Update from scikit-bio/scikit-bio@1aa4e4b

scikit-bio · Jun 7, 2024 · 9979a77 · 9979a77
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diff --git a/docs/dev/diversity.html b/docs/dev/diversity.html
@@ -907,14 +907,14 @@ <h2>Tutorial<a class="headerlink" href="#tutorial" title="Link to this heading">
 sample using the <code class="docutils literal notranslate"><span class="pre">alpha_diversity</span></code> driver function:</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.diversity</span> <span class="kn">import</span> <span class="n">alpha_diversity</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">adiv_sobs</span> <span class="o">=</span> <span class="n">alpha_diversity</span><span class="p">(</span><span class="s1">&#39;sobs&#39;</span><span class="p">,</span> <span class="n">data</span><span class="p">,</span> <span class="n">ids</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">adiv_sobs</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">adiv_sobs</span> 
 <span class="go">A    5</span>
 <span class="go">B    5</span>
 <span class="go">C    4</span>
 <span class="go">D    4</span>
 <span class="go">E    5</span>
 <span class="go">F    3</span>
-<span class="go">dtype: int64</span>
+<span class="go">dtype: ...</span>
 </pre></div>
 </div>
 <p>Next we’ll compute Faith’s PD on the same samples. Since this is a

diff --git a/docs/dev/generated/skbio.alignment.AlignPath.to_coordinates.html b/docs/dev/generated/skbio.alignment.AlignPath.to_coordinates.html
@@ -738,10 +738,10 @@ <h1>skbio.alignment.AlignPath.to_coordinates<a class="headerlink" href="#skbio-a
 <span class="gp">&gt;&gt;&gt; </span><span class="n">path</span> <span class="o">=</span> <span class="n">AlignPath</span><span class="p">(</span><span class="n">lengths</span><span class="o">=</span><span class="p">[</span><span class="mi">1</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="mi">1</span><span class="p">],</span>
 <span class="gp">... </span>                 <span class="n">states</span><span class="o">=</span><span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">5</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">6</span><span class="p">],</span>
 <span class="gp">... </span>                 <span class="n">starts</span><span class="o">=</span><span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">path</span><span class="o">.</span><span class="n">to_coordinates</span><span class="p">()</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">path</span><span class="o">.</span><span class="n">to_coordinates</span><span class="p">()</span> 
 <span class="go">array([[0, 1, 1, 3, 4],</span>
 <span class="go">       [0, 1, 3, 3, 3],</span>
-<span class="go">       [0, 1, 1, 3, 3]])</span>
+<span class="go">       [0, 1, 1, 3, 3]]...</span>
 </pre></div>
 </div>
 </dd></dl>

diff --git a/docs/dev/generated/skbio.alignment.PairAlignPath.to_coordinates.html b/docs/dev/generated/skbio.alignment.PairAlignPath.to_coordinates.html
@@ -740,10 +740,10 @@ <h1>skbio.alignment.PairAlignPath.to_coordinates<a class="headerlink" href="#skb
 <span class="gp">&gt;&gt;&gt; </span><span class="n">path</span> <span class="o">=</span> <span class="n">AlignPath</span><span class="p">(</span><span class="n">lengths</span><span class="o">=</span><span class="p">[</span><span class="mi">1</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="mi">1</span><span class="p">],</span>
 <span class="gp">... </span>                 <span class="n">states</span><span class="o">=</span><span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">5</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">6</span><span class="p">],</span>
 <span class="gp">... </span>                 <span class="n">starts</span><span class="o">=</span><span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">path</span><span class="o">.</span><span class="n">to_coordinates</span><span class="p">()</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">path</span><span class="o">.</span><span class="n">to_coordinates</span><span class="p">()</span> 
 <span class="go">array([[0, 1, 1, 3, 4],</span>
 <span class="go">       [0, 1, 3, 3, 3],</span>
-<span class="go">       [0, 1, 1, 3, 3]])</span>
+<span class="go">       [0, 1, 1, 3, 3]]...</span>
 </pre></div>
 </div>
 </dd></dl>

diff --git a/docs/dev/generated/skbio.sequence.DNA.complement.html b/docs/dev/generated/skbio.sequence.DNA.complement.html
@@ -827,8 +827,8 @@ <h1>skbio.sequence.DNA.complement<a class="headerlink" href="#skbio-sequence-dna
 <span class="go">    GC-content: 16.67%</span>
 <span class="go">-----------------------------</span>
 <span class="go">0 AATGAA</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">rc</span><span class="o">.</span><span class="n">positional_metadata</span><span class="p">[</span><span class="s1">&#39;quality&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">values</span>
-<span class="go">array([5, 4, 3, 2, 1, 0])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">rc</span><span class="o">.</span><span class="n">positional_metadata</span><span class="p">[</span><span class="s1">&#39;quality&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">values</span> 
+<span class="go">array([5, 4, 3, 2, 1, 0]...</span>
 </pre></div>
 </div>
 </dd></dl>

diff --git a/docs/dev/generated/skbio.sequence.DNA.reverse_complement.html b/docs/dev/generated/skbio.sequence.DNA.reverse_complement.html
@@ -796,8 +796,8 @@ <h1>skbio.sequence.DNA.reverse_complement<a class="headerlink" href="#skbio-sequ
 <span class="go">    GC-content: 16.67%</span>
 <span class="go">-----------------------------</span>
 <span class="go">0 AATGAA</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">seq</span><span class="o">.</span><span class="n">positional_metadata</span><span class="p">[</span><span class="s1">&#39;quality&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">values</span>
-<span class="go">array([5, 4, 3, 2, 1, 0])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">seq</span><span class="o">.</span><span class="n">positional_metadata</span><span class="p">[</span><span class="s1">&#39;quality&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">values</span> 
+<span class="go">array([5, 4, 3, 2, 1, 0]...</span>
 </pre></div>
 </div>
 </dd></dl>

diff --git a/docs/dev/generated/skbio.sequence.RNA.complement.html b/docs/dev/generated/skbio.sequence.RNA.complement.html
@@ -827,8 +827,8 @@ <h1>skbio.sequence.RNA.complement<a class="headerlink" href="#skbio-sequence-rna
 <span class="go">    GC-content: 16.67%</span>
 <span class="go">-----------------------------</span>
 <span class="go">0 AATGAA</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">rc</span><span class="o">.</span><span class="n">positional_metadata</span><span class="p">[</span><span class="s1">&#39;quality&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">values</span>
-<span class="go">array([5, 4, 3, 2, 1, 0])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">rc</span><span class="o">.</span><span class="n">positional_metadata</span><span class="p">[</span><span class="s1">&#39;quality&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">values</span> 
+<span class="go">array([5, 4, 3, 2, 1, 0]...</span>
 </pre></div>
 </div>
 </dd></dl>

diff --git a/docs/dev/generated/skbio.sequence.RNA.reverse_complement.html b/docs/dev/generated/skbio.sequence.RNA.reverse_complement.html
@@ -796,8 +796,8 @@ <h1>skbio.sequence.RNA.reverse_complement<a class="headerlink" href="#skbio-sequ
 <span class="go">    GC-content: 16.67%</span>
 <span class="go">-----------------------------</span>
 <span class="go">0 AATGAA</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">seq</span><span class="o">.</span><span class="n">positional_metadata</span><span class="p">[</span><span class="s1">&#39;quality&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">values</span>
-<span class="go">array([5, 4, 3, 2, 1, 0])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">seq</span><span class="o">.</span><span class="n">positional_metadata</span><span class="p">[</span><span class="s1">&#39;quality&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">values</span> 
+<span class="go">array([5, 4, 3, 2, 1, 0]...</span>
 </pre></div>
 </div>
 </dd></dl>

diff --git a/docs/dev/generated/skbio.stats.composition.ancom.html b/docs/dev/generated/skbio.stats.composition.ancom.html
@@ -889,15 +889,15 @@ <h1>skbio.stats.composition.ancom<a class="headerlink" href="#skbio-stats-compos
 results, and the second contains the percentile abundance data for each
 feature in each group.</p>
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">ancom_df</span><span class="p">,</span> <span class="n">percentile_df</span> <span class="o">=</span> <span class="n">ancom</span><span class="p">(</span><span class="n">table</span><span class="p">,</span> <span class="n">grouping</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">ancom_df</span><span class="p">[</span><span class="s1">&#39;W&#39;</span><span class="p">]</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">ancom_df</span><span class="p">[</span><span class="s1">&#39;W&#39;</span><span class="p">]</span> 
 <span class="go">b1    0</span>
 <span class="go">b2    4</span>
 <span class="go">b3    0</span>
 <span class="go">b4    1</span>
 <span class="go">b5    1</span>
 <span class="go">b6    0</span>
 <span class="go">b7    1</span>
-<span class="go">Name: W, dtype: int64</span>
+<span class="go">Name: W, dtype: ...</span>
 </pre></div>
 </div>
 <p>The <em>W</em>-statistic is the number of features that a single feature is tested

diff --git a/docs/dev/generated/skbio.stats.power.html b/docs/dev/generated/skbio.stats.power.html
@@ -764,8 +764,8 @@ <h2>Examples<a class="headerlink" href="#examples" title="Link to this heading">
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></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">20</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">ind</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">randint</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">20</span><span class="p">,</span> <span class="mi">15</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">ind</span>
-<span class="go">array([ 3, 15,  9, 11,  7,  2,  0,  8, 19, 16,  6,  6, 16,  9,  5])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">ind</span> 
+<span class="go">array([ 3, 15,  9, 11,  7,  2,  0,  8, 19, 16,  6,  6, 16,  9,  5]...</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">dep</span> <span class="o">=</span> <span class="p">(</span><span class="mi">3</span> <span class="o">*</span> <span class="n">ind</span> <span class="o">+</span> <span class="mi">5</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">randn</span><span class="p">(</span><span class="mi">15</span><span class="p">)</span> <span class="o">*</span> <span class="mi">5</span><span class="p">)</span><span class="o">.</span><span class="n">round</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">dep</span>
 <span class="go">array([ 15.617,  47.533,  28.04 ,  33.788,  19.602,  12.229,   4.779,</span>

diff --git a/docs/dev/generated/skbio.tree.TreeNode.to_array.html b/docs/dev/generated/skbio.tree.TreeNode.to_array.html
@@ -810,11 +810,11 @@ <h1>skbio.tree.TreeNode.to_array<a class="headerlink" href="#skbio-tree-treenode
 <span class="gp">&gt;&gt;&gt; </span><span class="n">res</span> <span class="o">=</span> <span class="n">t</span><span class="o">.</span><span class="n">to_array</span><span class="p">()</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="nb">sorted</span><span class="p">(</span><span class="n">res</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
 <span class="go">[&#39;child_index&#39;, &#39;id&#39;, &#39;id_index&#39;, &#39;length&#39;, &#39;name&#39;]</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">res</span><span class="p">[</span><span class="s1">&#39;child_index&#39;</span><span class="p">]</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">res</span><span class="p">[</span><span class="s1">&#39;child_index&#39;</span><span class="p">]</span> 
 <span class="go">array([[4, 0, 2],</span>
 <span class="go">       [5, 3, 3],</span>
 <span class="go">       [6, 4, 5],</span>
-<span class="go">       [7, 6, 6]])</span>
+<span class="go">       [7, 6, 6]]...</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">res</span><span class="p">[</span><span class="s1">&#39;id_index&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
 <span class="gp">... </span>    <span class="nb">print</span><span class="p">(</span><span class="n">k</span><span class="p">,</span> <span class="n">v</span><span class="p">)</span>
 <span class="gp">...</span>

diff --git a/docs/dev/searchindex.js b/docs/dev/searchindex.js