Update from scikit-bio/scikit-bio@bfabb46

Author: qiyunzhu

docs/dev/_sources/generated/skbio.metadata.IntervalMetadata.rst.txt

@@ -285,6 +285,7 @@ skbio.metadata.IntervalMetadata
       ~IntervalMetadata.__deepcopy__
       ~IntervalMetadata.__eq__
       ~IntervalMetadata.__ne__
+      ~IntervalMetadata.__str__
 
 
 
@@ -297,7 +298,6 @@ skbio.metadata.IntervalMetadata
       ~IntervalMetadata.__gt__
       ~IntervalMetadata.__le__
       ~IntervalMetadata.__lt__
-      ~IntervalMetadata.__str__
 
 
 
@@ -342,4 +342,8 @@ skbio.metadata.IntervalMetadata
    .. automethod:: IntervalMetadata.__ne__
 
 
+   
+   .. automethod:: IntervalMetadata.__str__
+   
+   
 

docs/dev/_sources/generated/skbio.metadata.SampleMetadata.rst.txt

@@ -303,6 +303,7 @@ skbio.metadata.SampleMetadata
 
       ~SampleMetadata.__eq__
       ~SampleMetadata.__ne__
+      ~SampleMetadata.__str__
 
 
 
@@ -315,7 +316,6 @@ skbio.metadata.SampleMetadata
       ~SampleMetadata.__gt__
       ~SampleMetadata.__le__
       ~SampleMetadata.__lt__
-      ~SampleMetadata.__str__
 
 
 
@@ -348,4 +348,8 @@ skbio.metadata.SampleMetadata
    .. automethod:: SampleMetadata.__ne__
 
 
+   
+   .. automethod:: SampleMetadata.__str__
+   
+   
 

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

@@ -711,7 +711,7 @@
 <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/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>
+<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#L20"><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

@@ -711,7 +711,7 @@
 <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/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>
+<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#L80"><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

@@ -691,7 +691,7 @@
 <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/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>
+<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#L20"><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

@@ -691,7 +691,7 @@
 <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/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>
+<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#L80"><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.html

@@ -710,7 +710,7 @@
 <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="k"><span class="pre">class</span></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#L667"><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="k"><span class="pre">class</span></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#L680"><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>

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

@@ -713,7 +713,7 @@
 <h1>skbio.io.registry.Format.reader<a class="headerlink" href="#skbio-io-registry-format-reader" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.io.registry.Format.reader">
-<span class="sig-prename descclassname"><span class="pre">Format.</span></span><span class="sig-name descname"><span class="pre">reader</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">override</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/io/registry.py#L825"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.io.registry.Format.reader" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">Format.</span></span><span class="sig-name descname"><span class="pre">reader</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">override</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/io/registry.py#L838"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.io.registry.Format.reader" title="Link to this definition">#</a></dt>
 <dd><p>Decorate a function to act as the reader for a class in this format.</p>
 <p>The function should take an argument which will be an implementation
 of either <a class="reference external" href="https://docs.python.org/3/library/io.html#io.TextIOBase" title="(in Python v3.14)"><code class="xref py py-class docutils literal notranslate"><span class="pre">io.TextIOBase</span></code></a> or <a class="reference external" href="https://docs.python.org/3/library/io.html#io.BufferedReader" title="(in Python v3.14)"><code class="xref py py-class docutils literal notranslate"><span class="pre">io.BufferedReader</span></code></a>
@@ -755,8 +755,11 @@ <h1>skbio.io.registry.Format.reader<a class="headerlink" href="#skbio-io-registr
 <span class="gp">... </span>        <span class="bp">self</span><span class="o">.</span><span class="n">content</span> <span class="o">=</span> <span class="n">content</span>
 <span class="gp">...</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="nd">@myformat</span><span class="o">.</span><span class="n">reader</span><span class="p">(</span><span class="n">MyObject</span><span class="p">)</span>
-<span class="gp">... </span><span class="k">def</span><span class="w"> </span><span class="nf">myformat_reader</span><span class="p">(</span><span class="n">fh</span><span class="p">):</span>
-<span class="gp">... </span>    <span class="k">return</span> <span class="n">MyObject</span><span class="p">(</span><span class="n">fh</span><span class="o">.</span><span class="n">readlines</span><span class="p">()[</span><span class="mi">1</span><span class="p">:])</span>
+<span class="gp">... </span><span class="k">def</span><span class="w"> </span><span class="nf">myformat_reader</span><span class="p">(</span><span class="n">fh</span><span class="p">,</span> <span class="bp">cls</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+<span class="gp">... </span>    <span class="c1"># These lines enable any subclass on your class to inherit this reader!</span>
+<span class="gp">... </span>    <span class="k">if</span> <span class="bp">cls</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+<span class="gp">... </span>        <span class="bp">cls</span> <span class="o">=</span> <span class="n">MyObject</span>
+<span class="gp">... </span>    <span class="k">return</span> <span class="bp">cls</span><span class="p">(</span><span class="n">fh</span><span class="o">.</span><span class="n">readlines</span><span class="p">()[</span><span class="mi">1</span><span class="p">:])</span>
 <span class="gp">...</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">MyObject</span><span class="o">.</span><span class="n">read</span><span class="p">([</span><span class="s2">&quot;myformat2</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">,</span> <span class="s2">&quot;some content here!</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">],</span>
 <span class="gp">... </span>              <span class="nb">format</span><span class="o">=</span><span class="s1">&#39;myformat&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">content</span>