Update from scikit-bio/scikit-bio@a089ac0

Author: qiyunzhu

docs/dev/_images/diversity-1.png

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

docs/dev/_images/diversity-2_00.png

@@ -240,6 +240,8 @@ skbio.tree.TreeNode
 
 
 
+
+   
 
 
 
@@ -310,6 +312,9 @@ skbio.tree.TreeNode
       ~TreeNode.cache_attr
 
 
+      ~TreeNode.clear_caches
+      
+      
       ~TreeNode.compare_rfd
 
 

docs/dev/_images/diversity-2_01.png

@@ -643,6 +643,7 @@
 <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.bifurcate.html">skbio.tree.TreeNode.bifurcate</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.cache_attr.html">skbio.tree.TreeNode.cache_attr</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.clear_caches.html">skbio.tree.TreeNode.clear_caches</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_subsets.html">skbio.tree.TreeNode.compare_subsets</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>
@@ -779,7 +780,7 @@
 <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#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>
+<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#L618"><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>
 

docs/dev/_images/diversity-3_00.png

@@ -643,6 +643,7 @@
 <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.bifurcate.html">skbio.tree.TreeNode.bifurcate</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.cache_attr.html">skbio.tree.TreeNode.cache_attr</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.clear_caches.html">skbio.tree.TreeNode.clear_caches</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_subsets.html">skbio.tree.TreeNode.compare_subsets</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>
@@ -779,7 +780,7 @@
 <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><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>
+<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#L622"><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>
 

docs/dev/_images/diversity-3_01.png

@@ -643,6 +643,7 @@
 <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.bifurcate.html">skbio.tree.TreeNode.bifurcate</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.cache_attr.html">skbio.tree.TreeNode.cache_attr</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.clear_caches.html">skbio.tree.TreeNode.clear_caches</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_subsets.html">skbio.tree.TreeNode.compare_subsets</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>

docs/dev/_images/diversity-3_02.png

@@ -643,6 +643,7 @@
 <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.bifurcate.html">skbio.tree.TreeNode.bifurcate</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.cache_attr.html">skbio.tree.TreeNode.cache_attr</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.clear_caches.html">skbio.tree.TreeNode.clear_caches</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_subsets.html">skbio.tree.TreeNode.compare_subsets</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>

docs/dev/_images/skbio-sequence-SubstitutionMatrix-plot-1.png

@@ -643,6 +643,7 @@
 <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.bifurcate.html">skbio.tree.TreeNode.bifurcate</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.cache_attr.html">skbio.tree.TreeNode.cache_attr</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.clear_caches.html">skbio.tree.TreeNode.clear_caches</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_subsets.html">skbio.tree.TreeNode.compare_subsets</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>
@@ -779,8 +780,8 @@
 <h1>skbio.tree.TreeNode.__getitem__<a class="headerlink" href="#skbio-tree-treenode-getitem" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.__getitem__">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">__getitem__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">i</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#L163"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.__getitem__" title="Link to this definition">#</a></dt>
-<dd><p>Node delegates slicing to <cite>children</cite>.</p>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">__getitem__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">i</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#L168"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.__getitem__" title="Link to this definition">#</a></dt>
+<dd><p>Node delegates slicing to <code class="docutils literal notranslate"><span class="pre">children</span></code>.</p>
 </dd></dl>
 
 </section>

docs/dev/_images/skbio-stats-distance-DissimilarityMatrix-plot-1.png

@@ -643,6 +643,7 @@
 <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.bifurcate.html">skbio.tree.TreeNode.bifurcate</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.cache_attr.html">skbio.tree.TreeNode.cache_attr</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.clear_caches.html">skbio.tree.TreeNode.clear_caches</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_subsets.html">skbio.tree.TreeNode.compare_subsets</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>

docs/dev/_images/skbio-stats-distance-DistanceMatrix-plot-1.png

@@ -643,6 +643,7 @@
 <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.bifurcate.html">skbio.tree.TreeNode.bifurcate</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.cache_attr.html">skbio.tree.TreeNode.cache_attr</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.clear_caches.html">skbio.tree.TreeNode.clear_caches</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_subsets.html">skbio.tree.TreeNode.compare_subsets</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>

docs/dev/_images/skbio-stats-ordination-OrdinationResults-plot-1.png

@@ -643,6 +643,7 @@
 <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.bifurcate.html">skbio.tree.TreeNode.bifurcate</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.cache_attr.html">skbio.tree.TreeNode.cache_attr</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.clear_caches.html">skbio.tree.TreeNode.clear_caches</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_subsets.html">skbio.tree.TreeNode.compare_subsets</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>

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

@@ -643,6 +643,7 @@
 <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.bifurcate.html">skbio.tree.TreeNode.bifurcate</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.cache_attr.html">skbio.tree.TreeNode.cache_attr</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.clear_caches.html">skbio.tree.TreeNode.clear_caches</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_subsets.html">skbio.tree.TreeNode.compare_subsets</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>
@@ -779,8 +780,8 @@
 <h1>skbio.tree.TreeNode.__iter__<a class="headerlink" href="#skbio-tree-treenode-iter" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.__iter__">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">__iter__</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#L156"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.__iter__" title="Link to this definition">#</a></dt>
-<dd><p>Node iter iterates over the <cite>children</cite>.</p>
+<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">__iter__</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#L161"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.__iter__" title="Link to this definition">#</a></dt>
+<dd><p>Node iter iterates over the <code class="docutils literal notranslate"><span class="pre">children</span></code>.</p>
 </dd></dl>
 
 </section>

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

@@ -643,6 +643,7 @@
 <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.bifurcate.html">skbio.tree.TreeNode.bifurcate</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.cache_attr.html">skbio.tree.TreeNode.cache_attr</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.clear_caches.html">skbio.tree.TreeNode.clear_caches</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_subsets.html">skbio.tree.TreeNode.compare_subsets</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>

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

@@ -643,6 +643,7 @@
 <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.bifurcate.html">skbio.tree.TreeNode.bifurcate</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.cache_attr.html">skbio.tree.TreeNode.cache_attr</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.clear_caches.html">skbio.tree.TreeNode.clear_caches</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_subsets.html">skbio.tree.TreeNode.compare_subsets</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>
@@ -779,7 +780,7 @@
 <h1>skbio.tree.TreeNode.__len__<a class="headerlink" href="#skbio-tree-treenode-len" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.tree.TreeNode.__len__">
-<span class="sig-prename descclassname"><span class="pre">TreeNode.</span></span><span class="sig-name descname"><span class="pre">__len__</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#L160"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.__len__" 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">__len__</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#L165"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.tree.TreeNode.__len__" title="Link to this definition">#</a></dt>
 <dd></dd></dl>
 
 </section>

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

@@ -643,6 +643,7 @@
 <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.bifurcate.html">skbio.tree.TreeNode.bifurcate</a></li>
 <li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.cache_attr.html">skbio.tree.TreeNode.cache_attr</a></li>
+<li class="toctree-l2"><a class="reference internal" href="skbio.tree.TreeNode.clear_caches.html">skbio.tree.TreeNode.clear_caches</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_subsets.html">skbio.tree.TreeNode.compare_subsets</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>