Update from scikit-bio/scikit-bio@74e1e14

Author: mataton

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

@@ -736,10 +736,10 @@ <h2>Format Specification<a class="headerlink" href="#format-specification" title
 <cite>matrix</cite> are all zeros.</p>
 <p>The dissimilarity between <cite>ids[i]</cite> and <cite>ids[j]</cite> is interpreted
 to be the value at <cite>matrix[i, j]</cite>. <cite>i</cite> and <cite>j</cite> are integer indices.</p>
-<p>Required attributes:</p>
+<p>Required datasets:</p>
 <div class="pst-scrollable-table-container"><table class="table">
 <thead>
-<tr class="row-odd"><th class="head"><p>Attribute</p></th>
+<tr class="row-odd"><th class="head"><p>Datasets</p></th>
 <th class="head"><p>Value
 type</p></th>
 <th class="head"><p>Description</p></th>
@@ -771,6 +771,9 @@ <h2>Format Specification<a class="headerlink" href="#format-specification" title
 </tbody>
 </table>
 </div>
+<p>Optionally, the file can contain several matrices.
+In such a case, the ‘matrix’ dataset will not exist and we will use
+‘matrix:0’ instead.</p>
 <div class="admonition note">
 <p class="admonition-title">Note</p>
 <p>This file format is most useful for storing large matrices that do

docs/dev/generated/skbio.table.Table.add_group_metadata.html

@@ -738,7 +738,7 @@
 <h1>skbio.table.Table.add_group_metadata<a class="headerlink" href="#skbio-table-table-add-group-metadata" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.table.Table.add_group_metadata">
-<span class="sig-prename descclassname"><span class="pre">Table.</span></span><span class="sig-name descname"><span class="pre">add_group_metadata</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">group_md</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axis</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'sample'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/../biom/table.py#L746"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.table.Table.add_group_metadata" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">Table.</span></span><span class="sig-name descname"><span class="pre">add_group_metadata</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">group_md</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axis</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'sample'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/../biom/table.py#L743"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.table.Table.add_group_metadata" title="Link to this definition">#</a></dt>
 <dd><p>Take a dict of group metadata and add it to an axis</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>

docs/dev/generated/skbio.table.Table.add_metadata.html

@@ -738,7 +738,7 @@
 <h1>skbio.table.Table.add_metadata<a class="headerlink" href="#skbio-table-table-add-metadata" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.table.Table.add_metadata">
-<span class="sig-prename descclassname"><span class="pre">Table.</span></span><span class="sig-name descname"><span class="pre">add_metadata</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">md</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axis</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'sample'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/../biom/table.py#L841"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.table.Table.add_metadata" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">Table.</span></span><span class="sig-name descname"><span class="pre">add_metadata</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">md</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axis</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'sample'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/../biom/table.py#L838"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.table.Table.add_metadata" title="Link to this definition">#</a></dt>
 <dd><p>Take a dict of metadata and add it to an axis.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>

docs/dev/generated/skbio.table.Table.align_to.html

@@ -738,7 +738,7 @@
 <h1>skbio.table.Table.align_to<a class="headerlink" href="#skbio-table-table-align-to" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.table.Table.align_to">
-<span class="sig-prename descclassname"><span class="pre">Table.</span></span><span class="sig-name descname"><span class="pre">align_to</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axis</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'detect'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/../biom/table.py#L3437"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.table.Table.align_to" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">Table.</span></span><span class="sig-name descname"><span class="pre">align_to</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axis</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'detect'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/../biom/table.py#L3436"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.table.Table.align_to" title="Link to this definition">#</a></dt>
 <dd><p>Align self to other over a requested axis</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>

docs/dev/generated/skbio.table.Table.align_to_dataframe.html

@@ -738,7 +738,7 @@
 <h1>skbio.table.Table.align_to_dataframe<a class="headerlink" href="#skbio-table-table-align-to-dataframe" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.table.Table.align_to_dataframe">
-<span class="sig-prename descclassname"><span class="pre">Table.</span></span><span class="sig-name descname"><span class="pre">align_to_dataframe</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">metadata</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axis</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'sample'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/../biom/table.py#L970"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.table.Table.align_to_dataframe" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">Table.</span></span><span class="sig-name descname"><span class="pre">align_to_dataframe</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">metadata</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axis</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'sample'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/../biom/table.py#L967"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.table.Table.align_to_dataframe" title="Link to this definition">#</a></dt>
 <dd><p>Aligns dataframe against biom table, only keeping common ids.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>

docs/dev/generated/skbio.table.Table.align_tree.html

@@ -738,7 +738,7 @@
 <h1>skbio.table.Table.align_tree<a class="headerlink" href="#skbio-table-table-align-tree" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.table.Table.align_tree">
-<span class="sig-prename descclassname"><span class="pre">Table.</span></span><span class="sig-name descname"><span class="pre">align_tree</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tree</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axis</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'observation'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/../biom/table.py#L1026"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.table.Table.align_tree" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">Table.</span></span><span class="sig-name descname"><span class="pre">align_tree</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tree</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axis</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'observation'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/../biom/table.py#L1023"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.table.Table.align_tree" title="Link to this definition">#</a></dt>
 <dd><p>Aligns biom table against tree, only keeping common ids.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>

docs/dev/generated/skbio.table.Table.collapse.html

@@ -738,7 +738,7 @@
 <h1>skbio.table.Table.collapse<a class="headerlink" href="#skbio-table-table-collapse" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.table.Table.collapse">
-<span class="sig-prename descclassname"><span class="pre">Table.</span></span><span class="sig-name descname"><span class="pre">collapse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">f</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">collapse_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">norm</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_group_size</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">include_collapsed_metadata</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">one_to_many</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">one_to_many_mode</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'add'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">one_to_many_md_key</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'Path'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">strict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axis</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'sample'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/../biom/table.py#L2533"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.table.Table.collapse" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">Table.</span></span><span class="sig-name descname"><span class="pre">collapse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">f</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">collapse_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">norm</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_group_size</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">include_collapsed_metadata</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">one_to_many</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">one_to_many_mode</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'add'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">one_to_many_md_key</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'Path'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">strict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axis</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'sample'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/../biom/table.py#L2530"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.table.Table.collapse" title="Link to this definition">#</a></dt>
 <dd><p>Collapse partitions in a table by metadata or by IDs</p>
 <p>Partition data by metadata or IDs and then collapse each partition into
 a single vector.</p>

docs/dev/generated/skbio.table.Table.concat.html

@@ -738,7 +738,7 @@
 <h1>skbio.table.Table.concat<a class="headerlink" href="#skbio-table-table-concat" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.table.Table.concat">
-<span class="sig-prename descclassname"><span class="pre">Table.</span></span><span class="sig-name descname"><span class="pre">concat</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">others</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axis</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'sample'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/../biom/table.py#L3515"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.table.Table.concat" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">Table.</span></span><span class="sig-name descname"><span class="pre">concat</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">others</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axis</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'sample'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/../biom/table.py#L3514"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.table.Table.concat" title="Link to this definition">#</a></dt>
 <dd><p>Concatenate tables if axis is disjoint</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>

docs/dev/generated/skbio.table.Table.copy.html

@@ -738,7 +738,7 @@
 <h1>skbio.table.Table.copy<a class="headerlink" href="#skbio-table-table-copy" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.table.Table.copy">
-<span class="sig-prename descclassname"><span class="pre">Table.</span></span><span class="sig-name descname"><span class="pre">copy</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/../biom/table.py#L1947"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.table.Table.copy" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">Table.</span></span><span class="sig-name descname"><span class="pre">copy</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/../biom/table.py#L1944"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.table.Table.copy" title="Link to this definition">#</a></dt>
 <dd><p>Returns a copy of the table</p>
 </dd></dl>