Update from scikit-bio/scikit-bio@4baf1db

Author: qiyunzhu

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

@@ -680,7 +680,7 @@
 <h1>skbio.alignment.local_pairwise_align_ssw<a class="headerlink" href="#skbio-alignment-local-pairwise-align-ssw" title="Link to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="skbio.alignment.local_pairwise_align_ssw">
-<span class="sig-prename descclassname"><span class="pre">skbio.alignment.</span></span><span class="sig-name descname"><span class="pre">local_pairwise_align_ssw</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sequence1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sequence2</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/util/_decorator.py#L141"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.alignment.local_pairwise_align_ssw" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">skbio.alignment.</span></span><span class="sig-name descname"><span class="pre">local_pairwise_align_ssw</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sequence1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sequence2</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/alignment/_pairwise.py#L597"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.alignment.local_pairwise_align_ssw" title="Link to this definition">#</a></dt>
 <dd><p>Align query and target sequences with Striped Smith-Waterman.</p>
 <div class="deprecated">
 <p><span class="versionmodified deprecated">Deprecated since version 0.5.8: </span>It will be removed in favor of more general purpose and performant aligners. Additional details at <a class="github reference external" href="https://github.com/scikit-bio/scikit-bio/issues/1814">scikit-bio/scikit-bio#1814</a>.</p>

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

@@ -680,7 +680,7 @@
 <h1>skbio.alignment.make_identity_substitution_matrix<a class="headerlink" href="#skbio-alignment-make-identity-substitution-matrix" title="Link to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="skbio.alignment.make_identity_substitution_matrix">
-<span class="sig-prename descclassname"><span class="pre">skbio.alignment.</span></span><span class="sig-name descname"><span class="pre">make_identity_substitution_matrix</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">match_score</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mismatch_score</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alphabet</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'ACGTU'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/util/_decorator.py#L141"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.alignment.make_identity_substitution_matrix" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">skbio.alignment.</span></span><span class="sig-name descname"><span class="pre">make_identity_substitution_matrix</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">match_score</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mismatch_score</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alphabet</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'ACGTU'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/alignment/_pairwise.py#L703"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.alignment.make_identity_substitution_matrix" title="Link to this definition">#</a></dt>
 <dd><p>Generate substitution matrix where all matches are scored equally.</p>
 <div class="deprecated">
 <p><span class="versionmodified deprecated">Deprecated since version 0.4.0: </span>It has been replaced by the SubstitutionMatrix class. Additional details at: <a class="github reference external" href="https://github.com/scikit-bio/scikit-bio/pull/1913">scikit-bio/scikit-bio#1913</a>.</p>

docs/dev/generated/skbio.diversity.alpha.berger_parker_d.html

@@ -722,7 +722,7 @@
 <h1>skbio.diversity.alpha.berger_parker_d<a class="headerlink" href="#skbio-diversity-alpha-berger-parker-d" title="Link to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="skbio.diversity.alpha.berger_parker_d">
-<span class="sig-prename descclassname"><span class="pre">skbio.diversity.alpha.</span></span><span class="sig-name descname"><span class="pre">berger_parker_d</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">counts</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/diversity/alpha/_base.py#L49"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.diversity.alpha.berger_parker_d" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">skbio.diversity.alpha.</span></span><span class="sig-name descname"><span class="pre">berger_parker_d</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">counts</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/diversity/alpha/_base.py#L70"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.diversity.alpha.berger_parker_d" title="Link to this definition">#</a></dt>
 <dd><p>Calculate Berger-Parker dominance index.</p>
 <p>Berger-Parker dominance index <span class="math notranslate nohighlight">\(d\)</span> is defined as the fraction of the
 sample that belongs to the most abundant taxon:</p>

docs/dev/generated/skbio.diversity.alpha.brillouin_d.html

@@ -722,7 +722,7 @@
 <h1>skbio.diversity.alpha.brillouin_d<a class="headerlink" href="#skbio-diversity-alpha-brillouin-d" title="Link to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="skbio.diversity.alpha.brillouin_d">
-<span class="sig-prename descclassname"><span class="pre">skbio.diversity.alpha.</span></span><span class="sig-name descname"><span class="pre">brillouin_d</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">counts</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/diversity/alpha/_base.py#L49"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.diversity.alpha.brillouin_d" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">skbio.diversity.alpha.</span></span><span class="sig-name descname"><span class="pre">brillouin_d</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">counts</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/diversity/alpha/_base.py#L108"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.diversity.alpha.brillouin_d" title="Link to this definition">#</a></dt>
 <dd><p>Calculate Brillouin’s diversity index.</p>
 <p>Brillouin’s diversity index (<span class="math notranslate nohighlight">\(H_B\)</span>) is defined as:</p>
 <div class="math notranslate nohighlight">

docs/dev/generated/skbio.diversity.alpha.dominance.html

@@ -722,7 +722,7 @@
 <h1>skbio.diversity.alpha.dominance<a class="headerlink" href="#skbio-diversity-alpha-dominance" title="Link to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="skbio.diversity.alpha.dominance">
-<span class="sig-prename descclassname"><span class="pre">skbio.diversity.alpha.</span></span><span class="sig-name descname"><span class="pre">dominance</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">counts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">finite</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/diversity/alpha/_base.py#L49"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.diversity.alpha.dominance" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">skbio.diversity.alpha.</span></span><span class="sig-name descname"><span class="pre">dominance</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">counts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">finite</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/diversity/alpha/_base.py#L145"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.diversity.alpha.dominance" title="Link to this definition">#</a></dt>
 <dd><p>Calculate Simpson’s dominance index.</p>
 <p>Simpson’s dominance index, a.k.a. Simpson’s <span class="math notranslate nohighlight">\(D\)</span>, measures the degree
 of concentration of taxon composition of a sample. It is defined as:</p>

docs/dev/generated/skbio.diversity.alpha.doubles.html

@@ -721,7 +721,7 @@
 <h1>skbio.diversity.alpha.doubles<a class="headerlink" href="#skbio-diversity-alpha-doubles" title="Link to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="skbio.diversity.alpha.doubles">
-<span class="sig-prename descclassname"><span class="pre">skbio.diversity.alpha.</span></span><span class="sig-name descname"><span class="pre">doubles</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">counts</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/diversity/alpha/_base.py#L49"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.diversity.alpha.doubles" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">skbio.diversity.alpha.</span></span><span class="sig-name descname"><span class="pre">doubles</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">counts</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/diversity/alpha/_base.py#L219"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.diversity.alpha.doubles" title="Link to this definition">#</a></dt>
 <dd><p>Calculate number of double-occurrence taxa (doubletons).</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>

docs/dev/generated/skbio.diversity.alpha.esty_ci.html

@@ -722,7 +722,7 @@
 <h1>skbio.diversity.alpha.esty_ci<a class="headerlink" href="#skbio-diversity-alpha-esty-ci" title="Link to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="skbio.diversity.alpha.esty_ci">
-<span class="sig-prename descclassname"><span class="pre">skbio.diversity.alpha.</span></span><span class="sig-name descname"><span class="pre">esty_ci</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">counts</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/diversity/alpha/_base.py#L49"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.diversity.alpha.esty_ci" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">skbio.diversity.alpha.</span></span><span class="sig-name descname"><span class="pre">esty_ci</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">counts</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/diversity/alpha/_base.py#L287"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.diversity.alpha.esty_ci" title="Link to this definition">#</a></dt>
 <dd><p>Calculate Esty’s confidence interval of Good’s coverage estimator.</p>
 <p>Esty’s confidence interval is defined as:</p>
 <div class="math notranslate nohighlight">

docs/dev/generated/skbio.diversity.alpha.fisher_alpha.html

@@ -722,7 +722,7 @@
 <h1>skbio.diversity.alpha.fisher_alpha<a class="headerlink" href="#skbio-diversity-alpha-fisher-alpha" title="Link to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="skbio.diversity.alpha.fisher_alpha">
-<span class="sig-prename descclassname"><span class="pre">skbio.diversity.alpha.</span></span><span class="sig-name descname"><span class="pre">fisher_alpha</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">counts</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/diversity/alpha/_base.py#L49"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.diversity.alpha.fisher_alpha" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">skbio.diversity.alpha.</span></span><span class="sig-name descname"><span class="pre">fisher_alpha</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">counts</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/diversity/alpha/_base.py#L343"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.diversity.alpha.fisher_alpha" title="Link to this definition">#</a></dt>
 <dd><p>Calculate Fisher’s alpha, a metric of diversity.</p>
 <p>Fisher’s alpha is estimated by solving the following equation for
 <span class="math notranslate nohighlight">\(\alpha\)</span>:</p>

docs/dev/generated/skbio.diversity.alpha.goods_coverage.html

@@ -722,7 +722,7 @@
 <h1>skbio.diversity.alpha.goods_coverage<a class="headerlink" href="#skbio-diversity-alpha-goods-coverage" title="Link to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="skbio.diversity.alpha.goods_coverage">
-<span class="sig-prename descclassname"><span class="pre">skbio.diversity.alpha.</span></span><span class="sig-name descname"><span class="pre">goods_coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">counts</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/diversity/alpha/_base.py#L49"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.diversity.alpha.goods_coverage" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">skbio.diversity.alpha.</span></span><span class="sig-name descname"><span class="pre">goods_coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">counts</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/diversity/alpha/_base.py#L413"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.diversity.alpha.goods_coverage" title="Link to this definition">#</a></dt>
 <dd><p>Calculate Good’s coverage estimator.</p>
 <p>Good’s coverage estimator <span class="math notranslate nohighlight">\(C\)</span>, a.k.a. Turing estimator or Good-
 Turing (GT) estimator, is an estimation of the proportion of the

docs/dev/generated/skbio.diversity.alpha.heip_e.html

@@ -722,7 +722,7 @@
 <h1>skbio.diversity.alpha.heip_e<a class="headerlink" href="#skbio-diversity-alpha-heip-e" title="Link to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="skbio.diversity.alpha.heip_e">
-<span class="sig-prename descclassname"><span class="pre">skbio.diversity.alpha.</span></span><span class="sig-name descname"><span class="pre">heip_e</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">counts</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/diversity/alpha/_base.py#L49"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.diversity.alpha.heip_e" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">skbio.diversity.alpha.</span></span><span class="sig-name descname"><span class="pre">heip_e</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">counts</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/diversity/alpha/_base.py#L456"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.diversity.alpha.heip_e" title="Link to this definition">#</a></dt>
 <dd><p>Calculate Heip’s evenness measure.</p>
 <p>Heip’s evenness is defined as:</p>
 <div class="math notranslate nohighlight">