scikit-bio
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diff --git a/‎docs/dev/generated/generated/skbio.util.config.set_config.html
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diff --git a/‎docs/dev/generated/skbio.stats.ordination.OrdinationResults.html
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@@ -0,0 +1,6 @@
+skbio.util.DataTable
+====================
+
+.. currentmodule:: skbio.util
+
+.. autodata:: DataTable
@@ -618,6 +618,9 @@
 <li class="toctree-l1"><a class="reference internal" href="../skbio.util.params_aliased.html">skbio.util.params_aliased</a></li>
 </ul>
 <ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="../skbio.util.DataTable.html">skbio.util.DataTable</a></li>
+</ul>
+<ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="../skbio.util.get_rng.html">skbio.util.get_rng</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../skbio.util.cardinal_to_ordinal.html">skbio.util.cardinal_to_ordinal</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../skbio.util.find_duplicates.html">skbio.util.find_duplicates</a></li>
@@ -689,7 +692,7 @@
 <h1>skbio.util.config.get_config<a class="headerlink" href="#skbio-util-config-get-config" title="Link to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="skbio.util.config.get_config">
-<span class="sig-prename descclassname"><span class="pre">skbio.util.config.</span></span><span class="sig-name descname"><span class="pre">get_config</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">option</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a></span></span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/util/config/_config.py#L32"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.util.config.get_config" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">skbio.util.config.</span></span><span class="sig-name descname"><span class="pre">get_config</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">option</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a></span></span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/util/config/_config.py#L48"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.util.config.get_config" title="Link to this definition">#</a></dt>
 <dd><p>Get the current value of an skbio config option.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 
@@ -6,7 +6,7 @@
 
   <head>
     <meta charset="utf-8" />
-    <meta name="description" content="Set an skbio config option." />
+    <meta name="description" content="Set a scikit-bio config option." />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
     <title>skbio.util.config.set_config &#8212; scikit-bio 0.6.4-dev documentation</title>
@@ -618,6 +618,9 @@
 <li class="toctree-l1"><a class="reference internal" href="../skbio.util.params_aliased.html">skbio.util.params_aliased</a></li>
 </ul>
 <ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="../skbio.util.DataTable.html">skbio.util.DataTable</a></li>
+</ul>
+<ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="../skbio.util.get_rng.html">skbio.util.get_rng</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../skbio.util.cardinal_to_ordinal.html">skbio.util.cardinal_to_ordinal</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../skbio.util.find_duplicates.html">skbio.util.find_duplicates</a></li>
@@ -690,17 +693,33 @@ <h1>skbio.util.config.set_config<a class="headerlink" href="#skbio-util-config-s
 <dl class="py function">
 <dt class="sig sig-object py" id="skbio.util.config.set_config">
 <span class="sig-prename descclassname"><span class="pre">skbio.util.config.</span></span><span class="sig-name descname"><span class="pre">set_config</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">option</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">value</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/util/config/_config.py#L12"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.util.config.set_config" title="Link to this definition">#</a></dt>
-<dd><p>Set an skbio config option.</p>
+<dd><p>Set a scikit-bio config option.</p>
+<p>This function enables users to set the configuration of scikit-bio functions
+globally.</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>option</strong><span class="classifier">str</span></dt><dd><p>The configuration option to be modified.</p>
+<dt><strong>option</strong><span class="classifier">str</span></dt><dd><p>The configuration option to be modified. Currently there is only one
+configurable option, <code class="docutils literal notranslate"><span class="pre">&quot;output&quot;</span></code>.</p>
+</dd>
+<dt><strong>value</strong><span class="classifier">str</span></dt><dd><p>The value to update the configuration dictionary with. For the
+<code class="docutils literal notranslate"><span class="pre">&quot;output&quot;</span></code> option, <code class="docutils literal notranslate"><span class="pre">value</span></code> may be set to <code class="docutils literal notranslate"><span class="pre">&quot;pandas&quot;</span></code>,
+<code class="docutils literal notranslate"><span class="pre">&quot;polars&quot;</span></code>, or <code class="docutils literal notranslate"><span class="pre">&quot;numpy&quot;</span></code>. Defaults to <code class="docutils literal notranslate"><span class="pre">&quot;pandas&quot;</span></code>.</p>
 </dd>
-<dt><strong>value</strong><span class="classifier">str</span></dt><dd><p>The value to update the configuration dictionary with.</p>
+</dl>
+</dd>
+<dt class="field-even">Raises<span class="colon">:</span></dt>
+<dd class="field-even"><dl class="simple">
+<dt>ValueError</dt><dd><p>If an unkown option is used or if an unsupported value for an option is used.</p>
 </dd>
 </dl>
 </dd>
 </dl>
+<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="w"> </span><span class="nn">skbio</span><span class="w"> </span><span class="kn">import</span> <span class="n">set_config</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">set_config</span><span class="p">(</span><span class="s2">&quot;output&quot;</span><span class="p">,</span> <span class="s2">&quot;numpy&quot;</span><span class="p">)</span>
+</pre></div>
+</div>
 </dd></dl>
 
 </section>
 
@@ -688,7 +688,7 @@
 <h1>skbio.stats.ordination.OrdinationResults<a class="headerlink" href="#skbio-stats-ordination-ordinationresults" title="Link to this heading">#</a></h1>
 <dl class="py class">
 <dt class="sig sig-object py" id="skbio.stats.ordination.OrdinationResults">
-<em class="property"><span class="k"><span class="pre">class</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">skbio.stats.ordination.</span></span><span class="sig-name descname"><span class="pre">OrdinationResults</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">short_method_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">long_method_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">eigvals</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">samples</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sample_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">features</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">feature_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">biplot_scores</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">sample_constraints</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">constraint_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">proportion_explained</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/ordination/_ordination_results.py#L21"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.ordination.OrdinationResults" title="Link to this definition">#</a></dt>
+<em class="property"><span class="k"><span class="pre">class</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">skbio.stats.ordination.</span></span><span class="sig-name descname"><span class="pre">OrdinationResults</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">short_method_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">long_method_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">eigvals</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">samples</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sample_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">features</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">feature_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">biplot_scores</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">sample_constraints</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">constraint_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">proportion_explained</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/ordination/_ordination_results.py#L22"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.ordination.OrdinationResults" title="Link to this definition">#</a></dt>
 <dd><p>Store ordination results, providing serialization and plotting support.</p>
 <p>Stores various components of ordination results. Provides methods for
 serializing/deserializing results, as well as generation of basic
@@ -701,27 +701,33 @@ <h1>skbio.stats.ordination.OrdinationResults<a class="headerlink" href="#skbio-s
 </dd>
 <dt><strong>long_method_name</strong><span class="classifier">str</span></dt><dd><p>Ordination method name.</p>
 </dd>
-<dt><strong>eigvals</strong><span class="classifier">ndarray</span></dt><dd><p>The resulting eigenvalues.  The index corresponds to the ordination
-axis labels</p>
+<dt><strong>eigvals</strong><span class="classifier">table_like</span></dt><dd><p>The resulting eigenvalues.  The index corresponds to the ordination
+axis labels. See the <a class="reference external" href="../../../docs/dev/generated/skbio.util.config.html#the-datatable-type">DataTable</a> type
+documentation for details.</p>
 </dd>
-<dt><strong>samples</strong><span class="classifier">ndarray</span></dt><dd><p>The position of the samples in the ordination space, row-indexed by the
-sample id.</p>
+<dt><strong>samples</strong><span class="classifier">table_like</span></dt><dd><p>The position of the samples in the ordination space, row-indexed by the
+sample id. See the <a class="reference external" href="../../../docs/dev/generated/skbio.util.config.html#the-datatable-type">DataTable</a> type
+documentation for details.</p>
 </dd>
-<dt><strong>sample_ids</strong><span class="classifier">list of str, or should it be pd.Index?</span></dt><dd><p>The names of the samples. Must be provided if samples is an array.</p>
+<dt><strong>features</strong><span class="classifier">table_like</span></dt><dd><p>The position of the features in the ordination space, row-indexed by
+the feature id. See the <a class="reference external" href="../../../docs/dev/generated/skbio.util.config.html#the-datatable-type">DataTable</a> type
+documentation for details.</p>
 </dd>
-<dt><strong>features</strong><span class="classifier">ndarray</span></dt><dd><p>The position of the features in the ordination space, row-indexed by
-the feature id.</p>
+<dt><strong>biplot_scores</strong><span class="classifier">table_like</span></dt><dd><p>Correlation coefficients of the samples with respect to the features.
+See the <a class="reference external" href="../../../docs/dev/generated/skbio.util.config.html#the-datatable-type">DataTable</a> type
+documentation for details.</p>
 </dd>
-<dt><strong>feature_ids</strong><span class="classifier">array-like of str</span></dt><dd><p>The names of the features. Must be provided if features is an array.</p>
-</dd>
-<dt><strong>biplot_scores</strong><span class="classifier">ndarray</span></dt><dd><p>Correlation coefficients of the samples with respect to the features.</p>
-</dd>
-<dt><strong>sample_constraints</strong><span class="classifier">ndarray</span></dt><dd><p>Site constraints (linear combinations of constraining variables):
+<dt><strong>sample_constraints</strong><span class="classifier">table_like</span></dt><dd><p>Site constraints (linear combinations of constraining variables):
 coordinates of the sites in the space of the explanatory variables X.
-These are the fitted site scores</p>
+These are the fitted site scores. See the <a class="reference external" href="../../../docs/dev/generated/skbio.util.config.html#the-datatable-type">DataTable</a> type
+documentation for details.</p>
+</dd>
+<dt><strong>proportion_explained</strong><span class="classifier">table_like</span></dt><dd><p>Proportion explained by each of the dimensions in the ordination space.
+The index corresponds to the ordination axis labels. See the
+<a class="reference external" href="../../../docs/dev/generated/skbio.util.config.html#the-datatable-type">DataTable</a> type documentation for details.</p>
 </dd>
-<dt><strong>proportion_explained</strong><span class="classifier">ndarray</span></dt><dd><p>Proportion explained by each of the dimensions in the ordination space.
-The index corresponds to the ordination axis labels</p>
+<dt><strong>sample_ids, feature_ids, constraint_ids, output_format</strong><span class="classifier">optional</span></dt><dd><p>Standard <code class="docutils literal notranslate"><span class="pre">DataTable</span></code> parameters. See the <a class="reference external" href="../../../docs/dev/generated/skbio.util.config.html#the-datatable-type">DataTable</a> type
+documentation for details.</p>
 </dd>
 </dl>
 </dd>
@@ -821,7 +827,7 @@ <h1>skbio.stats.ordination.OrdinationResults<a class="headerlink" href="#skbio-s
 
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.stats.ordination.OrdinationResults.__str__">
-<span class="sig-name descname"><span class="pre">__str__</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/ordination/_ordination_results.py#L107"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.ordination.OrdinationResults.__str__" title="Link to this definition">#</a></dt>
+<span class="sig-name descname"><span class="pre">__str__</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/ordination/_ordination_results.py#L123"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.ordination.OrdinationResults.__str__" title="Link to this definition">#</a></dt>
 <dd><p>Return a string representation of the ordination results.</p>
 <p>String representation lists ordination results attributes and indicates
 whether or not they are present. If an attribute is present, its