Update from scikit-bio/scikit-bio@d95160f

Author: qiyunzhu

docs/dev/generated/generated/skbio.util.config.get_config.html

@@ -692,7 +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#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>
+<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></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#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>

docs/dev/generated/generated/skbio.util.config.set_config.html

@@ -692,7 +692,7 @@
 <h1>skbio.util.config.set_config<a class="headerlink" href="#skbio-util-config-set-config" title="Link to this heading">#</a></h1>
 <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>
+<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></em>, <em class="sig-param"><span class="n"><span class="pre">value</span></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 a scikit-bio config option.</p>
 <p>This function enables users to set the configuration of scikit-bio functions
 globally.</p>

docs/dev/generated/skbio.embedding.ProteinVector.html

@@ -669,7 +669,7 @@
 <h1>skbio.embedding.ProteinVector<a class="headerlink" href="#skbio-embedding-proteinvector" title="Link to this heading">#</a></h1>
 <dl class="py class">
 <dt class="sig sig-object py" id="skbio.embedding.ProteinVector">
-<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.embedding.</span></span><span class="sig-name descname"><span class="pre">ProteinVector</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vector</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sequence</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="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/embedding/_protein.py#L123"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.embedding.ProteinVector" 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.embedding.</span></span><span class="sig-name descname"><span class="pre">ProteinVector</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vector</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sequence</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/embedding/_protein.py#L123"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.embedding.ProteinVector" title="Link to this definition">#</a></dt>
 <dd><p>Vector representation for a protein sequence.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>

docs/dev/generated/skbio.metadata.CategoricalMetadataColumn.html

@@ -670,7 +670,7 @@
 <h1>skbio.metadata.CategoricalMetadataColumn<a class="headerlink" href="#skbio-metadata-categoricalmetadatacolumn" title="Link to this heading">#</a></h1>
 <dl class="py class">
 <dt class="sig sig-object py" id="skbio.metadata.CategoricalMetadataColumn">
-<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.metadata.</span></span><span class="sig-name descname"><span class="pre">CategoricalMetadataColumn</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">series</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">missing_scheme</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'blank'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/metadata/_metadata.py#L1258"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.metadata.CategoricalMetadataColumn" 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.metadata.</span></span><span class="sig-name descname"><span class="pre">CategoricalMetadataColumn</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">series</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">missing_scheme</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'blank'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/metadata/_metadata.py#L1259"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.metadata.CategoricalMetadataColumn" title="Link to this definition">#</a></dt>
 <dd><p>A single metadata column containing categorical data.</p>
 <p>See the <code class="docutils literal notranslate"><span class="pre">Metadata</span></code> class docstring for details about <code class="docutils literal notranslate"><span class="pre">Metadata</span></code> and
 <code class="docutils literal notranslate"><span class="pre">MetadataColumn</span></code> objects, including a description of column types and

docs/dev/generated/skbio.metadata.MetadataColumn.drop_missing_values.html

@@ -683,7 +683,7 @@
 <h1>skbio.metadata.MetadataColumn.drop_missing_values<a class="headerlink" href="#skbio-metadata-metadatacolumn-drop-missing-values" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.metadata.MetadataColumn.drop_missing_values">
-<span class="sig-prename descclassname"><span class="pre">MetadataColumn.</span></span><span class="sig-name descname"><span class="pre">drop_missing_values</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/metadata/_metadata.py#L1180"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.metadata.MetadataColumn.drop_missing_values" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">MetadataColumn.</span></span><span class="sig-name descname"><span class="pre">drop_missing_values</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/metadata/_metadata.py#L1181"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.metadata.MetadataColumn.drop_missing_values" title="Link to this definition">#</a></dt>
 <dd><p>Filter out missing values from the metadata column.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Returns<span class="colon">:</span></dt>

docs/dev/generated/skbio.metadata.MetadataColumn.filter_ids.html

@@ -683,7 +683,7 @@
 <h1>skbio.metadata.MetadataColumn.filter_ids<a class="headerlink" href="#skbio-metadata-metadatacolumn-filter-ids" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.metadata.MetadataColumn.filter_ids">
-<span class="sig-prename descclassname"><span class="pre">MetadataColumn.</span></span><span class="sig-name descname"><span class="pre">filter_ids</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ids_to_keep</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/metadata/_metadata.py#L1227"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.metadata.MetadataColumn.filter_ids" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">MetadataColumn.</span></span><span class="sig-name descname"><span class="pre">filter_ids</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ids_to_keep</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/metadata/_metadata.py#L1228"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.metadata.MetadataColumn.filter_ids" title="Link to this definition">#</a></dt>
 <dd><p>Filter metadata column by IDs.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>

docs/dev/generated/skbio.metadata.MetadataColumn.get_ids.html

@@ -683,7 +683,7 @@
 <h1>skbio.metadata.MetadataColumn.get_ids<a class="headerlink" href="#skbio-metadata-metadatacolumn-get-ids" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.metadata.MetadataColumn.get_ids">
-<span class="sig-prename descclassname"><span class="pre">MetadataColumn.</span></span><span class="sig-name descname"><span class="pre">get_ids</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">where_values_missing</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/metadata/_metadata.py#L1198"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.metadata.MetadataColumn.get_ids" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">MetadataColumn.</span></span><span class="sig-name descname"><span class="pre">get_ids</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">where_values_missing</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/metadata/_metadata.py#L1199"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.metadata.MetadataColumn.get_ids" title="Link to this definition">#</a></dt>
 <dd><p>Retrieve IDs matching search criteria.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>

docs/dev/generated/skbio.metadata.MetadataColumn.get_missing.html

@@ -683,7 +683,7 @@
 <h1>skbio.metadata.MetadataColumn.get_missing<a class="headerlink" href="#skbio-metadata-metadatacolumn-get-missing" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.metadata.MetadataColumn.get_missing">
-<span class="sig-prename descclassname"><span class="pre">MetadataColumn.</span></span><span class="sig-name descname"><span class="pre">get_missing</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/metadata/_metadata.py#L1136"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.metadata.MetadataColumn.get_missing" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">MetadataColumn.</span></span><span class="sig-name descname"><span class="pre">get_missing</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/metadata/_metadata.py#L1137"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.metadata.MetadataColumn.get_missing" title="Link to this definition">#</a></dt>
 <dd><p>Return a series containing only missing values (with an index).</p>
 <p>If the column was constructed with a missing scheme, then the values
 of the series will be the original terms instead of NaN.</p>

docs/dev/generated/skbio.metadata.MetadataColumn.get_value.html

@@ -683,7 +683,7 @@
 <h1>skbio.metadata.MetadataColumn.get_value<a class="headerlink" href="#skbio-metadata-metadatacolumn-get-value" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.metadata.MetadataColumn.get_value">
-<span class="sig-prename descclassname"><span class="pre">MetadataColumn.</span></span><span class="sig-name descname"><span class="pre">get_value</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">id</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/metadata/_metadata.py#L1145"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.metadata.MetadataColumn.get_value" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">MetadataColumn.</span></span><span class="sig-name descname"><span class="pre">get_value</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">id</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/metadata/_metadata.py#L1146"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.metadata.MetadataColumn.get_value" title="Link to this definition">#</a></dt>
 <dd><p>Retrieve metadata column value associated with an ID.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>

docs/dev/generated/skbio.metadata.MetadataColumn.has_missing_values.html

@@ -683,7 +683,7 @@
 <h1>skbio.metadata.MetadataColumn.has_missing_values<a class="headerlink" href="#skbio-metadata-metadatacolumn-has-missing-values" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.metadata.MetadataColumn.has_missing_values">
-<span class="sig-prename descclassname"><span class="pre">MetadataColumn.</span></span><span class="sig-name descname"><span class="pre">has_missing_values</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/metadata/_metadata.py#L1163"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.metadata.MetadataColumn.has_missing_values" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">MetadataColumn.</span></span><span class="sig-name descname"><span class="pre">has_missing_values</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/metadata/_metadata.py#L1164"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.metadata.MetadataColumn.has_missing_values" title="Link to this definition">#</a></dt>
 <dd><p>Determine if the metadata column has one or more missing values.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Returns<span class="colon">:</span></dt>