Update from scikit-bio/scikit-bio@e534dde

Author: qiyunzhu

docs/dev/_sources/generated/skbio.stats.distance.DistanceMatrix.condensed_form.rst.txt

@@ -138,6 +138,10 @@ skbio.stats.distance.DistanceMatrix
 
 
 
+   
+
+   
+
 
 
 
@@ -279,6 +283,18 @@ skbio.stats.distance.DistanceMatrix
 
 
 
+   
+      
+         
+      
+   
+
+   
+      
+         
+      
+   
+
 
 
 
@@ -360,8 +376,6 @@ skbio.stats.distance.DistanceMatrix
    .. autosummary::
       :toctree:
 
-      ~DistanceMatrix.condensed_form
-   
       ~DistanceMatrix.to_series
 
 
@@ -370,7 +384,10 @@ skbio.stats.distance.DistanceMatrix
    .. rubric:: Methods (inherited)
 
    .. autoinherit::
+      ~DistanceMatrix.as_condensed
+      ~DistanceMatrix.as_redundant
       ~DistanceMatrix.between
+      ~DistanceMatrix.condensed_form
       ~DistanceMatrix.copy
       ~DistanceMatrix.filter
       ~DistanceMatrix.from_iterable

docs/dev/_sources/generated/skbio.stats.distance.DistanceMatrix.rst.txt

@@ -0,0 +1,8 @@
+:orphan:
+
+skbio.stats.distance.SymmetricMatrix.as_condensed
+=================================================
+
+.. currentmodule:: skbio.stats.distance
+
+.. automethod:: SymmetricMatrix.as_condensed

docs/dev/_sources/generated/skbio.stats.distance.SymmetricMatrix.as_condensed.rst.txt

@@ -0,0 +1,8 @@
+:orphan:
+
+skbio.stats.distance.SymmetricMatrix.as_redundant
+=================================================
+
+.. currentmodule:: skbio.stats.distance
+
+.. automethod:: SymmetricMatrix.as_redundant

docs/dev/_sources/generated/skbio.stats.distance.SymmetricMatrix.as_redundant.rst.txt

@@ -140,6 +140,10 @@ skbio.stats.distance.SymmetricMatrix
 
 
 
+   
+
+   
+
 
 
 
@@ -275,6 +279,18 @@ skbio.stats.distance.SymmetricMatrix
 
 
 
+   
+      
+         
+      
+   
+
+   
+      
+         
+      
+   
+
 
 
 
@@ -361,6 +377,10 @@ skbio.stats.distance.SymmetricMatrix
    .. autosummary::
       :toctree:
 
+      ~SymmetricMatrix.as_condensed
+   
+      ~SymmetricMatrix.as_redundant
+   
       ~SymmetricMatrix.condensed_form
 
       ~SymmetricMatrix.copy

docs/dev/_sources/generated/skbio.stats.distance.SymmetricMatrix.rst.txt

@@ -69,7 +69,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="skbio.stats.distance.randdm" href="skbio.stats.distance.randdm.html" />
-    <link rel="prev" title="skbio.stats.distance.DistanceMatrix.condensed_form" href="skbio.stats.distance.DistanceMatrix.condensed_form.html" />
+    <link rel="prev" title="skbio.stats.distance.DistanceMatrix" href="skbio.stats.distance.DistanceMatrix.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   <meta name="docsearch:version" content="0.7.1-dev" />
@@ -703,7 +703,7 @@
 <h1>skbio.stats.distance.DistanceMatrix.to_series<a class="headerlink" href="#skbio-stats-distance-distancematrix-to-series" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.stats.distance.DistanceMatrix.to_series">
-<span class="sig-prename descclassname"><span class="pre">DistanceMatrix.</span></span><span class="sig-name descname"><span class="pre">to_series</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/stats/distance/_base.py#L1878"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.distance.DistanceMatrix.to_series" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">DistanceMatrix.</span></span><span class="sig-name descname"><span class="pre">to_series</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/stats/distance/_base.py#L2106"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.distance.DistanceMatrix.to_series" title="Link to this definition">#</a></dt>
 <dd><p>Create a pandas Series from this <code class="docutils literal notranslate"><span class="pre">DistanceMatrix</span></code>.</p>
 <p>The series will contain distances in condensed form: only distances from one
 matrix triangle are included, and the diagonal is excluded. The series’ index
@@ -712,7 +712,7 @@ <h1>skbio.stats.distance.DistanceMatrix.to_series<a class="headerlink" href="#sk
 triangle.</p>
 <p>To obtain all distances (i.e. both upper and lower matrix triangles and the
 diagonal), use <code class="xref py py-meth docutils literal notranslate"><span class="pre">to_data_frame</span></code>. To obtain <em>only</em> the distances in
-condensed form (e.g. for use with SciPy), use <a class="reference internal" href="skbio.stats.distance.DistanceMatrix.condensed_form.html#skbio.stats.distance.DistanceMatrix.condensed_form" title="skbio.stats.distance.DistanceMatrix.condensed_form"><code class="xref py py-meth docutils literal notranslate"><span class="pre">condensed_form</span></code></a>.</p>
+condensed form (e.g. for use with SciPy), use <code class="xref py py-meth docutils literal notranslate"><span class="pre">condensed_form</span></code>.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Returns<span class="colon">:</span></dt>
 <dd class="field-odd"><dl class="simple">
@@ -725,7 +725,7 @@ <h1>skbio.stats.distance.DistanceMatrix.to_series<a class="headerlink" href="#sk
 <p class="admonition-title">See also</p>
 <dl class="simple">
 <dt><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_data_frame</span></code></dt><dd></dd>
-<dt><a class="reference internal" href="skbio.stats.distance.DistanceMatrix.condensed_form.html#skbio.stats.distance.DistanceMatrix.condensed_form" title="skbio.stats.distance.DistanceMatrix.condensed_form"><code class="xref py py-obj docutils literal notranslate"><span class="pre">condensed_form</span></code></a></dt><dd></dd>
+<dt><code class="xref py py-obj docutils literal notranslate"><span class="pre">condensed_form</span></code></dt><dd></dd>
 <dt><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.distance.squareform.html#scipy.spatial.distance.squareform" title="(in SciPy v1.16.2)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scipy.spatial.distance.squareform</span></code></a></dt><dd></dd>
 </dl>
 </div>
@@ -760,12 +760,12 @@ <h1>skbio.stats.distance.DistanceMatrix.to_series<a class="headerlink" href="#sk
 
 <div class="prev-next-area">
     <a class="left-prev"
-       href="skbio.stats.distance.DistanceMatrix.condensed_form.html"
+       href="skbio.stats.distance.DistanceMatrix.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">skbio.stats.distance.DistanceMatrix.condensed_form</p>
+        <p class="prev-next-title">skbio.stats.distance.DistanceMatrix</p>
       </div>
     </a>
     <a class="right-next"

docs/dev/generated/skbio.stats.distance.DistanceMatrix.html

@@ -703,7 +703,7 @@
 <h1>skbio.stats.distance.PairwiseMatrix.between<a class="headerlink" href="#skbio-stats-distance-pairwisematrix-between" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.stats.distance.PairwiseMatrix.between">
-<span class="sig-prename descclassname"><span class="pre">PairwiseMatrix.</span></span><span class="sig-name descname"><span class="pre">between</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">from_</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">to_</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allow_overlap</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/stats/distance/_base.py#L617"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.distance.PairwiseMatrix.between" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">PairwiseMatrix.</span></span><span class="sig-name descname"><span class="pre">between</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">from_</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">to_</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allow_overlap</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/stats/distance/_base.py#L624"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.distance.PairwiseMatrix.between" title="Link to this definition">#</a></dt>
 <dd><p>Obtain the pairwise values between the two groups of IDs.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>

docs/dev/generated/skbio.stats.distance.DistanceMatrix.to_series.html

@@ -703,7 +703,7 @@
 <h1>skbio.stats.distance.PairwiseMatrix.copy<a class="headerlink" href="#skbio-stats-distance-pairwisematrix-copy" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.stats.distance.PairwiseMatrix.copy">
-<span class="sig-prename descclassname"><span class="pre">PairwiseMatrix.</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/stats/distance/_base.py#L410"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.distance.PairwiseMatrix.copy" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">PairwiseMatrix.</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/stats/distance/_base.py#L417"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.distance.PairwiseMatrix.copy" title="Link to this definition">#</a></dt>
 <dd><p>Return a deep copy of the matrix.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Returns<span class="colon">:</span></dt>

docs/dev/generated/skbio.stats.distance.PairwiseMatrix.between.html

@@ -703,7 +703,7 @@
 <h1>skbio.stats.distance.PairwiseMatrix.filter<a class="headerlink" href="#skbio-stats-distance-pairwisematrix-filter" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.stats.distance.PairwiseMatrix.filter">
-<span class="sig-prename descclassname"><span class="pre">PairwiseMatrix.</span></span><span class="sig-name descname"><span class="pre">filter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ids</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">strict</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/stats/distance/_base.py#L482"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.distance.PairwiseMatrix.filter" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">PairwiseMatrix.</span></span><span class="sig-name descname"><span class="pre">filter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ids</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">strict</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/stats/distance/_base.py#L489"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.distance.PairwiseMatrix.filter" title="Link to this definition">#</a></dt>
 <dd><p>Filter the matrix by IDs.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>