Update from scikit-bio/scikit-bio@dfdf30b

Author: mataton

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

@@ -266,6 +266,8 @@ skbio.tree.TreeNode
 
 
 
+   
+
 
 
 
@@ -763,6 +765,12 @@ skbio.tree.TreeNode
 
 
 
+   
+      
+         
+      
+   
+
 
 
 
@@ -957,6 +965,7 @@ skbio.tree.TreeNode
       ~TreeNode.is_bifurcating
       ~TreeNode.observed_node_counts
       ~TreeNode.accumulate_to_ancestor
+      ~TreeNode.total_length
       ~TreeNode.descending_branch_length
       ~TreeNode.distance
       ~TreeNode.maxdist

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

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

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

@@ -73,7 +73,7 @@
     <link rel="icon" href="../_static/favicon.ico"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="skbio.tree.TreeNode.descending_branch_length" href="skbio.tree.TreeNode.descending_branch_length.html" />
+    <link rel="next" title="skbio.tree.TreeNode.total_length" href="skbio.tree.TreeNode.total_length.html" />
     <link rel="prev" title="skbio.tree.TreeNode.observed_node_counts" href="skbio.tree.TreeNode.observed_node_counts.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -657,6 +657,7 @@
 <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>
 <li class="toctree-l2 current active"><a class="current reference internal" href="#">skbio.tree.TreeNode.accumulate_to_ancestor</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.total_length.html">skbio.tree.TreeNode.total_length</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.descending_branch_length.html">skbio.tree.TreeNode.descending_branch_length</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.distance.html">skbio.tree.TreeNode.distance</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.maxdist.html">skbio.tree.TreeNode.maxdist</a></li>
@@ -751,7 +752,7 @@
 <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#L3745"><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#L3762"><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>
@@ -816,11 +817,11 @@ <h1>skbio.tree.TreeNode.accumulate_to_ancestor<a class="headerlink" href="#skbio
       </div>
     </a>
     <a class="right-next"
-       href="skbio.tree.TreeNode.descending_branch_length.html"
+       href="skbio.tree.TreeNode.total_length.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">skbio.tree.TreeNode.descending_branch_length</p>
+        <p class="prev-next-title">skbio.tree.TreeNode.total_length</p>
       </div>
       <i class="fa-solid fa-angle-right"></i>
     </a>

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

@@ -657,6 +657,7 @@
 <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>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.accumulate_to_ancestor.html">skbio.tree.TreeNode.accumulate_to_ancestor</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.total_length.html">skbio.tree.TreeNode.total_length</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.descending_branch_length.html">skbio.tree.TreeNode.descending_branch_length</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.distance.html">skbio.tree.TreeNode.distance</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.maxdist.html">skbio.tree.TreeNode.maxdist</a></li>

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

@@ -657,6 +657,7 @@
 <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>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.accumulate_to_ancestor.html">skbio.tree.TreeNode.accumulate_to_ancestor</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.total_length.html">skbio.tree.TreeNode.total_length</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.descending_branch_length.html">skbio.tree.TreeNode.descending_branch_length</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.distance.html">skbio.tree.TreeNode.distance</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.maxdist.html">skbio.tree.TreeNode.maxdist</a></li>
@@ -751,7 +752,7 @@
 <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#L1178"><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#L1195"><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

@@ -657,6 +657,7 @@
 <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>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.accumulate_to_ancestor.html">skbio.tree.TreeNode.accumulate_to_ancestor</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.total_length.html">skbio.tree.TreeNode.total_length</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.descending_branch_length.html">skbio.tree.TreeNode.descending_branch_length</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.distance.html">skbio.tree.TreeNode.distance</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.maxdist.html">skbio.tree.TreeNode.maxdist</a></li>
@@ -751,7 +752,7 @@
 <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#L5647"><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#L5751"><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

@@ -657,6 +657,7 @@
 <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>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.accumulate_to_ancestor.html">skbio.tree.TreeNode.accumulate_to_ancestor</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.total_length.html">skbio.tree.TreeNode.total_length</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.descending_branch_length.html">skbio.tree.TreeNode.descending_branch_length</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.distance.html">skbio.tree.TreeNode.distance</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.maxdist.html">skbio.tree.TreeNode.maxdist</a></li>
@@ -751,7 +752,7 @@
 <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#L5249"><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#L5353"><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

@@ -657,6 +657,7 @@
 <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>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.accumulate_to_ancestor.html">skbio.tree.TreeNode.accumulate_to_ancestor</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.total_length.html">skbio.tree.TreeNode.total_length</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.descending_branch_length.html">skbio.tree.TreeNode.descending_branch_length</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.distance.html">skbio.tree.TreeNode.distance</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.maxdist.html">skbio.tree.TreeNode.maxdist</a></li>
@@ -751,7 +752,7 @@
 <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#L3608"><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#L3625"><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

@@ -657,6 +657,7 @@
 <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>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.accumulate_to_ancestor.html">skbio.tree.TreeNode.accumulate_to_ancestor</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.total_length.html">skbio.tree.TreeNode.total_length</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.descending_branch_length.html">skbio.tree.TreeNode.descending_branch_length</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.distance.html">skbio.tree.TreeNode.distance</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.maxdist.html">skbio.tree.TreeNode.maxdist</a></li>
@@ -751,7 +752,7 @@
 <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#L1869"><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#L1886"><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>