Update from scikit-bio/scikit-bio@8db9860

Author: qiyunzhu

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

@@ -772,7 +772,7 @@
 <h1>skbio.tree.TreeNode.accumulate_to_ancestor<a class="headerlink" href="#skbio-tree-treenode-accumulate-to-ancestor" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.accumulate_to_ancestor">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">accumulate_to_ancestor</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ancestor</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#L2212"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.accumulate_to_ancestor" 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">accumulate_to_ancestor</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ancestor</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#L2217"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.accumulate_to_ancestor" title="Link to this definition">#</a></dt>
 <dd><p>Return the sum of the distance between self and ancestor.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>

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

@@ -772,7 +772,7 @@
 <h1>skbio.tree.TreeNode.ascii_art<a class="headerlink" href="#skbio-tree-treenode-ascii-art" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.ascii_art">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">ascii_art</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">show_internal</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">compact</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#L2177"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.ascii_art" 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">ascii_art</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">show_internal</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">compact</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#L2182"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.ascii_art" title="Link to this definition">#</a></dt>
 <dd><p>Return a string containing an ascii drawing of the tree.</p>
 <p>Note, this method calls a private recursive function and is not safe
 for large trees.</p>

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

@@ -772,7 +772,7 @@
 <h1>skbio.tree.TreeNode.assign_ids<a class="headerlink" href="#skbio-tree-treenode-assign-ids" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.assign_ids">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">assign_ids</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L2827"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.assign_ids" 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">assign_ids</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L2832"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.assign_ids" title="Link to this definition">#</a></dt>
 <dd><p>Assign topologically stable unique ids to self.</p>
 <p>Following the call, all nodes in the tree will have their id
 attribute set.</p>

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

@@ -772,7 +772,7 @@
 <h1>skbio.tree.TreeNode.assign_supports<a class="headerlink" href="#skbio-tree-treenode-assign-supports" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.assign_supports">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">assign_supports</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3117"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.assign_supports" 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">assign_supports</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/tree/_tree.py#L3122"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.assign_supports" title="Link to this definition">#</a></dt>
 <dd><p>Extract support values from internal node labels of a tree.</p>
 <p class="rubric">Notes</p>
 <p>A “support value” measures the confidence or frequency of the incoming

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

@@ -772,7 +772,7 @@
 <h1>skbio.tree.TreeNode.bifurcate<a class="headerlink" href="#skbio-tree-treenode-bifurcate" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.bifurcate">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">bifurcate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">insert_length</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/tree/_tree.py#L2721"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.bifurcate" 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">bifurcate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">insert_length</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/tree/_tree.py#L2726"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.bifurcate" title="Link to this definition">#</a></dt>
 <dd><p>Reorder the tree into a bifurcating tree.</p>
 <p>All nodes that have more than 2 children will
 have additional intermediate nodes inserted to ensure that

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

@@ -772,7 +772,7 @@
 <h1>skbio.tree.TreeNode.cache_attr<a class="headerlink" href="#skbio-tree-treenode-cache-attr" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.cache_attr">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">cache_attr</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">func</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cache_attrname</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cache_type=&lt;class</span> <span class="pre">'list'&gt;</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#L2907"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.cache_attr" 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">cache_attr</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">func</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cache_attrname</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cache_type=&lt;class</span> <span class="pre">'list'&gt;</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#L2912"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.cache_attr" title="Link to this definition">#</a></dt>
 <dd><p>Cache attributes on internal nodes of the tree.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>

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

@@ -772,7 +772,7 @@
 <h1>skbio.tree.TreeNode.compare_rfd<a class="headerlink" href="#skbio-tree-treenode-compare-rfd" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.compare_rfd">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">compare_rfd</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">proportion</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#L2519"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.compare_rfd" 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">compare_rfd</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">proportion</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#L2524"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.compare_rfd" title="Link to this definition">#</a></dt>
 <dd><p>Calculate the Robinson and Foulds symmetric difference.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>

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

@@ -772,7 +772,7 @@
 <h1>skbio.tree.TreeNode.compare_subsets<a class="headerlink" href="#skbio-tree-treenode-compare-subsets" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.compare_subsets">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">compare_subsets</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_absent_taxa</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#L2590"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.compare_subsets" 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">compare_subsets</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_absent_taxa</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#L2595"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.compare_subsets" title="Link to this definition">#</a></dt>
 <dd><p>Return fraction of overlapping subsets where self and other differ.</p>
 <p>Names present in only one of the two trees will count as mismatches,
 if you don’t want this behavior, strip out the non-matching tips first.</p>

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

@@ -772,7 +772,7 @@
 <h1>skbio.tree.TreeNode.compare_tip_distances<a class="headerlink" href="#skbio-tree-treenode-compare-tip-distances" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.compare_tip_distances">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">compare_tip_distances</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sample=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dist_f=&lt;function</span> <span class="pre">distance_from_r&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">shuffle_f=&lt;built-in</span> <span class="pre">method</span> <span class="pre">shuffle</span> <span class="pre">of</span> <span class="pre">numpy.random.mtrand.RandomState</span> <span class="pre">object&gt;</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#L2640"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.compare_tip_distances" 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">compare_tip_distances</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sample=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dist_f=&lt;function</span> <span class="pre">distance_from_r&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">shuffle_f=&lt;built-in</span> <span class="pre">method</span> <span class="pre">shuffle</span> <span class="pre">of</span> <span class="pre">numpy.random.mtrand.RandomState</span> <span class="pre">object&gt;</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#L2645"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.compare_tip_distances" title="Link to this definition">#</a></dt>
 <dd><p>Compare self to other using tip-to-tip distance matrices.</p>
 <p>Value returned is <cite>dist_f(m1, m2)</cite> for the two matrices. Default is
 to use the Pearson correlation coefficient, with +1 giving a distance

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

@@ -772,7 +772,7 @@
 <h1>skbio.tree.TreeNode.descending_branch_length<a class="headerlink" href="#skbio-tree-treenode-descending-branch-length" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.descending_branch_length">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">descending_branch_length</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tip_subset</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/tree/_tree.py#L2841"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.descending_branch_length" 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">descending_branch_length</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tip_subset</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/tree/_tree.py#L2846"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.descending_branch_length" title="Link to this definition">#</a></dt>
 <dd><p>Find total descending branch length from self or subset of self tips.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>