Update from scikit-bio/scikit-bio@e641751

Author: mataton

docs/dev/.buildinfo

@@ -903,10 +903,10 @@ <h2>Coverage metrics<a class="headerlink" href="#coverage-metrics" title="Link t
 <tr class="row-even"><td><p><a class="reference internal" href="skbio.diversity.alpha.goods_coverage.html#skbio.diversity.alpha.goods_coverage" title="skbio.diversity.alpha.goods_coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">goods_coverage</span></code></a>(counts)</p></td>
 <td><p>Calculate Good's coverage estimator.</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="skbio.diversity.alpha.lladser_ci.html#skbio.diversity.alpha.lladser_ci" title="skbio.diversity.alpha.lladser_ci"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lladser_ci</span></code></a>(counts, r[, alpha, f, ci_type])</p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="skbio.diversity.alpha.lladser_ci.html#skbio.diversity.alpha.lladser_ci" title="skbio.diversity.alpha.lladser_ci"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lladser_ci</span></code></a>(counts, r[, alpha, f, ci_type, seed])</p></td>
 <td><p>Calculate single CI of the conditional uncovered probability.</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="skbio.diversity.alpha.lladser_pe.html#skbio.diversity.alpha.lladser_pe" title="skbio.diversity.alpha.lladser_pe"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lladser_pe</span></code></a>(counts[, r])</p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="skbio.diversity.alpha.lladser_pe.html#skbio.diversity.alpha.lladser_pe" title="skbio.diversity.alpha.lladser_pe"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lladser_pe</span></code></a>(counts[, r, seed])</p></td>
 <td><p>Calculate single point estimate of conditional uncovered probability.</p></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="skbio.diversity.alpha.robbins.html#skbio.diversity.alpha.robbins" title="skbio.diversity.alpha.robbins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">robbins</span></code></a>(counts)</p></td>

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

@@ -740,11 +740,11 @@
 <h1>skbio.diversity.alpha.lladser_ci<a class="headerlink" href="#skbio-diversity-alpha-lladser-ci" title="Link to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="skbio.diversity.alpha.lladser_ci">
-<span class="sig-prename descclassname"><span class="pre">skbio.diversity.alpha.</span></span><span class="sig-name descname"><span class="pre">lladser_ci</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">r</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alpha</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.95</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">f</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ci_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'ULCL'</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/_lladser.py#L60"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.diversity.alpha.lladser_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">lladser_ci</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">r</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alpha</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.95</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">f</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ci_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'ULCL'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seed</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/diversity/alpha/_lladser.py#L66"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.diversity.alpha.lladser_ci" title="Link to this definition">#</a></dt>
 <dd><p>Calculate single CI of the conditional uncovered probability.</p>
-<dl class="field-list simple">
+<dl class="field-list">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><dl class="simple">
+<dd class="field-odd"><dl>
 <dt><strong>counts</strong><span class="classifier">1-D array_like, int</span></dt><dd><p>Vector of counts.</p>
 </dd>
 <dt><strong>r</strong><span class="classifier">int</span></dt><dd><p>Number of new colors that are required for the next prediction.</p>
@@ -758,6 +758,11 @@ <h1>skbio.diversity.alpha.lladser_ci<a class="headerlink" href="#skbio-diversity
 conservative upper bound. If <code class="docutils literal notranslate"><span class="pre">'U'</span></code>, upper bound only, lower bound
 fixed to 0.0. If <code class="docutils literal notranslate"><span class="pre">'L'</span></code>, lower bound only, upper bound fixed to 1.0.</p>
 </dd>
+<dt><strong>seed</strong><span class="classifier">int or np.random.Generator, optional</span></dt><dd><p>A user-provided random seed or random generator instance.</p>
+<div class="versionadded">
+<p><span class="versionmodified added">Added in version 0.6.3.</span></p>
+</div>
+</dd>
 </dl>
 </dd>
 <dt class="field-even">Returns<span class="colon">:</span></dt>

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

@@ -740,15 +740,20 @@
 <h1>skbio.diversity.alpha.lladser_pe<a class="headerlink" href="#skbio-diversity-alpha-lladser-pe" title="Link to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="skbio.diversity.alpha.lladser_pe">
-<span class="sig-prename descclassname"><span class="pre">skbio.diversity.alpha.</span></span><span class="sig-name descname"><span class="pre">lladser_pe</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">r</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</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/_lladser.py#L14"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.diversity.alpha.lladser_pe" 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">lladser_pe</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">r</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seed</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/diversity/alpha/_lladser.py#L15"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.diversity.alpha.lladser_pe" title="Link to this definition">#</a></dt>
 <dd><p>Calculate single point estimate of conditional uncovered probability.</p>
-<dl class="field-list simple">
+<dl class="field-list">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><dl class="simple">
+<dd class="field-odd"><dl>
 <dt><strong>counts</strong><span class="classifier">1-D array_like, int</span></dt><dd><p>Vector of counts.</p>
 </dd>
 <dt><strong>r</strong><span class="classifier">int, optional</span></dt><dd><p>Number of new colors that are required for the next prediction.</p>
 </dd>
+<dt><strong>seed</strong><span class="classifier">int or np.random.Generator, optional</span></dt><dd><p>A user-provided random seed or random generator instance.</p>
+<div class="versionadded">
+<p><span class="versionmodified added">Added in version 0.6.3.</span></p>
+</div>
+</dd>
 </dl>
 </dd>
 <dt class="field-even">Returns<span class="colon">:</span></dt>

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

@@ -698,15 +698,15 @@
 <h1>skbio.stats.isubsample<a class="headerlink" href="#skbio-stats-isubsample" title="Link to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="skbio.stats.isubsample">
-<span class="sig-prename descclassname"><span class="pre">skbio.stats.</span></span><span class="sig-name descname"><span class="pre">isubsample</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">items</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">maximum</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">minimum</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">buf_size</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1000</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bin_f</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/stats/_subsample.py#L21"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.isubsample" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">skbio.stats.</span></span><span class="sig-name descname"><span class="pre">isubsample</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">items</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">maximum</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">minimum</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">buf_size</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1000</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bin_f</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">seed</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/stats/_subsample.py#L21"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.stats.isubsample" title="Link to this definition">#</a></dt>
 <dd><p>Randomly subsample items from bins, without replacement.</p>
 <p>Randomly subsample items without replacement from an unknown number of
 input items, that may fall into an unknown number of bins. This method is
 intended for data that either a) cannot fit into memory or b) subsampling
 collections of arbitrary datatypes.</p>
-<dl class="field-list simple">
+<dl class="field-list">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><dl class="simple">
+<dd class="field-odd"><dl>
 <dt><strong>items</strong><span class="classifier">Iterable</span></dt><dd><p>The items to evaluate.</p>
 </dd>
 <dt><strong>maximum</strong><span class="classifier">unsigned int</span></dt><dd><p>The maximum number of items per bin.</p>
@@ -726,6 +726,11 @@ <h1>skbio.stats.isubsample<a class="headerlink" href="#skbio-stats-isubsample" t
 return a hashable value indicating the bin that that entry should be
 placed in.</p>
 </dd>
+<dt><strong>seed</strong><span class="classifier">int or np.random.Generator, optional</span></dt><dd><p>A user-provided random seed or random generator instance.</p>
+<div class="versionadded">
+<p><span class="versionmodified added">Added in version 0.6.3.</span></p>
+</div>
+</dd>
 </dl>
 </dd>
 <dt class="field-even">Returns<span class="colon">:</span></dt>
@@ -760,32 +765,30 @@ <h1>skbio.stats.isubsample<a class="headerlink" href="#skbio-stats-isubsample" t
 <p>Randomly keep up to 2 sequences per sample from a set of demultiplexed
 sequences:</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="nn">skbio.stats</span> <span class="kn">import</span> <span class="n">isubsample</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">seed</span><span class="p">(</span><span class="mi">123</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">seqs</span> <span class="o">=</span> <span class="p">[(</span><span class="s1">&#39;sampleA&#39;</span><span class="p">,</span> <span class="s1">&#39;AATTGG&#39;</span><span class="p">),</span>
 <span class="gp">... </span>        <span class="p">(</span><span class="s1">&#39;sampleB&#39;</span><span class="p">,</span> <span class="s1">&#39;ATATATAT&#39;</span><span class="p">),</span>
 <span class="gp">... </span>        <span class="p">(</span><span class="s1">&#39;sampleC&#39;</span><span class="p">,</span> <span class="s1">&#39;ATGGCC&#39;</span><span class="p">),</span>
 <span class="gp">... </span>        <span class="p">(</span><span class="s1">&#39;sampleB&#39;</span><span class="p">,</span> <span class="s1">&#39;ATGGCT&#39;</span><span class="p">),</span>
 <span class="gp">... </span>        <span class="p">(</span><span class="s1">&#39;sampleB&#39;</span><span class="p">,</span> <span class="s1">&#39;ATGGCG&#39;</span><span class="p">),</span>
 <span class="gp">... </span>        <span class="p">(</span><span class="s1">&#39;sampleA&#39;</span><span class="p">,</span> <span class="s1">&#39;ATGGCA&#39;</span><span class="p">)]</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">bin_f</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">item</span><span class="p">:</span> <span class="n">item</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="k">for</span> <span class="n">bin_</span><span class="p">,</span> <span class="n">item</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">isubsample</span><span class="p">(</span><span class="n">seqs</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="n">bin_f</span><span class="o">=</span><span class="n">bin_f</span><span class="p">)):</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="k">for</span> <span class="n">bin_</span><span class="p">,</span> <span class="n">item</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">isubsample</span><span class="p">(</span><span class="n">seqs</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="n">bin_f</span><span class="o">=</span><span class="n">bin_f</span><span class="p">,</span> <span class="n">seed</span><span class="o">=</span><span class="mi">123</span><span class="p">)):</span>
 <span class="gp">... </span>    <span class="nb">print</span><span class="p">(</span><span class="n">bin_</span><span class="p">,</span> <span class="n">item</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
 <span class="go">sampleA AATTGG</span>
 <span class="go">sampleA ATGGCA</span>
-<span class="go">sampleB ATATATAT</span>
 <span class="go">sampleB ATGGCG</span>
+<span class="go">sampleB ATGGCT</span>
 <span class="go">sampleC ATGGCC</span>
 </pre></div>
 </div>
 <p>Now, let’s set the minimum to 2:</p>
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">bin_f</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">item</span><span class="p">:</span> <span class="n">item</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="k">for</span> <span class="n">bin_</span><span class="p">,</span> <span class="n">item</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">isubsample</span><span class="p">(</span><span class="n">seqs</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="n">bin_f</span><span class="o">=</span><span class="n">bin_f</span><span class="p">)):</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="k">for</span> <span class="n">bin_</span><span class="p">,</span> <span class="n">item</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">isubsample</span><span class="p">(</span><span class="n">seqs</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="n">bin_f</span><span class="o">=</span><span class="n">bin_f</span><span class="p">,</span> <span class="n">seed</span><span class="o">=</span><span class="mi">123</span><span class="p">)):</span>
 <span class="gp">... </span>    <span class="nb">print</span><span class="p">(</span><span class="n">bin_</span><span class="p">,</span> <span class="n">item</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
 <span class="go">sampleA AATTGG</span>
 <span class="go">sampleA ATGGCA</span>
-<span class="go">sampleB ATATATAT</span>
 <span class="go">sampleB ATGGCG</span>
+<span class="go">sampleB ATGGCT</span>
 </pre></div>
 </div>
 </dd></dl>