Update from scikit-bio/scikit-bio@b288528

Author: qiyunzhu

docs/dev/generated/skbio.alignment.TabularMSA.read.html

@@ -693,7 +693,7 @@
 <h1>skbio.alignment.TabularMSA.read<a class="headerlink" href="#skbio-alignment-tabularmsa-read" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.alignment.TabularMSA.read">
-<span class="sig-prename descclassname"><span class="pre">TabularMSA.</span></span><span class="sig-name descname"><span class="pre">read</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">format</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="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/io/registry.py#L1084"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.alignment.TabularMSA.read" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TabularMSA.</span></span><span class="sig-name descname"><span class="pre">read</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">format</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="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/io/descriptors.py#L23"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.alignment.TabularMSA.read" title="Link to this definition">#</a></dt>
 <dd><p>Create a new <code class="docutils literal notranslate"><span class="pre">TabularMSA</span></code> instance from a file.</p>
 <p>This is a convenience method for <a class="reference internal" href="skbio.io.registry.read.html#skbio.io.registry.read" title="skbio.io.registry.read"><code class="xref py py-func docutils literal notranslate"><span class="pre">skbio.io.registry.read</span></code></a>. For more information
 about the I/O system in scikit-bio, please see <a class="reference internal" href="../io.html#module-skbio.io" title="skbio.io"><code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io</span></code></a>.</p>

docs/dev/generated/skbio.alignment.TabularMSA.write.html

@@ -693,7 +693,7 @@
 <h1>skbio.alignment.TabularMSA.write<a class="headerlink" href="#skbio-alignment-tabularmsa-write" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.alignment.TabularMSA.write">
-<span class="sig-prename descclassname"><span class="pre">TabularMSA.</span></span><span class="sig-name descname"><span class="pre">write</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">format</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="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/io/registry.py#L1143"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.alignment.TabularMSA.write" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">TabularMSA.</span></span><span class="sig-name descname"><span class="pre">write</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">format</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="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/io/descriptors.py#L82"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.alignment.TabularMSA.write" title="Link to this definition">#</a></dt>
 <dd><p>Write an instance of <code class="docutils literal notranslate"><span class="pre">TabularMSA</span></code> to a file.</p>
 <p>This is a convenience method for <a class="reference internal" href="skbio.io.registry.write.html#skbio.io.registry.write" title="skbio.io.registry.write"><code class="xref py py-func docutils literal notranslate"><span class="pre">skbio.io.registry.write</span></code></a>. For more
 information about the I/O system in scikit-bio, please see <a class="reference internal" href="../io.html#module-skbio.io" title="skbio.io"><code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io</span></code></a>.</p>

docs/dev/generated/skbio.embedding.Embedding.read.html

@@ -677,7 +677,7 @@
 <h1>skbio.embedding.Embedding.read<a class="headerlink" href="#skbio-embedding-embedding-read" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.embedding.Embedding.read">
-<span class="sig-prename descclassname"><span class="pre">Embedding.</span></span><span class="sig-name descname"><span class="pre">read</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">format</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="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/io/registry.py#L1084"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.embedding.Embedding.read" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">Embedding.</span></span><span class="sig-name descname"><span class="pre">read</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">format</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="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/io/descriptors.py#L23"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.embedding.Embedding.read" title="Link to this definition">#</a></dt>
 <dd><p>Create a new <code class="docutils literal notranslate"><span class="pre">Embedding</span></code> instance from a file.</p>
 <p>This is a convenience method for <a class="reference internal" href="skbio.io.registry.read.html#skbio.io.registry.read" title="skbio.io.registry.read"><code class="xref py py-func docutils literal notranslate"><span class="pre">skbio.io.registry.read</span></code></a>. For more information
 about the I/O system in scikit-bio, please see <a class="reference internal" href="../io.html#module-skbio.io" title="skbio.io"><code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io</span></code></a>.</p>

docs/dev/generated/skbio.embedding.Embedding.write.html

@@ -677,7 +677,7 @@
 <h1>skbio.embedding.Embedding.write<a class="headerlink" href="#skbio-embedding-embedding-write" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.embedding.Embedding.write">
-<span class="sig-prename descclassname"><span class="pre">Embedding.</span></span><span class="sig-name descname"><span class="pre">write</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">format</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="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/io/registry.py#L1143"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.embedding.Embedding.write" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">Embedding.</span></span><span class="sig-name descname"><span class="pre">write</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">format</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="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/io/descriptors.py#L82"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.embedding.Embedding.write" title="Link to this definition">#</a></dt>
 <dd><p>Write an instance of <code class="docutils literal notranslate"><span class="pre">Embedding</span></code> to a file.</p>
 <p>This is a convenience method for <a class="reference internal" href="skbio.io.registry.write.html#skbio.io.registry.write" title="skbio.io.registry.write"><code class="xref py py-func docutils literal notranslate"><span class="pre">skbio.io.registry.write</span></code></a>. For more
 information about the I/O system in scikit-bio, please see <a class="reference internal" href="../io.html#module-skbio.io" title="skbio.io"><code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io</span></code></a>.</p>

docs/dev/generated/skbio.io.registry.Format.reader.html

@@ -729,7 +729,7 @@ <h1>skbio.io.registry.Format.reader<a class="headerlink" href="#skbio-io-registr
 </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.io.registry</span><span class="w"> </span><span class="kn">import</span> <span class="n">Format</span><span class="p">,</span> <span class="n">io_registry</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span><span class="w"> </span><span class="nn">skbio.io.registry</span><span class="w"> </span><span class="kn">import</span> <span class="n">Read</span><span class="p">,</span> <span class="n">Write</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span><span class="w"> </span><span class="nn">skbio.io.descriptors</span><span class="w"> </span><span class="kn">import</span> <span class="n">Read</span><span class="p">,</span> <span class="n">Write</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">myformat</span> <span class="o">=</span> <span class="n">Format</span><span class="p">(</span><span class="s1">&#39;myformat&#39;</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">io_registry</span><span class="o">.</span><span class="n">add_format</span><span class="p">(</span><span class="n">myformat</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="c1"># If developing a new format for skbio, use the create_format()</span>

docs/dev/generated/skbio.io.registry.Format.writer.html

@@ -730,7 +730,7 @@ <h1>skbio.io.registry.Format.writer<a class="headerlink" href="#skbio-io-registr
 </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.io.registry</span><span class="w"> </span><span class="kn">import</span> <span class="n">Format</span><span class="p">,</span> <span class="n">io_registry</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span><span class="w"> </span><span class="nn">skbio.io.registry</span><span class="w"> </span><span class="kn">import</span> <span class="n">Read</span><span class="p">,</span> <span class="n">Write</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span><span class="w"> </span><span class="nn">skbio.io.descriptors</span><span class="w"> </span><span class="kn">import</span> <span class="n">Read</span><span class="p">,</span> <span class="n">Write</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">myformat</span> <span class="o">=</span> <span class="n">Format</span><span class="p">(</span><span class="s1">&#39;myformat&#39;</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">io_registry</span><span class="o">.</span><span class="n">add_format</span><span class="p">(</span><span class="n">myformat</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="c1"># If developing a new format for skbio, use the create_format()</span>

docs/dev/generated/skbio.metadata.IntervalMetadata.read.html

@@ -683,7 +683,7 @@
 <h1>skbio.metadata.IntervalMetadata.read<a class="headerlink" href="#skbio-metadata-intervalmetadata-read" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.metadata.IntervalMetadata.read">
-<span class="sig-prename descclassname"><span class="pre">IntervalMetadata.</span></span><span class="sig-name descname"><span class="pre">read</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">format</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="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/io/registry.py#L1084"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.metadata.IntervalMetadata.read" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">IntervalMetadata.</span></span><span class="sig-name descname"><span class="pre">read</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">format</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="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/io/descriptors.py#L23"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.metadata.IntervalMetadata.read" title="Link to this definition">#</a></dt>
 <dd><p>Create a new <code class="docutils literal notranslate"><span class="pre">IntervalMetadata</span></code> instance from a file.</p>
 <p>This is a convenience method for <a class="reference internal" href="skbio.io.registry.read.html#skbio.io.registry.read" title="skbio.io.registry.read"><code class="xref py py-func docutils literal notranslate"><span class="pre">skbio.io.registry.read</span></code></a>. For more information
 about the I/O system in scikit-bio, please see <a class="reference internal" href="../io.html#module-skbio.io" title="skbio.io"><code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io</span></code></a>.</p>

docs/dev/generated/skbio.metadata.IntervalMetadata.write.html

@@ -683,7 +683,7 @@
 <h1>skbio.metadata.IntervalMetadata.write<a class="headerlink" href="#skbio-metadata-intervalmetadata-write" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.metadata.IntervalMetadata.write">
-<span class="sig-prename descclassname"><span class="pre">IntervalMetadata.</span></span><span class="sig-name descname"><span class="pre">write</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">format</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="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/io/registry.py#L1143"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.metadata.IntervalMetadata.write" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">IntervalMetadata.</span></span><span class="sig-name descname"><span class="pre">write</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">format</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="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/io/descriptors.py#L82"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.metadata.IntervalMetadata.write" title="Link to this definition">#</a></dt>
 <dd><p>Write an instance of <code class="docutils literal notranslate"><span class="pre">IntervalMetadata</span></code> to a file.</p>
 <p>This is a convenience method for <a class="reference internal" href="skbio.io.registry.write.html#skbio.io.registry.write" title="skbio.io.registry.write"><code class="xref py py-func docutils literal notranslate"><span class="pre">skbio.io.registry.write</span></code></a>. For more
 information about the I/O system in scikit-bio, please see <a class="reference internal" href="../io.html#module-skbio.io" title="skbio.io"><code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io</span></code></a>.</p>