Update from scikit-bio/scikit-bio@2516f46

Author: qiyunzhu

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

@@ -722,7 +722,7 @@
 <h1>skbio.diversity.alpha.faith_pd<a class="headerlink" href="#skbio-diversity-alpha-faith-pd" title="Link to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="skbio.diversity.alpha.faith_pd">
-<span class="sig-prename descclassname"><span class="pre">skbio.diversity.alpha.</span></span><span class="sig-name descname"><span class="pre">faith_pd</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">counts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">taxa</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">tree</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>, <em class="sig-param"><span class="n"><span class="pre">otu_ids</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/diversity/alpha/_pd.py#L53"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.diversity.alpha.faith_pd" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">skbio.diversity.alpha.</span></span><span class="sig-name descname"><span class="pre">faith_pd</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">counts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">taxa</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tree</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/diversity/alpha/_pd.py#L53"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.diversity.alpha.faith_pd" title="Link to this definition">#</a></dt>
 <dd><p>Calculate Faith’s phylogenetic diversity (Faith’s PD) metric.</p>
 <p>The Faith’s PD metric is defined as:</p>
 <div class="math notranslate nohighlight">
@@ -731,13 +731,16 @@ <h1>skbio.diversity.alpha.faith_pd<a class="headerlink" href="#skbio-diversity-a
 connect all taxa in a community. <span class="math notranslate nohighlight">\(R\)</span> is a set of branches from the lowest
 common ancestor (LCA) of the taxa to the root of the tree. <span class="math notranslate nohighlight">\(PD\)</span> is the sum of
 lengths (<span class="math notranslate nohighlight">\(l\)</span>) of branches in both sets.</p>
-<dl class="field-list simple">
+<dl class="field-list">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><dl class="simple">
+<dd class="field-odd"><dl>
 <dt><strong>counts</strong><span class="classifier">1-D array_like, int</span></dt><dd><p>Vectors of counts/abundances of taxa for one sample.</p>
 </dd>
 <dt><strong>taxa</strong><span class="classifier">list, np.array</span></dt><dd><p>Vector of taxon IDs corresponding to tip names in <code class="docutils literal notranslate"><span class="pre">tree</span></code>. Must be the same
 length as <code class="docutils literal notranslate"><span class="pre">counts</span></code>. Required.</p>
+<div class="versionchanged">
+<p><span class="versionmodified changed">Changed in version 0.6.0: </span>Renamed from <code class="docutils literal notranslate"><span class="pre">otu_ids</span></code>. The old name is kept as an alias but is deprecated.</p>
+</div>
 </dd>
 <dt><strong>tree</strong><span class="classifier">skbio.TreeNode</span></dt><dd><p>Tree relating taxa. The set of tip names in the tree can be a superset of
 <code class="docutils literal notranslate"><span class="pre">taxa</span></code>, but not a subset. Required.</p>
@@ -749,9 +752,6 @@ <h1>skbio.diversity.alpha.faith_pd<a class="headerlink" href="#skbio-diversity-a
 are valid. See <a class="reference internal" href="../diversity.html#module-skbio.diversity" title="skbio.diversity"><code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.diversity</span></code></a> for the description of what validation
 entails so you can determine if you can safely disable validation.</p>
 </dd>
-<dt><strong>otu_ids</strong><span class="classifier">list, np.array</span></dt><dd><p>Alias of <code class="docutils literal notranslate"><span class="pre">taxa</span></code> for backward compatibility. Deprecated and to be removed in a
-future release.</p>
-</dd>
 </dl>
 </dd>
 <dt class="field-even">Returns<span class="colon">:</span></dt>

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

@@ -741,7 +741,7 @@ <h2>Richness metrics<a class="headerlink" href="#richness-metrics" title="Link t
 <tr class="row-even"><td><p><a class="reference internal" href="skbio.diversity.alpha.doubles.html#skbio.diversity.alpha.doubles" title="skbio.diversity.alpha.doubles"><code class="xref py py-obj docutils literal notranslate"><span class="pre">doubles</span></code></a>(counts)</p></td>
 <td><p>Calculate number of double-occurrence taxa (doubletons).</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="skbio.diversity.alpha.faith_pd.html#skbio.diversity.alpha.faith_pd" title="skbio.diversity.alpha.faith_pd"><code class="xref py py-obj docutils literal notranslate"><span class="pre">faith_pd</span></code></a>(counts[, taxa, tree, validate, otu_ids])</p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="skbio.diversity.alpha.faith_pd.html#skbio.diversity.alpha.faith_pd" title="skbio.diversity.alpha.faith_pd"><code class="xref py py-obj docutils literal notranslate"><span class="pre">faith_pd</span></code></a>(counts, taxa, tree[, validate])</p></td>
 <td><p>Calculate Faith's phylogenetic diversity (Faith's PD) metric.</p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="skbio.diversity.alpha.margalef.html#skbio.diversity.alpha.margalef" title="skbio.diversity.alpha.margalef"><code class="xref py py-obj docutils literal notranslate"><span class="pre">margalef</span></code></a>(counts)</p></td>
@@ -796,7 +796,7 @@ <h2>Diversity metrics<a class="headerlink" href="#diversity-metrics" title="Link
 <tr class="row-even"><td><p><a class="reference internal" href="skbio.diversity.alpha.kempton_taylor_q.html#skbio.diversity.alpha.kempton_taylor_q" title="skbio.diversity.alpha.kempton_taylor_q"><code class="xref py py-obj docutils literal notranslate"><span class="pre">kempton_taylor_q</span></code></a>(counts[, lower_quantile, ...])</p></td>
 <td><p>Calculate Kempton-Taylor Q index of alpha diversity.</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="skbio.diversity.alpha.phydiv.html#skbio.diversity.alpha.phydiv" title="skbio.diversity.alpha.phydiv"><code class="xref py py-obj docutils literal notranslate"><span class="pre">phydiv</span></code></a>(counts[, taxa, tree, rooted, weight, ...])</p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="skbio.diversity.alpha.phydiv.html#skbio.diversity.alpha.phydiv" title="skbio.diversity.alpha.phydiv"><code class="xref py py-obj docutils literal notranslate"><span class="pre">phydiv</span></code></a>(counts, taxa, tree[, rooted, weight, ...])</p></td>
 <td><p>Calculate generalized phylogenetic diversity (PD) metrics.</p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="skbio.diversity.alpha.renyi.html#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>(counts[, order, base])</p></td>

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

@@ -722,15 +722,18 @@
 <h1>skbio.diversity.alpha.phydiv<a class="headerlink" href="#skbio-diversity-alpha-phydiv" title="Link to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="skbio.diversity.alpha.phydiv">
-<span class="sig-prename descclassname"><span class="pre">skbio.diversity.alpha.</span></span><span class="sig-name descname"><span class="pre">phydiv</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">counts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">taxa</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">tree</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">rooted</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">weight</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">validate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">otu_ids</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/diversity/alpha/_pd.py#L248"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.diversity.alpha.phydiv" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">skbio.diversity.alpha.</span></span><span class="sig-name descname"><span class="pre">phydiv</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">counts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">taxa</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tree</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rooted</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">weight</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">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/diversity/alpha/_pd.py#L244"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.diversity.alpha.phydiv" title="Link to this definition">#</a></dt>
 <dd><p>Calculate generalized phylogenetic diversity (PD) metrics.</p>
-<dl class="field-list simple">
+<dl class="field-list">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><dl class="simple">
+<dd class="field-odd"><dl>
 <dt><strong>counts</strong><span class="classifier">1-D array_like, int</span></dt><dd><p>Vectors of counts/abundances of taxa for one sample.</p>
 </dd>
 <dt><strong>taxa</strong><span class="classifier">list, np.array</span></dt><dd><p>Vector of taxon IDs corresponding to tip names in <code class="docutils literal notranslate"><span class="pre">tree</span></code>. Must be the same
 length as <code class="docutils literal notranslate"><span class="pre">counts</span></code>. Required.</p>
+<div class="versionchanged">
+<p><span class="versionmodified changed">Changed in version 0.6.0: </span>Renamed from <code class="docutils literal notranslate"><span class="pre">otu_ids</span></code>. The old name is kept as an alias but is deprecated.</p>
+</div>
 </dd>
 <dt><strong>tree</strong><span class="classifier">skbio.TreeNode</span></dt><dd><p>Tree relating taxa. The set of tip names in the tree can be a superset of
 <code class="docutils literal notranslate"><span class="pre">taxa</span></code>, but not a subset. Required.</p>
@@ -745,9 +748,6 @@ <h1>skbio.diversity.alpha.phydiv<a class="headerlink" href="#skbio-diversity-alp
 </dd>
 <dt><strong>validate</strong><span class="classifier">bool, optional</span></dt><dd><p>Whether validate the input data. See <a class="reference internal" href="skbio.diversity.alpha.faith_pd.html#skbio.diversity.alpha.faith_pd" title="skbio.diversity.alpha.faith_pd"><code class="xref py py-func docutils literal notranslate"><span class="pre">faith_pd</span></code></a> for details.</p>
 </dd>
-<dt><strong>otu_ids</strong><span class="classifier">list, np.array</span></dt><dd><p>Alias of <code class="docutils literal notranslate"><span class="pre">taxa</span></code> for backward compatibility. Deprecated and to be removed in a
-future release.</p>
-</dd>
 </dl>
 </dd>
 <dt class="field-even">Returns<span class="colon">:</span></dt>

docs/dev/generated/skbio.diversity.beta.html

@@ -687,10 +687,10 @@
 <h2>Functions<a class="headerlink" href="#functions" title="Link to this heading">#</a></h2>
 <div class="pst-scrollable-table-container"><table class="autosummary longtable table autosummary">
 <tbody>
-<tr class="row-odd"><td><p><a class="reference internal" href="skbio.diversity.beta.unweighted_unifrac.html#skbio.diversity.beta.unweighted_unifrac" title="skbio.diversity.beta.unweighted_unifrac"><code class="xref py py-obj docutils literal notranslate"><span class="pre">unweighted_unifrac</span></code></a>(u_counts, v_counts[, ...])</p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="skbio.diversity.beta.unweighted_unifrac.html#skbio.diversity.beta.unweighted_unifrac" title="skbio.diversity.beta.unweighted_unifrac"><code class="xref py py-obj docutils literal notranslate"><span class="pre">unweighted_unifrac</span></code></a>(u_counts, v_counts, taxa, ...)</p></td>
 <td><p>Compute unweighted UniFrac.</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="skbio.diversity.beta.weighted_unifrac.html#skbio.diversity.beta.weighted_unifrac" title="skbio.diversity.beta.weighted_unifrac"><code class="xref py py-obj docutils literal notranslate"><span class="pre">weighted_unifrac</span></code></a>(u_counts, v_counts[, taxa, ...])</p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="skbio.diversity.beta.weighted_unifrac.html#skbio.diversity.beta.weighted_unifrac" title="skbio.diversity.beta.weighted_unifrac"><code class="xref py py-obj docutils literal notranslate"><span class="pre">weighted_unifrac</span></code></a>(u_counts, v_counts, taxa, tree)</p></td>
 <td><p>Compute weighted UniFrac with or without branch length normalization.</p></td>
 </tr>
 </tbody>