Update from scikit-bio/scikit-bio@a79322a

Author: qiyunzhu

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

@@ -819,28 +819,28 @@ skbio.tree.TreeNode
    .. autosummary::
       :toctree:
 
-      ~TreeNode.is_tip
-      ~TreeNode.is_root
-      ~TreeNode.has_children
-      ~TreeNode.root
       ~TreeNode.ancestors
-      ~TreeNode.siblings
-      ~TreeNode.neighbors
+      ~TreeNode.has_children
+      ~TreeNode.is_root
+      ~TreeNode.is_tip
       ~TreeNode.lca
+      ~TreeNode.neighbors
       ~TreeNode.path
+      ~TreeNode.root
+      ~TreeNode.siblings
 
    .. rubric:: Tree traversal
 
    .. autosummary::
       :toctree:
 
-      ~TreeNode.traverse
-      ~TreeNode.preorder
+      ~TreeNode.levelorder
+      ~TreeNode.non_tips
       ~TreeNode.postorder
       ~TreeNode.pre_and_postorder
-      ~TreeNode.levelorder
+      ~TreeNode.preorder
       ~TreeNode.tips
-      ~TreeNode.non_tips
+      ~TreeNode.traverse
 
    .. rubric:: Tree copying
 
@@ -857,78 +857,77 @@ skbio.tree.TreeNode
       :toctree:
 
       ~TreeNode.append
+      ~TreeNode.bifurcate
       ~TreeNode.extend
       ~TreeNode.insert
       ~TreeNode.pop
+      ~TreeNode.prune
       ~TreeNode.remove
       ~TreeNode.remove_by_func
       ~TreeNode.remove_deleted
-      ~TreeNode.prune
       ~TreeNode.shear
+      ~TreeNode.shuffle
       ~TreeNode.unpack
       ~TreeNode.unpack_by_func
-      ~TreeNode.bifurcate
-      ~TreeNode.shuffle
 
    .. rubric:: Tree rerooting
 
    .. autosummary::
       :toctree:
 
+      ~TreeNode.root_at
+      ~TreeNode.root_at_midpoint
+      ~TreeNode.root_by_outgroup
       ~TreeNode.unroot
       ~TreeNode.unrooted_copy
       ~TreeNode.unrooted_deepcopy
       ~TreeNode.unrooted_move
-      ~TreeNode.root_at
-      ~TreeNode.root_at_midpoint
-      ~TreeNode.root_by_outgroup
 
    .. rubric:: Tree searching
 
    .. autosummary::
       :toctree:
 
-      ~TreeNode.has_caches
-      ~TreeNode.clear_caches
-      ~TreeNode.cache_attr
       ~TreeNode.assign_ids
-      ~TreeNode.index_tree
+      ~TreeNode.cache_attr
+      ~TreeNode.clear_caches
       ~TreeNode.create_caches
+      ~TreeNode.has_caches
       ~TreeNode.find
       ~TreeNode.find_all
-      ~TreeNode.find_by_id
       ~TreeNode.find_by_func
+      ~TreeNode.find_by_id
+      ~TreeNode.index_tree
 
    .. rubric:: Tree analysis
 
    .. autosummary::
       :toctree:
 
-      ~TreeNode.count
-      ~TreeNode.subset
-      ~TreeNode.subsets
       ~TreeNode.bipart
       ~TreeNode.biparts
-      ~TreeNode.assign_supports
-      ~TreeNode.is_bifurcating
-      ~TreeNode.observed_node_counts
+      ~TreeNode.cophenet
+      ~TreeNode.count
       ~TreeNode.depth
-      ~TreeNode.height
-      ~TreeNode.total_length
       ~TreeNode.distance
+      ~TreeNode.height
+      ~TreeNode.is_bifurcating
       ~TreeNode.maxdist
-      ~TreeNode.cophenet
+      ~TreeNode.observed_node_counts
+      ~TreeNode.subset
+      ~TreeNode.subsets
+      ~TreeNode.total_length
 
    .. rubric:: Tree comparison
 
    .. autosummary::
       :toctree:
 
-      ~TreeNode.compare_rfd
-      ~TreeNode.compare_wrfd
-      ~TreeNode.compare_subsets
       ~TreeNode.compare_biparts
       ~TreeNode.compare_cophenet
+      ~TreeNode.compare_rfd
+      ~TreeNode.compare_subsets
+      ~TreeNode.compare_wrfd
 
    .. rubric:: Tree visualization
 
@@ -942,11 +941,12 @@ skbio.tree.TreeNode
    .. autosummary::
       :toctree:
 
+      ~TreeNode.assign_supports
       ~TreeNode.from_linkage_matrix
-      ~TreeNode.from_taxonomy
-      ~TreeNode.to_taxonomy
       ~TreeNode.from_taxdump
+      ~TreeNode.from_taxonomy
       ~TreeNode.to_array
+      ~TreeNode.to_taxonomy
 
 
 

docs/dev/diversity.html

@@ -780,7 +780,7 @@ <h2>Introduction<a class="headerlink" href="#introduction" title="Link to this h
 Counts vectors are <cite>array_like</cite>: anything that can be converted into a 1-D
 numpy array is acceptable input. For example, you can provide a numpy array or
 a native Python list and the results will be identical.</p>
-<p>The driver functions <a class="reference internal" href="generated/skbio.diversity.alpha_diversity.html#skbio.diversity.alpha_diversity" title="skbio.diversity.alpha_diversity"><code class="xref py py-func docutils literal notranslate"><span class="pre">alpha_diversity()</span></code></a> and <a class="reference internal" href="generated/skbio.diversity.beta_diversity.html#skbio.diversity.beta_diversity" title="skbio.diversity.beta_diversity"><code class="xref py py-func docutils literal notranslate"><span class="pre">beta_diversity()</span></code></a> are
+<p>The driver functions <a class="reference internal" href="generated/skbio.diversity.alpha_diversity.html#skbio.diversity.alpha_diversity" title="skbio.diversity.alpha_diversity"><code class="xref py py-func docutils literal notranslate"><span class="pre">alpha_diversity</span></code></a> and <a class="reference internal" href="generated/skbio.diversity.beta_diversity.html#skbio.diversity.beta_diversity" title="skbio.diversity.beta_diversity"><code class="xref py py-func docutils literal notranslate"><span class="pre">beta_diversity</span></code></a> are
 designed to compute alpha diversity for one or more samples, or beta diversity
 for one or more pairs of samples. The driver functions accept a matrix
 containing vectors of frequencies of taxa within each sample. Each row in the

docs/dev/generated/skbio.alignment.AlignPath.from_bits.html

@@ -776,7 +776,7 @@ <h1>skbio.alignment.AlignPath.from_bits<a class="headerlink" href="#skbio-alignm
   </div>
   <nav class="bd-toc-nav page-toc" aria-labelledby="pst-page-navigation-heading-2">
     <ul class="visible nav section-nav flex-column">
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#skbio.alignment.AlignPath.from_bits"><code class="docutils literal notranslate"><span class="pre">AlignPath.from_bits()</span></code></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#skbio.alignment.AlignPath.from_bits"><code class="docutils literal notranslate"><span class="pre">AlignPath.from_bits</span></code></a></li>
 </ul>
   </nav></div>
 

docs/dev/generated/skbio.alignment.AlignPath.from_coordinates.html

@@ -774,7 +774,7 @@ <h1>skbio.alignment.AlignPath.from_coordinates<a class="headerlink" href="#skbio
   </div>
   <nav class="bd-toc-nav page-toc" aria-labelledby="pst-page-navigation-heading-2">
     <ul class="visible nav section-nav flex-column">
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#skbio.alignment.AlignPath.from_coordinates"><code class="docutils literal notranslate"><span class="pre">AlignPath.from_coordinates()</span></code></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#skbio.alignment.AlignPath.from_coordinates"><code class="docutils literal notranslate"><span class="pre">AlignPath.from_coordinates</span></code></a></li>
 </ul>
   </nav></div>
 

docs/dev/generated/skbio.alignment.AlignPath.from_indices.html

@@ -780,7 +780,7 @@ <h1>skbio.alignment.AlignPath.from_indices<a class="headerlink" href="#skbio-ali
   </div>
   <nav class="bd-toc-nav page-toc" aria-labelledby="pst-page-navigation-heading-2">
     <ul class="visible nav section-nav flex-column">
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#skbio.alignment.AlignPath.from_indices"><code class="docutils literal notranslate"><span class="pre">AlignPath.from_indices()</span></code></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#skbio.alignment.AlignPath.from_indices"><code class="docutils literal notranslate"><span class="pre">AlignPath.from_indices</span></code></a></li>
 </ul>
   </nav></div>
 

docs/dev/generated/skbio.alignment.AlignPath.from_tabular.html

@@ -768,7 +768,7 @@ <h1>skbio.alignment.AlignPath.from_tabular<a class="headerlink" href="#skbio-ali
   </div>
   <nav class="bd-toc-nav page-toc" aria-labelledby="pst-page-navigation-heading-2">
     <ul class="visible nav section-nav flex-column">
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#skbio.alignment.AlignPath.from_tabular"><code class="docutils literal notranslate"><span class="pre">AlignPath.from_tabular()</span></code></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#skbio.alignment.AlignPath.from_tabular"><code class="docutils literal notranslate"><span class="pre">AlignPath.from_tabular</span></code></a></li>
 </ul>
   </nav></div>
 

docs/dev/generated/skbio.alignment.AlignPath.html

@@ -933,7 +933,7 @@ <h1>skbio.alignment.AlignPath<a class="headerlink" href="#skbio-alignment-alignp
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#skbio.alignment.AlignPath.shape"><code class="docutils literal notranslate"><span class="pre">AlignPath.shape</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#skbio.alignment.AlignPath.starts"><code class="docutils literal notranslate"><span class="pre">AlignPath.starts</span></code></a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#skbio.alignment.AlignPath.states"><code class="docutils literal notranslate"><span class="pre">AlignPath.states</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#skbio.alignment.AlignPath.__str__"><code class="docutils literal notranslate"><span class="pre">AlignPath.__str__()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#skbio.alignment.AlignPath.__str__"><code class="docutils literal notranslate"><span class="pre">AlignPath.__str__</span></code></a></li>
 </ul>
 </li>
 </ul>

docs/dev/generated/skbio.alignment.AlignPath.to_bits.html

@@ -769,7 +769,7 @@ <h1>skbio.alignment.AlignPath.to_bits<a class="headerlink" href="#skbio-alignmen
   </div>
   <nav class="bd-toc-nav page-toc" aria-labelledby="pst-page-navigation-heading-2">
     <ul class="visible nav section-nav flex-column">
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#skbio.alignment.AlignPath.to_bits"><code class="docutils literal notranslate"><span class="pre">AlignPath.to_bits()</span></code></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#skbio.alignment.AlignPath.to_bits"><code class="docutils literal notranslate"><span class="pre">AlignPath.to_bits</span></code></a></li>
 </ul>
   </nav></div>
 

docs/dev/generated/skbio.alignment.AlignPath.to_coordinates.html

@@ -765,7 +765,7 @@ <h1>skbio.alignment.AlignPath.to_coordinates<a class="headerlink" href="#skbio-a
   </div>
   <nav class="bd-toc-nav page-toc" aria-labelledby="pst-page-navigation-heading-2">
     <ul class="visible nav section-nav flex-column">
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#skbio.alignment.AlignPath.to_coordinates"><code class="docutils literal notranslate"><span class="pre">AlignPath.to_coordinates()</span></code></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#skbio.alignment.AlignPath.to_coordinates"><code class="docutils literal notranslate"><span class="pre">AlignPath.to_coordinates</span></code></a></li>
 </ul>
   </nav></div>
 

docs/dev/generated/skbio.alignment.AlignPath.to_indices.html

@@ -772,7 +772,7 @@ <h1>skbio.alignment.AlignPath.to_indices<a class="headerlink" href="#skbio-align
   </div>
   <nav class="bd-toc-nav page-toc" aria-labelledby="pst-page-navigation-heading-2">
     <ul class="visible nav section-nav flex-column">
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#skbio.alignment.AlignPath.to_indices"><code class="docutils literal notranslate"><span class="pre">AlignPath.to_indices()</span></code></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#skbio.alignment.AlignPath.to_indices"><code class="docutils literal notranslate"><span class="pre">AlignPath.to_indices</span></code></a></li>
 </ul>
   </nav></div>