Update from scikit-bio/scikit-bio@e8c5688

Author: qiyunzhu

docs/dev/_sources/generated/skbio.io.registry.IORegistry.rst.txt

@@ -116,6 +116,8 @@ skbio.io.registry.IORegistry
 
 
 
+   
+
 
 
 

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

@@ -720,7 +720,7 @@
 <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">
-<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><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">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#L646"><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>
+<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><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">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#L658"><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

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

@@ -720,7 +720,7 @@
 <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">'fasta'</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#L669"><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">'fasta'</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#L681"><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

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

@@ -703,7 +703,7 @@
 <h1>skbio.embedding.ProteinEmbedding.read<a class="headerlink" href="#skbio-embedding-proteinembedding-read" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.embedding.ProteinEmbedding.read">
-<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">ProteinEmbedding.</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">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#L646"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.embedding.ProteinEmbedding.read" title="Link to this definition">#</a></dt>
+<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">ProteinEmbedding.</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">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#L658"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.embedding.ProteinEmbedding.read" title="Link to this definition">#</a></dt>
 <dd><p>Create a new <code class="docutils literal notranslate"><span class="pre">ProteinEmbedding</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

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

@@ -703,7 +703,7 @@
 <h1>skbio.embedding.ProteinEmbedding.write<a class="headerlink" href="#skbio-embedding-proteinembedding-write" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.embedding.ProteinEmbedding.write">
-<span class="sig-prename descclassname"><span class="pre">ProteinEmbedding.</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">'embed'</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#L669"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.embedding.ProteinEmbedding.write" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">ProteinEmbedding.</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">'embed'</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#L681"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.embedding.ProteinEmbedding.write" title="Link to this definition">#</a></dt>
 <dd><p>Write an instance of <code class="docutils literal notranslate"><span class="pre">ProteinEmbedding</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

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

@@ -703,7 +703,7 @@
 <h1>skbio.embedding.ProteinVector.read<a class="headerlink" href="#skbio-embedding-proteinvector-read" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.embedding.ProteinVector.read">
-<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">ProteinVector.</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">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#L646"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.embedding.ProteinVector.read" title="Link to this definition">#</a></dt>
+<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">ProteinVector.</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">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#L658"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.embedding.ProteinVector.read" title="Link to this definition">#</a></dt>
 <dd><p>Create a new <code class="docutils literal notranslate"><span class="pre">ProteinVector</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

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

@@ -703,7 +703,7 @@
 <h1>skbio.embedding.ProteinVector.write<a class="headerlink" href="#skbio-embedding-proteinvector-write" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.embedding.ProteinVector.write">
-<span class="sig-prename descclassname"><span class="pre">ProteinVector.</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">'embed'</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#L669"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.embedding.ProteinVector.write" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">ProteinVector.</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">'embed'</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#L681"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.embedding.ProteinVector.write" title="Link to this definition">#</a></dt>
 <dd><p>Write an instance of <code class="docutils literal notranslate"><span class="pre">ProteinVector</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

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

@@ -723,7 +723,7 @@
 <h1>skbio.io.registry.Format<a class="headerlink" href="#skbio-io-registry-format" title="Link to this heading">#</a></h1>
 <dl class="py class">
 <dt class="sig sig-object py" id="skbio.io.registry.Format">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">skbio.io.registry.</span></span><span class="sig-name descname"><span class="pre">Format</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">encoding</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">newline</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/io/registry.py#L769"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.io.registry.Format" title="Link to this definition">#</a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">skbio.io.registry.</span></span><span class="sig-name descname"><span class="pre">Format</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">encoding</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">newline</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/io/registry.py#L781"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.io.registry.Format" title="Link to this definition">#</a></dt>
 <dd><p>Defines a format on which readers/writers/sniffer can be registered.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>