Update from scikit-bio/scikit-bio@b262b1e

Author: qiyunzhu

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

@@ -688,7 +688,7 @@
 <h1>skbio.stats.distance.DistanceMatrix.condensed_form<a class="headerlink" href="#skbio-stats-distance-distancematrix-condensed-form" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.stats.distance.DistanceMatrix.condensed_form">
-<span class="sig-prename descclassname"><span class="pre">DistanceMatrix.</span></span><span class="sig-name descname"><span class="pre">condensed_form</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#L1087"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.distance.DistanceMatrix.condensed_form" 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">condensed_form</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#L1107"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.distance.DistanceMatrix.condensed_form" title="Link to this definition">#</a></dt>
 <dd><p>Return an array of distances in condensed format.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Returns<span class="colon">:</span></dt>

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

@@ -688,7 +688,7 @@
 <h1>skbio.stats.distance.DistanceMatrix.from_iterable<a class="headerlink" href="#skbio-stats-distance-distancematrix-from-iterable" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.stats.distance.DistanceMatrix.from_iterable">
-<em class="property"><span class="k"><span class="pre">classmethod</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">DistanceMatrix.</span></span><span class="sig-name descname"><span class="pre">from_iterable</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">iterable</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metric</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">key</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">keys</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">validate</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#L1027"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.distance.DistanceMatrix.from_iterable" title="Link to this definition">#</a></dt>
+<em class="property"><span class="k"><span class="pre">classmethod</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">DistanceMatrix.</span></span><span class="sig-name descname"><span class="pre">from_iterable</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">iterable</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metric</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">key</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">keys</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">validate</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#L1047"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.distance.DistanceMatrix.from_iterable" title="Link to this definition">#</a></dt>
 <dd><p>Create DistanceMatrix from all pairs in an iterable given a metric.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>

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

@@ -690,6 +690,29 @@ <h1>skbio.stats.distance.DistanceMatrix<a class="headerlink" href="#skbio-stats-
 <p>A <cite>DistanceMatrix</cite> is a <cite>DissimilarityMatrix</cite> with the additional
 requirement that the matrix data is symmetric. There are additional methods
 made available that take advantage of this symmetry.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><dl class="simple">
+<dt><strong>data</strong><span class="classifier">array_like or DissimilarityMatrix</span></dt><dd><p>Square, hollow, two-dimensional <code class="docutils literal notranslate"><span class="pre">numpy.ndarray</span></code> of distances
+(floats), or a structure that can be converted to a <code class="docutils literal notranslate"><span class="pre">numpy.ndarray</span></code>
+using <code class="docutils literal notranslate"><span class="pre">numpy.asarray</span></code> or a one-dimensional vector of distances
+(floats), as defined by <cite>scipy.spatial.distance.squareform</cite>. Can
+instead be a <cite>DissimilarityMatrix</cite> (or <cite>DistanceMatrix</cite>) instance,
+in which case the instance’s data will be used.
+Data will be converted to a float <code class="docutils literal notranslate"><span class="pre">dtype</span></code> if necessary. A copy will
+<em>not</em> be made if already a <code class="docutils literal notranslate"><span class="pre">numpy.ndarray</span></code> with a float <code class="docutils literal notranslate"><span class="pre">dtype</span></code>.</p>
+</dd>
+<dt><strong>ids</strong><span class="classifier">sequence of str, optional</span></dt><dd><p>Sequence of strings to be used as object IDs. Must match the number of
+rows/cols in <cite>data</cite>. If <code class="docutils literal notranslate"><span class="pre">None</span></code> (the default), IDs will be
+monotonically-increasing integers cast as strings, with numbering
+starting from zero, e.g., <code class="docutils literal notranslate"><span class="pre">('0',</span> <span class="pre">'1',</span> <span class="pre">'2',</span> <span class="pre">'3',</span> <span class="pre">...)</span></code>.</p>
+</dd>
+<dt><strong>validate</strong><span class="classifier">bool, optional</span></dt><dd><p>If <cite>validate</cite> is <code class="docutils literal notranslate"><span class="pre">True</span></code> (the default) and data is not a
+DistanceMatrix object, the input data will be validated.</p>
+</dd>
+</dl>
+</dd>
+</dl>
 <div class="admonition seealso">
 <p class="admonition-title">See also</p>
 <dl class="simple">

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

@@ -688,7 +688,7 @@
 <h1>skbio.stats.distance.DistanceMatrix.permute<a class="headerlink" href="#skbio-stats-distance-distancematrix-permute" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.stats.distance.DistanceMatrix.permute">
-<span class="sig-prename descclassname"><span class="pre">DistanceMatrix.</span></span><span class="sig-name descname"><span class="pre">permute</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">condensed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</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#L1109"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.distance.DistanceMatrix.permute" 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">permute</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">condensed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</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#L1129"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.distance.DistanceMatrix.permute" title="Link to this definition">#</a></dt>
 <dd><p>Randomly permute both rows and columns in the matrix.</p>
 <p>Randomly permutes the ordering of rows and columns in the matrix. The
 same permutation is applied to both rows and columns in order to

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

@@ -688,7 +688,7 @@
 <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#L1176"><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#L1196"><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 <code class="docutils literal notranslate"><span class="pre">pandas.Series</span></code> 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.

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

@@ -685,7 +685,7 @@
 <h1>skbio.stats.distance.randdm<a class="headerlink" href="#skbio-stats-distance-randdm" title="Link to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="skbio.stats.distance.randdm">
-<span class="sig-prename descclassname"><span class="pre">skbio.stats.distance.</span></span><span class="sig-name descname"><span class="pre">randdm</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">num_objects</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ids</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">constructor</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">random_fn</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</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#L1226"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.distance.randdm" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">skbio.stats.distance.</span></span><span class="sig-name descname"><span class="pre">randdm</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">num_objects</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ids</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">constructor</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">random_fn</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</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#L1246"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.distance.randdm" title="Link to this definition">#</a></dt>
 <dd><p>Generate a distance matrix populated with random distances.</p>
 <p>Using the default <code class="docutils literal notranslate"><span class="pre">random_fn</span></code>, distances are randomly drawn from a uniform
 distribution over <code class="docutils literal notranslate"><span class="pre">[0,</span> <span class="pre">1)</span></code>.</p>