Update from scikit-bio/scikit-bio@d160747

Author: qiyunzhu

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

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

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

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

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

@@ -218,6 +218,18 @@ skbio.tree.TreeNode
 
 
 
+
+   
+
+   
+
+   
+
+   
+
+   
+
+   
 
 
 
@@ -358,6 +370,9 @@ skbio.tree.TreeNode
       ~TreeNode.index_tree
 
 
+      ~TreeNode.insert
+      
+      
       ~TreeNode.invalidate_caches
 
 
@@ -418,6 +433,9 @@ skbio.tree.TreeNode
       ~TreeNode.root_at_midpoint
 
 
+      ~TreeNode.root_by_outgroup
+      
+      
       ~TreeNode.shear
 
 
@@ -457,12 +475,18 @@ skbio.tree.TreeNode
       ~TreeNode.unpack_by_func
 
 
+      ~TreeNode.unroot
+      
+      
       ~TreeNode.unrooted_copy
 
 
       ~TreeNode.unrooted_deepcopy
 
 
+      ~TreeNode.unrooted_move
+      
+      
       ~TreeNode.write
 
 

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

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

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

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

docs/dev/generated/skbio.diversity.alpha.renyi.html

@@ -771,8 +771,8 @@ <h1>skbio.diversity.alpha.renyi<a class="headerlink" href="#skbio-diversity-alph
 <dl class="simple">
 <dt><a class="reference internal" href="skbio.diversity.alpha.hill.html#skbio.diversity.alpha.hill" title="skbio.diversity.alpha.hill"><code class="xref py py-obj docutils literal notranslate"><span class="pre">hill</span></code></a></dt><dd></dd>
 <dt><a class="reference internal" href="skbio.diversity.alpha.inv_simpson.html#skbio.diversity.alpha.inv_simpson" title="skbio.diversity.alpha.inv_simpson"><code class="xref py py-obj docutils literal notranslate"><span class="pre">inv_simpson</span></code></a></dt><dd></dd>
-<dt><a class="reference internal" href="#skbio.diversity.alpha.renyi" title="skbio.diversity.alpha.renyi"><code class="xref py py-obj docutils literal notranslate"><span class="pre">renyi</span></code></a></dt><dd></dd>
 <dt><a class="reference internal" href="skbio.diversity.alpha.shannon.html#skbio.diversity.alpha.shannon" title="skbio.diversity.alpha.shannon"><code class="xref py py-obj docutils literal notranslate"><span class="pre">shannon</span></code></a></dt><dd></dd>
+<dt><a class="reference internal" href="skbio.diversity.alpha.tsallis.html#skbio.diversity.alpha.tsallis" title="skbio.diversity.alpha.tsallis"><code class="xref py py-obj docutils literal notranslate"><span class="pre">tsallis</span></code></a></dt><dd></dd>
 </dl>
 </div>
 <p class="rubric">Notes</p>

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

@@ -663,6 +663,7 @@
 <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.has_children.html">skbio.tree.TreeNode.has_children</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.index_tree.html">skbio.tree.TreeNode.index_tree</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.insert.html">skbio.tree.TreeNode.insert</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.invalidate_caches.html">skbio.tree.TreeNode.invalidate_caches</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.is_root.html">skbio.tree.TreeNode.is_root</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.is_tip.html">skbio.tree.TreeNode.is_tip</a></li>
@@ -683,6 +684,7 @@
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.root.html">skbio.tree.TreeNode.root</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.root_at.html">skbio.tree.TreeNode.root_at</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.root_at_midpoint.html">skbio.tree.TreeNode.root_at_midpoint</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.root_by_outgroup.html">skbio.tree.TreeNode.root_by_outgroup</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.shear.html">skbio.tree.TreeNode.shear</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.shuffle.html">skbio.tree.TreeNode.shuffle</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.siblings.html">skbio.tree.TreeNode.siblings</a></li>
@@ -696,8 +698,10 @@
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.traverse.html">skbio.tree.TreeNode.traverse</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.unpack.html">skbio.tree.TreeNode.unpack</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.unpack_by_func.html">skbio.tree.TreeNode.unpack_by_func</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.unroot.html">skbio.tree.TreeNode.unroot</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.unrooted_copy.html">skbio.tree.TreeNode.unrooted_copy</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.unrooted_deepcopy.html">skbio.tree.TreeNode.unrooted_deepcopy</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.unrooted_move.html">skbio.tree.TreeNode.unrooted_move</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.write.html">skbio.tree.TreeNode.write</a></li>
 </ul>
 </details></li>
@@ -771,36 +775,8 @@
 <h1>skbio.tree.TreeNode.__copy__<a class="headerlink" href="#skbio-tree-treenode-copy" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.__copy__">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">__copy__</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#L471"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.__copy__" title="Link to this definition">#</a></dt>
-<dd><p>Return a copy of self using an iterative approach.</p>
-<p>Perform an iterative deepcopy of self. It is not assured that the copy
-of node attributes will be performed iteratively as that depends on
-the copy method of the types being copied</p>
-<dl class="field-list simple">
-<dt class="field-odd">Returns<span class="colon">:</span></dt>
-<dd class="field-odd"><dl class="simple">
-<dt>TreeNode</dt><dd><p>A new copy of self</p>
-</dd>
-</dl>
-</dd>
-</dl>
-<div class="admonition seealso">
-<p class="admonition-title">See also</p>
-<dl class="simple">
-<dt><a class="reference internal" href="skbio.tree.TreeNode.unrooted_deepcopy.html#skbio.tree.TreeNode.unrooted_deepcopy" title="skbio.tree.TreeNode.unrooted_deepcopy"><code class="xref py py-obj docutils literal notranslate"><span class="pre">unrooted_deepcopy</span></code></a></dt><dd></dd>
-<dt><a class="reference internal" href="skbio.tree.TreeNode.unrooted_copy.html#skbio.tree.TreeNode.unrooted_copy" title="skbio.tree.TreeNode.unrooted_copy"><code class="xref py py-obj docutils literal notranslate"><span class="pre">unrooted_copy</span></code></a></dt><dd></dd>
-</dl>
-</div>
-<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>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">tree</span> <span class="o">=</span> <span class="n">TreeNode</span><span class="o">.</span><span class="n">read</span><span class="p">([</span><span class="s2">&quot;((a,b)c,(d,e)f)root;&quot;</span><span class="p">])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">tree_copy</span> <span class="o">=</span> <span class="n">tree</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">tree_nodes</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([</span><span class="nb">id</span><span class="p">(</span><span class="n">n</span><span class="p">)</span> <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">tree</span><span class="o">.</span><span class="n">traverse</span><span class="p">()])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">tree_copy_nodes</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([</span><span class="nb">id</span><span class="p">(</span><span class="n">n</span><span class="p">)</span> <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">tree_copy</span><span class="o">.</span><span class="n">traverse</span><span class="p">()])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="nb">print</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">tree_nodes</span><span class="o">.</span><span class="n">intersection</span><span class="p">(</span><span class="n">tree_copy_nodes</span><span class="p">)))</span>
-<span class="go">0</span>
-</pre></div>
-</div>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">__copy__</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#L613"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.__copy__" title="Link to this definition">#</a></dt>
+<dd><p>Return a shallow copy.</p>
 </dd></dl>
 
 </section>

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

@@ -663,6 +663,7 @@
 <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.has_children.html">skbio.tree.TreeNode.has_children</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.index_tree.html">skbio.tree.TreeNode.index_tree</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.insert.html">skbio.tree.TreeNode.insert</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.invalidate_caches.html">skbio.tree.TreeNode.invalidate_caches</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.is_root.html">skbio.tree.TreeNode.is_root</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.is_tip.html">skbio.tree.TreeNode.is_tip</a></li>
@@ -683,6 +684,7 @@
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.root.html">skbio.tree.TreeNode.root</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.root_at.html">skbio.tree.TreeNode.root_at</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.root_at_midpoint.html">skbio.tree.TreeNode.root_at_midpoint</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.root_by_outgroup.html">skbio.tree.TreeNode.root_by_outgroup</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.shear.html">skbio.tree.TreeNode.shear</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.shuffle.html">skbio.tree.TreeNode.shuffle</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.siblings.html">skbio.tree.TreeNode.siblings</a></li>
@@ -696,8 +698,10 @@
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.traverse.html">skbio.tree.TreeNode.traverse</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.unpack.html">skbio.tree.TreeNode.unpack</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.unpack_by_func.html">skbio.tree.TreeNode.unpack_by_func</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.unroot.html">skbio.tree.TreeNode.unroot</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.unrooted_copy.html">skbio.tree.TreeNode.unrooted_copy</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.unrooted_deepcopy.html">skbio.tree.TreeNode.unrooted_deepcopy</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.unrooted_move.html">skbio.tree.TreeNode.unrooted_move</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.write.html">skbio.tree.TreeNode.write</a></li>
 </ul>
 </details></li>
@@ -771,36 +775,8 @@
 <h1>skbio.tree.TreeNode.__deepcopy__<a class="headerlink" href="#skbio-tree-treenode-deepcopy" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.__deepcopy__">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">__deepcopy__</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#L471"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.__deepcopy__" title="Link to this definition">#</a></dt>
-<dd><p>Return a copy of self using an iterative approach.</p>
-<p>Perform an iterative deepcopy of self. It is not assured that the copy
-of node attributes will be performed iteratively as that depends on
-the copy method of the types being copied</p>
-<dl class="field-list simple">
-<dt class="field-odd">Returns<span class="colon">:</span></dt>
-<dd class="field-odd"><dl class="simple">
-<dt>TreeNode</dt><dd><p>A new copy of self</p>
-</dd>
-</dl>
-</dd>
-</dl>
-<div class="admonition seealso">
-<p class="admonition-title">See also</p>
-<dl class="simple">
-<dt><a class="reference internal" href="skbio.tree.TreeNode.unrooted_deepcopy.html#skbio.tree.TreeNode.unrooted_deepcopy" title="skbio.tree.TreeNode.unrooted_deepcopy"><code class="xref py py-obj docutils literal notranslate"><span class="pre">unrooted_deepcopy</span></code></a></dt><dd></dd>
-<dt><a class="reference internal" href="skbio.tree.TreeNode.unrooted_copy.html#skbio.tree.TreeNode.unrooted_copy" title="skbio.tree.TreeNode.unrooted_copy"><code class="xref py py-obj docutils literal notranslate"><span class="pre">unrooted_copy</span></code></a></dt><dd></dd>
-</dl>
-</div>
-<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>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">tree</span> <span class="o">=</span> <span class="n">TreeNode</span><span class="o">.</span><span class="n">read</span><span class="p">([</span><span class="s2">&quot;((a,b)c,(d,e)f)root;&quot;</span><span class="p">])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">tree_copy</span> <span class="o">=</span> <span class="n">tree</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">tree_nodes</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([</span><span class="nb">id</span><span class="p">(</span><span class="n">n</span><span class="p">)</span> <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">tree</span><span class="o">.</span><span class="n">traverse</span><span class="p">()])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">tree_copy_nodes</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([</span><span class="nb">id</span><span class="p">(</span><span class="n">n</span><span class="p">)</span> <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">tree_copy</span><span class="o">.</span><span class="n">traverse</span><span class="p">()])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="nb">print</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">tree_nodes</span><span class="o">.</span><span class="n">intersection</span><span class="p">(</span><span class="n">tree_copy_nodes</span><span class="p">)))</span>
-<span class="go">0</span>
-</pre></div>
-</div>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">__deepcopy__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">memo</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#L617"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.__deepcopy__" title="Link to this definition">#</a></dt>
+<dd><p>Return a deep copy.</p>
 </dd></dl>
 
 </section>