literal notranslate"><span class="pre">beta_diversity</span></code></a></dt><dd></dd>
 <dt><a class="reference internal" href="skbio.diversity.get_alpha_diversity_metrics.html#skbio.diversity.get_alpha_diversity_metrics" title="skbio.diversity.get_alpha_diversity_metrics"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_alpha_diversity_metrics</span></code></a></dt><dd></dd>
-<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.distance.pdist.html#scipy.spatial.distance.pdist" title="(in SciPy v1.15.0)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.spatial.distance.pdist</span></code></a></dt><dd></dd>
+<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.distance.pdist.html#scipy.spatial.distance.pdist" title="(in SciPy v1.15.1)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.spatial.distance.pdist</span></code></a></dt><dd></dd>
 </dl>
 </div>
 <p class="rubric">Notes</p>

docs/dev/generated/skbio.sequence.distance.hamming.html

@@ -714,7 +714,7 @@ <h1>skbio.sequence.distance.hamming<a class="headerlink" href="#skbio-sequence-d
 <div class="admonition seealso">
 <p class="admonition-title">See also</p>
 <dl class="simple">
-<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.distance.hamming.html#scipy.spatial.distance.hamming" title="(in SciPy v1.15.0)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.spatial.distance.hamming</span></code></a></dt><dd></dd>
+<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.distance.hamming.html#scipy.spatial.distance.hamming" title="(in SciPy v1.15.1)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.spatial.distance.hamming</span></code></a></dt><dd></dd>
 </dl>
 </div>
 <p class="rubric">Notes</p>

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

@@ -788,10 +788,10 @@ <h1>skbio.stats.composition.ancom<a class="headerlink" href="#skbio-stats-compos
 <p class="admonition-title">See also</p>
 <dl class="simple">
 <dt><a class="reference internal" href="skbio.stats.composition.multi_replace.html#skbio.stats.composition.multi_replace" title="skbio.stats.composition.multi_replace"><code class="xref py py-obj docutils literal notranslate"><span class="pre">multi_replace</span></code></a></dt><dd></dd>
-<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.ttest_ind.html#scipy.stats.ttest_ind" title="(in SciPy v1.15.0)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.stats.ttest_ind</span></code></a></dt><dd></dd>
-<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.f_oneway.html#scipy.stats.f_oneway" title="(in SciPy v1.15.0)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.stats.f_oneway</span></code></a></dt><dd></dd>
-<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.wilcoxon.html#scipy.stats.wilcoxon" title="(in SciPy v1.15.0)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.stats.wilcoxon</span></code></a></dt><dd></dd>
-<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.kruskal.html#scipy.stats.kruskal" title="(in SciPy v1.15.0)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.stats.kruskal</span></code></a></dt><dd></dd>
+<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.ttest_ind.html#scipy.stats.ttest_ind" title="(in SciPy v1.15.1)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.stats.ttest_ind</span></code></a></dt><dd></dd>
+<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.f_oneway.html#scipy.stats.f_oneway" title="(in SciPy v1.15.1)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.stats.f_oneway</span></code></a></dt><dd></dd>
+<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.wilcoxon.html#scipy.stats.wilcoxon" title="(in SciPy v1.15.1)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.stats.wilcoxon</span></code></a></dt><dd></dd>
+<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.kruskal.html#scipy.stats.kruskal" title="(in SciPy v1.15.1)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.stats.kruskal</span></code></a></dt><dd></dd>
 </dl>
 </div>
 <p class="rubric">Notes</p>

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

@@ -786,7 +786,7 @@ <h1>skbio.stats.composition.dirmult_ttest<a class="headerlink" href="#skbio-stat
 <div class="admonition seealso">
 <p class="admonition-title">See also</p>
 <dl class="simple">
-<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.ttest_ind.html#scipy.stats.ttest_ind" title="(in SciPy v1.15.0)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.stats.ttest_ind</span></code></a></dt><dd></dd>
+<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.ttest_ind.html#scipy.stats.ttest_ind" title="(in SciPy v1.15.1)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.stats.ttest_ind</span></code></a></dt><dd></dd>
 </dl>
 </div>
 <p class="rubric">Notes</p>

docs/dev/generated/skbio.stats.distance.DissimilarityMatrix.html

@@ -727,7 +727,7 @@ <h1>skbio.stats.distance.DissimilarityMatrix<a class="headerlink" href="#skbio-s
 <p class="admonition-title">See also</p>
 <dl class="simple">
 <dt><a class="reference internal" href="skbio.stats.distance.DistanceMatrix.html#skbio.stats.distance.DistanceMatrix" title="skbio.stats.distance.DistanceMatrix"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DistanceMatrix</span></code></a></dt><dd></dd>
-<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.distance.squareform.html#scipy.spatial.distance.squareform" title="(in SciPy v1.15.0)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.spatial.distance.squareform</span></code></a></dt><dd></dd>
+<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.distance.squareform.html#scipy.spatial.distance.squareform" title="(in SciPy v1.15.1)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.spatial.distance.squareform</span></code></a></dt><dd></dd>
 </dl>
 </div>
 <p class="rubric">Notes</p>

docs/dev/generated/skbio.stats.distance.DistanceMatrix.to_series.html

@@ -718,7 +718,7 @@ <h1>skbio.stats.distance.DistanceMatrix.to_series<a class="headerlink" href="#sk
 <dl class="simple">
 <dt><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_data_frame</span></code></dt><dd></dd>
 <dt><a class="reference internal" href="skbio.stats.distance.DistanceMatrix.condensed_form.html#skbio.stats.distance.DistanceMatrix.condensed_form" title="skbio.stats.distance.DistanceMatrix.condensed_form"><code class="xref py py-obj docutils literal notranslate"><span class="pre">condensed_form</span></code></a></dt><dd></dd>
-<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.distance.squareform.html#scipy.spatial.distance.squareform" title="(in SciPy v1.15.0)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.spatial.distance.squareform</span></code></a></dt><dd></dd>
+<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.distance.squareform.html#scipy.spatial.distance.squareform" title="(in SciPy v1.15.1)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.spatial.distance.squareform</span></code></a></dt><dd></dd>
 </dl>
 </div>
 <p class="rubric">Examples</p>

docs/dev/generated/skbio.stats.distance.bioenv.html

@@ -752,7 +752,7 @@ <h1>skbio.stats.distance.bioenv<a class="headerlink" href="#skbio-stats-distance
 <div class="admonition seealso">
 <p class="admonition-title">See also</p>
 <dl class="simple">
-<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.spearmanr.html#scipy.stats.spearmanr" title="(in SciPy v1.15.0)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.stats.spearmanr</span></code></a></dt><dd></dd>
+<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.spearmanr.html#scipy.stats.spearmanr" title="(in SciPy v1.15.1)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.stats.spearmanr</span></code></a></dt><dd></dd>
 </dl>
 </div>
 <p class="rubric">Notes</p>

docs/dev/generated/skbio.stats.distance.mantel.html

@@ -803,8 +803,8 @@ <h1>skbio.stats.distance.mantel<a class="headerlink" href="#skbio-stats-distance
 <p class="admonition-title">See also</p>
 <dl class="simple">
 <dt><a class="reference internal" href="skbio.stats.distance.DistanceMatrix.html#skbio.stats.distance.DistanceMatrix" title="skbio.stats.distance.DistanceMatrix"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DistanceMatrix</span></code></a></dt><dd></dd>
-<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.pearsonr.html#scipy.stats.pearsonr" title="(in SciPy v1.15.0)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.stats.pearsonr</span></code></a></dt><dd></dd>
-<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.spearmanr.html#scipy.stats.spearmanr" title="(in SciPy v1.15.0)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.stats.spearmanr</span></code></a></dt><dd></dd>
+<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.pearsonr.html#scipy.stats.pearsonr" title="(in SciPy v1.15.1)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.stats.pearsonr</span></code></a></dt><dd></dd>
+<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.spearmanr.html#scipy.stats.spearmanr" title="(in SciPy v1.15.1)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.stats.spearmanr</span></code></a></dt><dd></dd>
 <dt><a class="reference internal" href="skbio.stats.distance.pwmantel.html#skbio.stats.distance.pwmantel" title="skbio.stats.distance.pwmantel"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pwmantel</span></code></a></dt><dd></dd>
 </dl>
 </div>

docs/dev/generated/skbio.stats.evolve.hommola_cospeciation.html

@@ -764,7 +764,7 @@ <h1>skbio.stats.evolve.hommola_cospeciation<a class="headerlink" href="#skbio-st
 <p class="admonition-title">See also</p>
 <dl class="simple">
 <dt><a class="reference internal" href="skbio.stats.distance.mantel.html#skbio.stats.distance.mantel" title="skbio.stats.distance.mantel"><code class="xref py py-obj docutils literal notranslate"><span class="pre">skbio.stats.distance.mantel</span></code></a></dt><dd></dd>
-<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.pearsonr.html#scipy.stats.pearsonr" title="(in SciPy v1.15.0)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.stats.pearsonr</span></code></a></dt><dd></dd>
+<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.pearsonr.html#scipy.stats.pearsonr" title="(in SciPy v1.15.1)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.stats.pearsonr</span></code></a></dt><dd></dd>
 </dl>
 </div>
 <p class="rubric">Notes</p>

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

@@ -750,7 +750,7 @@ <h2>Examples<a class="headerlink" href="#examples" title="Link to this heading">
 </pre></div>
 </div>
 <p>Let’s define a test that will draw a list of sample pairs and determine
-if they’re correlated. We’ll use <a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.pearsonr.html#scipy.stats.pearsonr" title="(in SciPy v1.15.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">scipy.stats.pearsonr()</span></code></a> which takes
+if they’re correlated. We’ll use <a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.pearsonr.html#scipy.stats.pearsonr" title="(in SciPy v1.15.1)"><code class="xref py py-func docutils literal notranslate"><span class="pre">scipy.stats.pearsonr()</span></code></a> which takes
 two arrays and returns a correlation coefficient and a p-value representing
 the probability the two distributions are correlated.</p>
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span><span class="w"> </span><span class="nn">scipy.stats</span><span class="w"> </span><span class="kn">import</span> <span class="n">pearsonr</span>

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

@@ -794,7 +794,7 @@ <h1>skbio.stats.power.subsample_power<a class="headerlink" href="#skbio-stats-po
 </div>
 <p>Let’s set up a test function, so we can test the probability of
 finding a difference in frequency between the two groups. We’ll use
-<a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.chisquare.html#scipy.stats.chisquare" title="(in SciPy v1.15.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">scipy.stats.chisquare()</span></code></a> to look for the difference in frequency
+<a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.chisquare.html#scipy.stats.chisquare" title="(in SciPy v1.15.1)"><code class="xref py py-func docutils literal notranslate"><span class="pre">scipy.stats.chisquare()</span></code></a> to look for the difference in frequency
 between groups.</p>
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span><span class="w"> </span><span class="nn">scipy.stats</span><span class="w"> </span><span class="kn">import</span> <span class="n">chisquare</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">test</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">chisquare</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">x</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span>

docs/dev/generated/skbio.table.Table.rankdata.html

@@ -757,7 +757,7 @@ <h1>skbio.table.Table.rankdata<a class="headerlink" href="#skbio-table-table-ran
 <div class="admonition seealso">
 <p class="admonition-title">See also</p>
 <dl class="simple">
-<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.rankdata.html#scipy.stats.rankdata" title="(in SciPy v1.15.0)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.stats.rankdata</span></code></a></dt><dd></dd>
+<dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.rankdata.html#scipy.stats.rankdata" title="(in SciPy v1.15.1)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.stats.rankdata</span></code></a></dt><dd></dd>
 </dl>
 </div>
 <p class="rubric">Examples</p>

docs/dev/generated/skbio.tree.TreeNode.ancestors.html

@@ -760,7 +760,7 @@
 <h1>skbio.tree.TreeNode.ancestors<a class="headerlink" href="#skbio-tree-treenode-ancestors" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.ancestors">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">ancestors</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">include_self</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L452"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.ancestors" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">ancestors</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">include_self</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L451"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.ancestors" title="Link to this definition">#</a></dt>
 <dd><p>Return all ancestral nodes from self back to the root.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>