Update from scikit-bio/scikit-bio@9764be1

Author: qiyunzhu

docs/dev/config.html

@@ -683,8 +683,8 @@ <h2>Functions<a class="headerlink" href="#functions" title="Link to this heading
 </table>
 </div>
 </section>
-<section id="configuraton-options">
-<h2>Configuraton options<a class="headerlink" href="#configuraton-options" title="Link to this heading">#</a></h2>
+<section id="id1">
+<h2>Configuration options<a class="headerlink" href="#id1" title="Link to this heading">#</a></h2>
 <p>At present, only one configuration option is available:</p>
 <dl>
 <dt><strong>table_output</strong><span class="classifier"><em>{“pandas”, “numpy”, “polars”}, default=”pandas”</em></span></dt><dd><p>The preferred output format of tables. See <a class="reference internal" href="table.html#table-output"><span class="std std-ref">details</span></a>.</p>
@@ -741,7 +741,7 @@ <h2>Configuraton options<a class="headerlink" href="#configuraton-options" title
   <nav class="bd-toc-nav page-toc" aria-labelledby="pst-page-navigation-heading-2">
     <ul class="visible nav section-nav flex-column">
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#functions">Functions</a></li>
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#configuraton-options">Configuraton options</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#id1">Configuration options</a></li>
 </ul>
   </nav></div>
 

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

@@ -1175,7 +1175,7 @@ <h1>skbio.alignment.TabularMSA<a class="headerlink" href="#skbio-alignment-tabul
 </div>
 <p>Here we sliced the first axis by a boolean vector, but then restricted
 the columns to a single column. Because the second axis was given a
-nonscalar we still recieve an MSA even though only one column is
+nonscalar we still receive an MSA even though only one column is
 present.</p>
 </dd></dl>
 
@@ -1411,7 +1411,7 @@ <h1>skbio.alignment.TabularMSA<a class="headerlink" href="#skbio-alignment-tabul
 </div>
 <p>Here we sliced the first axis by a boolean vector, but then restricted
 the columns to a single column. Because the second axis was given a
-nonscalar we still recieve an MSA even though only one column is
+nonscalar we still receive an MSA even though only one column is
 present.</p>
 <p>Duplicate labels can be an unfortunate reality in the real world,
 however <cite>loc</cite> is capable of handling this:</p>

docs/dev/generated/skbio.alignment.global_pairwise_align.html

@@ -701,10 +701,10 @@ <h1>skbio.alignment.global_pairwise_align<a class="headerlink" href="#skbio-alig
 </dd>
 <dt><strong>seq2</strong><span class="classifier">GrammaredSequence or TabularMSA</span></dt><dd><p>The second unaligned sequence(s).</p>
 </dd>
-<dt><strong>gap_open_penalty</strong><span class="classifier">int or float</span></dt><dd><p>Penalty for opening a gap (this is substracted from previous best
+<dt><strong>gap_open_penalty</strong><span class="classifier">int or float</span></dt><dd><p>Penalty for opening a gap (this is subtracted from previous best
 alignment score, so is typically positive).</p>
 </dd>
-<dt><strong>gap_extend_penalty</strong><span class="classifier">int or float</span></dt><dd><p>Penalty for extending a gap (this is substracted from previous best
+<dt><strong>gap_extend_penalty</strong><span class="classifier">int or float</span></dt><dd><p>Penalty for extending a gap (this is subtracted from previous best
 alignment score, so is typically positive).</p>
 </dd>
 <dt><strong>substitution_matrix: 2D dict (or similar)</strong></dt><dd><p>Lookup for substitution scores (these values are added to the

docs/dev/generated/skbio.alignment.global_pairwise_align_nucleotide.html

@@ -701,10 +701,10 @@ <h1>skbio.alignment.global_pairwise_align_nucleotide<a class="headerlink" href="
 </dd>
 <dt><strong>seq2</strong><span class="classifier">DNA, RNA, or TabularMSA[DNA|RNA]</span></dt><dd><p>The second unaligned sequence(s).</p>
 </dd>
-<dt><strong>gap_open_penalty</strong><span class="classifier">int or float, optional</span></dt><dd><p>Penalty for opening a gap (this is substracted from previous best
+<dt><strong>gap_open_penalty</strong><span class="classifier">int or float, optional</span></dt><dd><p>Penalty for opening a gap (this is subtracted from previous best
 alignment score, so is typically positive).</p>
 </dd>
-<dt><strong>gap_extend_penalty</strong><span class="classifier">int or float, optional</span></dt><dd><p>Penalty for extending a gap (this is substracted from previous best
+<dt><strong>gap_extend_penalty</strong><span class="classifier">int or float, optional</span></dt><dd><p>Penalty for extending a gap (this is subtracted from previous best
 alignment score, so is typically positive).</p>
 </dd>
 <dt><strong>match_score</strong><span class="classifier">int or float, optional</span></dt><dd><p>The score to add for a match between a pair of bases (this is added

docs/dev/generated/skbio.alignment.global_pairwise_align_protein.html

@@ -701,10 +701,10 @@ <h1>skbio.alignment.global_pairwise_align_protein<a class="headerlink" href="#sk
 </dd>
 <dt><strong>seq2</strong><span class="classifier">Protein or TabularMSA[Protein]</span></dt><dd><p>The second unaligned sequence(s).</p>
 </dd>
-<dt><strong>gap_open_penalty</strong><span class="classifier">int or float, optional</span></dt><dd><p>Penalty for opening a gap (this is substracted from previous best
+<dt><strong>gap_open_penalty</strong><span class="classifier">int or float, optional</span></dt><dd><p>Penalty for opening a gap (this is subtracted from previous best
 alignment score, so is typically positive).</p>
 </dd>
-<dt><strong>gap_extend_penalty</strong><span class="classifier">int or float, optional</span></dt><dd><p>Penalty for extending a gap (this is substracted from previous best
+<dt><strong>gap_extend_penalty</strong><span class="classifier">int or float, optional</span></dt><dd><p>Penalty for extending a gap (this is subtracted from previous best
 alignment score, so is typically positive).</p>
 </dd>
 <dt><strong>substitution_matrix: 2D dict (or similar), optional</strong></dt><dd><p>Lookup for substitution scores (these values are added to the

docs/dev/generated/skbio.alignment.local_pairwise_align.html

@@ -701,10 +701,10 @@ <h1>skbio.alignment.local_pairwise_align<a class="headerlink" href="#skbio-align
 </dd>
 <dt><strong>seq2</strong><span class="classifier">GrammaredSequence</span></dt><dd><p>The second unaligned sequence.</p>
 </dd>
-<dt><strong>gap_open_penalty</strong><span class="classifier">int or float</span></dt><dd><p>Penalty for opening a gap (this is substracted from previous best
+<dt><strong>gap_open_penalty</strong><span class="classifier">int or float</span></dt><dd><p>Penalty for opening a gap (this is subtracted from previous best
 alignment score, so is typically positive).</p>
 </dd>
-<dt><strong>gap_extend_penalty</strong><span class="classifier">int or float</span></dt><dd><p>Penalty for extending a gap (this is substracted from previous best
+<dt><strong>gap_extend_penalty</strong><span class="classifier">int or float</span></dt><dd><p>Penalty for extending a gap (this is subtracted from previous best
 alignment score, so is typically positive).</p>
 </dd>
 <dt><strong>substitution_matrix: 2D dict (or similar)</strong></dt><dd><p>Lookup for substitution scores (these values are added to the

docs/dev/generated/skbio.alignment.local_pairwise_align_nucleotide.html

@@ -701,10 +701,10 @@ <h1>skbio.alignment.local_pairwise_align_nucleotide<a class="headerlink" href="#
 </dd>
 <dt><strong>seq2</strong><span class="classifier">DNA or RNA</span></dt><dd><p>The second unaligned sequence.</p>
 </dd>
-<dt><strong>gap_open_penalty</strong><span class="classifier">int or float, optional</span></dt><dd><p>Penalty for opening a gap (this is substracted from previous best
+<dt><strong>gap_open_penalty</strong><span class="classifier">int or float, optional</span></dt><dd><p>Penalty for opening a gap (this is subtracted from previous best
 alignment score, so is typically positive).</p>
 </dd>
-<dt><strong>gap_extend_penalty</strong><span class="classifier">int or float, optional</span></dt><dd><p>Penalty for extending a gap (this is substracted from previous best
+<dt><strong>gap_extend_penalty</strong><span class="classifier">int or float, optional</span></dt><dd><p>Penalty for extending a gap (this is subtracted from previous best
 alignment score, so is typically positive).</p>
 </dd>
 <dt><strong>match_score</strong><span class="classifier">int or float, optional</span></dt><dd><p>The score to add for a match between a pair of bases (this is added

docs/dev/generated/skbio.alignment.local_pairwise_align_protein.html

@@ -701,10 +701,10 @@ <h1>skbio.alignment.local_pairwise_align_protein<a class="headerlink" href="#skb
 </dd>
 <dt><strong>seq2</strong><span class="classifier">Protein</span></dt><dd><p>The second unaligned sequence.</p>
 </dd>
-<dt><strong>gap_open_penalty</strong><span class="classifier">int or float, optional</span></dt><dd><p>Penalty for opening a gap (this is substracted from previous best
+<dt><strong>gap_open_penalty</strong><span class="classifier">int or float, optional</span></dt><dd><p>Penalty for opening a gap (this is subtracted from previous best
 alignment score, so is typically positive).</p>
 </dd>
-<dt><strong>gap_extend_penalty</strong><span class="classifier">int or float, optional</span></dt><dd><p>Penalty for extending a gap (this is substracted from previous best
+<dt><strong>gap_extend_penalty</strong><span class="classifier">int or float, optional</span></dt><dd><p>Penalty for extending a gap (this is subtracted from previous best
 alignment score, so is typically positive).</p>
 </dd>
 <dt><strong>substitution_matrix: 2D dict (or similar), optional</strong></dt><dd><p>Lookup for substitution scores (these values are added to the

docs/dev/generated/skbio.io.format.embl.html

@@ -715,7 +715,7 @@ <h2>Feature Level Products<a class="headerlink" href="#feature-level-products" t
 ENA records, with each flatfile representing a single feature”</em>.
 While only the sequence of the feature is included in such entries, features
 are derived from the parent entry, and can’t be applied as interval metadata.
-For such reason, interval metatdata are ignored from Feature-level products,
+For such reason, interval metadata are ignored from Feature-level products,
 as they will be ignored by subsetting a generic Sequence object.</p>
 <section id="format-support">
 <h3>Format Support<a class="headerlink" href="#format-support" title="Link to this heading">#</a></h3>

docs/dev/generated/skbio.io.format.fasta.html

@@ -712,7 +712,7 @@
 </pre></div>
 </div>
 <p>The QUAL file format is an additional format related to FASTA. A FASTA file is
-sometimes accompanied by a QUAL file, particuarly when the FASTA file contains
+sometimes accompanied by a QUAL file, particularly when the FASTA file contains
 sequences generated on a high-throughput sequencing instrument. QUAL files
 store a Phred quality score (nonnegative integer) for each base in a sequence
 stored in FASTA format (see <a class="reference internal" href="#rc6adbf0d8a87-4" id="id4">[4]</a> for more details). scikit-bio supports reading
@@ -802,7 +802,7 @@ <h4>Sequence Header<a class="headerlink" href="#sequence-header" title="Link to
 <p class="admonition-title">Note</p>
 <p>When reading a FASTA-formatted file, the sequence ID and description
 are stored in the sequence <cite>metadata</cite> attribute, under the <cite>‘id’</cite> and
-<cite>‘description’</cite> keys, repectively. Both are optional. Each will be
+<cite>‘description’</cite> keys, respectively. Both are optional. Each will be
 represented as the empty string (<code class="docutils literal notranslate"><span class="pre">''</span></code>) in <cite>metadata</cite> if it is not present
 in the header.</p>
 <p>When writing a FASTA-formatted file, sequence <cite>metadata</cite> identified by keys
@@ -881,7 +881,7 @@ <h3>QUAL Format<a class="headerlink" href="#qual-format" title="Link to this hea
 in the same order in both files (i.e., each FASTA and QUAL record must have
 the same ID and description after being parsed). In addition to having the
 same order, the number of FASTA records must match the number of QUAL
-records (i.e., missing or additonal records are not allowed). scikit-bio
+records (i.e., missing or additional records are not allowed). scikit-bio
 also requires that the number of quality scores match the number of bases in
 the corresponding sequence.</p>
 <p>When writing FASTA and QUAL files, scikit-bio will maintain the same