Update from scikit-bio/scikit-bio@0855846

Author: qiyunzhu

docs/dev/_sources/generated/skbio.tree.TreeNode.rst.txt

@@ -250,6 +250,8 @@ skbio.tree.TreeNode
 
 
 
+   
+
 
 
 
@@ -699,6 +701,12 @@ skbio.tree.TreeNode
 
 
 
+   
+      
+         
+      
+   
+
 
 
 

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

@@ -770,7 +770,7 @@
 <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#L3212"><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#L3277"><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>Calculate the distance between self and an ancestor.</p>
 <p>The distance is the sum of branch lengths connecting the current node and the
 given ancestral node.</p>

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

@@ -770,7 +770,7 @@
 <h1>skbio.tree.TreeNode.append<a class="headerlink" href="#skbio-tree-treenode-append" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.append">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">append</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">node</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uncache</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</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#L1095"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.append" 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">append</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">node</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uncache</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</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#L1160"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.append" title="Link to this definition">#</a></dt>
 <dd><p>Add a node to self’s children.</p>
 <dl class="field-list">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>

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

@@ -770,7 +770,7 @@
 <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#L4462"><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#L4527"><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

@@ -770,7 +770,7 @@
 <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#L4078"><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#L4143"><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 all nodes of the tree.</p>
 <div class="admonition seealso">
 <p class="admonition-title">See also</p>

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

@@ -770,7 +770,7 @@
 <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#L3075"><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#L3140"><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

@@ -770,7 +770,7 @@
 <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>, <em class="sig-param"><span class="n"><span class="pre">uncache</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</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#L1785"><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>, <em class="sig-param"><span class="n"><span class="pre">uncache</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</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#L1850"><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>Convert the tree into a bifurcating tree.</p>
 <p>All nodes that have more than two children will have additional intermediate
 nodes inserted to ensure that every node has only two children.</p>

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

@@ -770,7 +770,7 @@
 <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>, <em class="sig-param"><span class="n"><span class="pre">register=True</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#L3927"><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>, <em class="sig-param"><span class="n"><span class="pre">register=True</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#L3992"><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 nodes of the tree through a postorder traversal.</p>
 <dl class="field-list">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>

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

@@ -770,7 +770,7 @@
 <h1>skbio.tree.TreeNode.clear_caches<a class="headerlink" href="#skbio-tree-treenode-clear-caches" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.clear_caches">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">clear_caches</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">attr</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">lookup</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</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#L3854"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.clear_caches" 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">clear_caches</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">attr</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">lookup</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</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#L3919"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.clear_caches" title="Link to this definition">#</a></dt>
 <dd><p>Delete node attribute and lookup caches of a tree.</p>
 <div class="versionchanged">
 <p><span class="versionmodified changed">Changed in version 0.6.3: </span>Renamed from <code class="docutils literal notranslate"><span class="pre">invalidate_caches</span></code>. The old name is preserved as an alias.

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

@@ -770,7 +770,7 @@
 <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#L3589"><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#L3654"><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

@@ -770,7 +770,7 @@
 <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#L3660"><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#L3725"><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>