Update from scikit-bio/scikit-bio@1a1e65d

Author: qiyunzhu

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

@@ -0,0 +1,8 @@
+:orphan:
+
+skbio.tree.TreeNode.bipart
+==========================
+
+.. currentmodule:: skbio.tree
+
+.. automethod:: TreeNode.bipart

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

@@ -0,0 +1,8 @@
+:orphan:
+
+skbio.tree.TreeNode.biparts
+===========================
+
+.. currentmodule:: skbio.tree
+
+.. automethod:: TreeNode.biparts

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

@@ -0,0 +1,8 @@
+:orphan:
+
+skbio.tree.TreeNode.compare_biparts
+===================================
+
+.. currentmodule:: skbio.tree
+
+.. automethod:: TreeNode.compare_biparts

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

@@ -0,0 +1,8 @@
+:orphan:
+
+skbio.tree.TreeNode.compare_wrfd
+================================
+
+.. currentmodule:: skbio.tree
+
+.. automethod:: TreeNode.compare_wrfd

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

@@ -252,6 +252,14 @@ skbio.tree.TreeNode
 
 
 
+   
+
+   
+
+   
+
+   
+
 
 
 
@@ -707,6 +715,30 @@ skbio.tree.TreeNode
 
 
 
+   
+      
+         
+      
+   
+
+   
+      
+         
+      
+   
+
+   
+      
+         
+      
+   
+
+   
+      
+         
+      
+   
+
 
 
 
@@ -895,6 +927,8 @@ skbio.tree.TreeNode
       ~TreeNode.count
       ~TreeNode.subset
       ~TreeNode.subsets
+      ~TreeNode.bipart
+      ~TreeNode.biparts
       ~TreeNode.assign_supports
       ~TreeNode.is_bifurcating
       ~TreeNode.observed_node_counts
@@ -904,7 +938,9 @@ skbio.tree.TreeNode
       ~TreeNode.get_max_distance
       ~TreeNode.tip_tip_distances
       ~TreeNode.compare_rfd
+      ~TreeNode.compare_wrfd
       ~TreeNode.compare_subsets
+      ~TreeNode.compare_biparts
       ~TreeNode.compare_tip_distances
 
    .. rubric:: Tree visualization

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

@@ -651,6 +651,8 @@
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.count.html">skbio.tree.TreeNode.count</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.subset.html">skbio.tree.TreeNode.subset</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.subsets.html">skbio.tree.TreeNode.subsets</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.bipart.html">skbio.tree.TreeNode.bipart</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.biparts.html">skbio.tree.TreeNode.biparts</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.assign_supports.html">skbio.tree.TreeNode.assign_supports</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.is_bifurcating.html">skbio.tree.TreeNode.is_bifurcating</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.observed_node_counts.html">skbio.tree.TreeNode.observed_node_counts</a></li>
@@ -660,7 +662,9 @@
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.get_max_distance.html">skbio.tree.TreeNode.get_max_distance</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.tip_tip_distances.html">skbio.tree.TreeNode.tip_tip_distances</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.compare_rfd.html">skbio.tree.TreeNode.compare_rfd</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.compare_wrfd.html">skbio.tree.TreeNode.compare_wrfd</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.compare_subsets.html">skbio.tree.TreeNode.compare_subsets</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.compare_biparts.html">skbio.tree.TreeNode.compare_biparts</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.compare_tip_distances.html">skbio.tree.TreeNode.compare_tip_distances</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.ascii_art.html">skbio.tree.TreeNode.ascii_art</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.from_linkage_matrix.html">skbio.tree.TreeNode.from_linkage_matrix</a></li>
@@ -744,7 +748,7 @@
 <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#L3301"><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#L3742"><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.ancestors.html

@@ -651,6 +651,8 @@
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.count.html">skbio.tree.TreeNode.count</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.subset.html">skbio.tree.TreeNode.subset</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.subsets.html">skbio.tree.TreeNode.subsets</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.bipart.html">skbio.tree.TreeNode.bipart</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.biparts.html">skbio.tree.TreeNode.biparts</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.assign_supports.html">skbio.tree.TreeNode.assign_supports</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.is_bifurcating.html">skbio.tree.TreeNode.is_bifurcating</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.observed_node_counts.html">skbio.tree.TreeNode.observed_node_counts</a></li>
@@ -660,7 +662,9 @@
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.get_max_distance.html">skbio.tree.TreeNode.get_max_distance</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.tip_tip_distances.html">skbio.tree.TreeNode.tip_tip_distances</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.compare_rfd.html">skbio.tree.TreeNode.compare_rfd</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.compare_wrfd.html">skbio.tree.TreeNode.compare_wrfd</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.compare_subsets.html">skbio.tree.TreeNode.compare_subsets</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.compare_biparts.html">skbio.tree.TreeNode.compare_biparts</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.compare_tip_distances.html">skbio.tree.TreeNode.compare_tip_distances</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.ascii_art.html">skbio.tree.TreeNode.ascii_art</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.from_linkage_matrix.html">skbio.tree.TreeNode.from_linkage_matrix</a></li>
@@ -744,17 +748,21 @@
 <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#L470"><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#L445"><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">Returns<span class="colon">:</span></dt>
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><dl class="simple">
-<dt>list of TreeNode</dt><dd><p>The path, toward the root, from self.</p>
-</dd>
 <dt><strong>include_self</strong><span class="classifier">bool, optional</span></dt><dd><p>Whether to include the initial node in the path (default: False).</p>
 </dd>
 </dl>
 </dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><dl class="simple">
+<dt>list of TreeNode</dt><dd><p>The path from self toward the root.</p>
+</dd>
+</dl>
+</dd>
 </dl>
 <p class="rubric">Examples</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="nn">skbio</span> <span class="kn">import</span> <span class="n">TreeNode</span>
@@ -767,7 +775,9 @@ <h1>skbio.tree.TreeNode.ancestors<a class="headerlink" href="#skbio-tree-treenod
 <span class="go">         |          /-d</span>
 <span class="go">          \f-------|</span>
 <span class="go">                    \-e</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">tip</span> <span class="o">=</span> <span class="n">tree</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;a&#39;</span><span class="p">)</span>
+</pre></div>
+</div>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">tip</span> <span class="o">=</span> <span class="n">tree</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;a&#39;</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="p">[</span><span class="n">node</span><span class="o">.</span><span class="n">name</span> <span class="k">for</span> <span class="n">node</span> <span class="ow">in</span> <span class="n">tip</span><span class="o">.</span><span class="n">ancestors</span><span class="p">()]</span>
 <span class="go">[&#39;c&#39;, &#39;g&#39;]</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="p">[</span><span class="n">node</span><span class="o">.</span><span class="n">name</span> <span class="k">for</span> <span class="n">node</span> <span class="ow">in</span> <span class="n">tip</span><span class="o">.</span><span class="n">ancestors</span><span class="p">(</span><span class="n">include_self</span><span class="o">=</span><span class="kc">True</span><span class="p">)]</span>

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

@@ -651,6 +651,8 @@
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.count.html">skbio.tree.TreeNode.count</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.subset.html">skbio.tree.TreeNode.subset</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.subsets.html">skbio.tree.TreeNode.subsets</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.bipart.html">skbio.tree.TreeNode.bipart</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.biparts.html">skbio.tree.TreeNode.biparts</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.assign_supports.html">skbio.tree.TreeNode.assign_supports</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.is_bifurcating.html">skbio.tree.TreeNode.is_bifurcating</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.observed_node_counts.html">skbio.tree.TreeNode.observed_node_counts</a></li>
@@ -660,7 +662,9 @@
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.get_max_distance.html">skbio.tree.TreeNode.get_max_distance</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.tip_tip_distances.html">skbio.tree.TreeNode.tip_tip_distances</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.compare_rfd.html">skbio.tree.TreeNode.compare_rfd</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.compare_wrfd.html">skbio.tree.TreeNode.compare_wrfd</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.compare_subsets.html">skbio.tree.TreeNode.compare_subsets</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.compare_biparts.html">skbio.tree.TreeNode.compare_biparts</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.compare_tip_distances.html">skbio.tree.TreeNode.compare_tip_distances</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.ascii_art.html">skbio.tree.TreeNode.ascii_art</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.from_linkage_matrix.html">skbio.tree.TreeNode.from_linkage_matrix</a></li>
@@ -744,7 +748,7 @@
 <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#L1184"><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#L1176"><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>