Update from scikit-bio/scikit-bio@3271cbb

scikit-bio · Jan 13, 2025 · 1dc51df · 1dc51df
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diff --git a/docs/dev/_static/documentation_options.js b/docs/dev/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '0.6.3',
+    VERSION: '0.6.4-dev',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/docs/dev/alignment.html b/docs/dev/alignment.html
@@ -9,7 +9,7 @@
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 <meta content="Computing and manipulating biological sequence alignments." name="description" />
 
-    <title>Sequence Alignments (skbio.alignment) &#8212; scikit-bio 0.6.3 documentation</title>
+    <title>Sequence Alignments (skbio.alignment) &#8212; scikit-bio 0.6.4-dev documentation</title>
 
 
 
@@ -43,7 +43,7 @@
   <link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=8878045cc6db502f8baf" />
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=8878045cc6db502f8baf" />
 
-    <script src="_static/documentation_options.js?v=b8503983"></script>
+    <script src="_static/documentation_options.js?v=dcd4525e"></script>
     <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/clipboard.min.js?v=a7894cd8"></script>
@@ -66,7 +66,7 @@
     <script>
         DOCUMENTATION_OPTIONS.theme_version = '0.16.1';
         DOCUMENTATION_OPTIONS.theme_switcher_json_url = 'https://scikit.bio/versions.json';
-        DOCUMENTATION_OPTIONS.theme_switcher_version_match = '0.6.3';
+        DOCUMENTATION_OPTIONS.theme_switcher_version_match = 'dev';
         DOCUMENTATION_OPTIONS.show_version_warning_banner =
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         </script>
@@ -78,7 +78,7 @@
     <link rel="prev" title="skbio.sequence.NucleotideMixin.reverse_complement" href="generated/skbio.sequence.NucleotideMixin.reverse_complement.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-  <meta name="docsearch:version" content="0.6.3" />
+  <meta name="docsearch:version" content="0.6.4-dev" />
   </head>
 
 
@@ -144,8 +144,8 @@
 
 
 
-    <img src="_static/logo.svg" class="logo__image only-light" alt="scikit-bio 0.6.3 documentation"/>
-    <img src="_static/logo_inv.svg" class="logo__image only-dark pst-js-only" alt="scikit-bio 0.6.3 documentation"/>
+    <img src="_static/logo.svg" class="logo__image only-light" alt="scikit-bio 0.6.4-dev documentation"/>
+    <img src="_static/logo_inv.svg" class="logo__image only-dark pst-js-only" alt="scikit-bio 0.6.4-dev documentation"/>
 
 
 </a></div>

diff --git a/docs/dev/diversity.html b/docs/dev/diversity.html
@@ -9,7 +9,7 @@
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 <meta content="Analyzing biodiversity of communities -- groups of organisms living in the same area." name="description" />
 
-    <title>Community Diversity (skbio.diversity) &#8212; scikit-bio 0.6.3 documentation</title>
+    <title>Community Diversity (skbio.diversity) &#8212; scikit-bio 0.6.4-dev documentation</title>
 
 
 
@@ -43,7 +43,7 @@
   <link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=8878045cc6db502f8baf" />
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=8878045cc6db502f8baf" />
 
-    <script src="_static/documentation_options.js?v=b8503983"></script>
+    <script src="_static/documentation_options.js?v=dcd4525e"></script>
     <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/clipboard.min.js?v=a7894cd8"></script>
@@ -67,7 +67,7 @@
     <script>
         DOCUMENTATION_OPTIONS.theme_version = '0.16.1';
         DOCUMENTATION_OPTIONS.theme_switcher_json_url = 'https://scikit.bio/versions.json';
-        DOCUMENTATION_OPTIONS.theme_switcher_version_match = '0.6.3';
+        DOCUMENTATION_OPTIONS.theme_switcher_version_match = 'dev';
         DOCUMENTATION_OPTIONS.show_version_warning_banner =
             false;
         </script>
@@ -79,7 +79,7 @@
     <link rel="prev" title="skbio.tree.majority_rule" href="generated/skbio.tree.majority_rule.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-  <meta name="docsearch:version" content="0.6.3" />
+  <meta name="docsearch:version" content="0.6.4-dev" />
   </head>
 
 
@@ -145,8 +145,8 @@
 
 
 
-    <img src="_static/logo.svg" class="logo__image only-light" alt="scikit-bio 0.6.3 documentation"/>
-    <img src="_static/logo_inv.svg" class="logo__image only-dark pst-js-only" alt="scikit-bio 0.6.3 documentation"/>
+    <img src="_static/logo.svg" class="logo__image only-light" alt="scikit-bio 0.6.4-dev documentation"/>
+    <img src="_static/logo_inv.svg" class="logo__image only-dark pst-js-only" alt="scikit-bio 0.6.4-dev documentation"/>
 
 
 </a></div>

diff --git a/docs/dev/embedding.html b/docs/dev/embedding.html
@@ -9,7 +9,7 @@
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 <meta content="Storing and working with embeddings of biological objects for machine learning." name="description" />
 
-    <title>Biological Embeddings (skbio.embedding) &#8212; scikit-bio 0.6.3 documentation</title>
+    <title>Biological Embeddings (skbio.embedding) &#8212; scikit-bio 0.6.4-dev documentation</title>
 
 
 
@@ -43,7 +43,7 @@
   <link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=8878045cc6db502f8baf" />
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=8878045cc6db502f8baf" />
 
-    <script src="_static/documentation_options.js?v=b8503983"></script>
+    <script src="_static/documentation_options.js?v=dcd4525e"></script>
     <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/clipboard.min.js?v=a7894cd8"></script>
@@ -66,7 +66,7 @@
     <script>
         DOCUMENTATION_OPTIONS.theme_version = '0.16.1';
         DOCUMENTATION_OPTIONS.theme_switcher_json_url = 'https://scikit.bio/versions.json';
-        DOCUMENTATION_OPTIONS.theme_switcher_version_match = '0.6.3';
+        DOCUMENTATION_OPTIONS.theme_switcher_version_match = 'dev';
         DOCUMENTATION_OPTIONS.show_version_warning_banner =
             false;
         </script>
@@ -78,7 +78,7 @@
     <link rel="prev" title="skbio.stats.power.paired_subsamples" href="generated/skbio.stats.power.paired_subsamples.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-  <meta name="docsearch:version" content="0.6.3" />
+  <meta name="docsearch:version" content="0.6.4-dev" />
   </head>
 
 
@@ -144,8 +144,8 @@
 
 
 
-    <img src="_static/logo.svg" class="logo__image only-light" alt="scikit-bio 0.6.3 documentation"/>
-    <img src="_static/logo_inv.svg" class="logo__image only-dark pst-js-only" alt="scikit-bio 0.6.3 documentation"/>
+    <img src="_static/logo.svg" class="logo__image only-light" alt="scikit-bio 0.6.4-dev documentation"/>
+    <img src="_static/logo_inv.svg" class="logo__image only-dark pst-js-only" alt="scikit-bio 0.6.4-dev documentation"/>
 
 
 </a></div>

diff --git a/docs/dev/generated/skbio.alignment.AlignPath.from_bits.html b/docs/dev/generated/skbio.alignment.AlignPath.from_bits.html
@@ -9,7 +9,7 @@
     <meta name="description" content="Create an alignment path from a bit array (0 - character, 1 - gap)." />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>skbio.alignment.AlignPath.from_bits &#8212; scikit-bio 0.6.3 documentation</title>
+    <title>skbio.alignment.AlignPath.from_bits &#8212; scikit-bio 0.6.4-dev documentation</title>
 
 
 
@@ -43,7 +43,7 @@
   <link rel="preload" as="script" href="../_static/scripts/bootstrap.js?digest=8878045cc6db502f8baf" />
 <link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=8878045cc6db502f8baf" />
 
-    <script src="../_static/documentation_options.js?v=b8503983"></script>
+    <script src="../_static/documentation_options.js?v=dcd4525e"></script>
     <script src="../_static/doctools.js?v=9bcbadda"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -66,7 +66,7 @@
     <script>
         DOCUMENTATION_OPTIONS.theme_version = '0.16.1';
         DOCUMENTATION_OPTIONS.theme_switcher_json_url = 'https://scikit.bio/versions.json';
-        DOCUMENTATION_OPTIONS.theme_switcher_version_match = '0.6.3';
+        DOCUMENTATION_OPTIONS.theme_switcher_version_match = 'dev';
         DOCUMENTATION_OPTIONS.show_version_warning_banner =
             false;
         </script>
@@ -78,7 +78,7 @@
     <link rel="prev" title="skbio.alignment.AlignPath" href="skbio.alignment.AlignPath.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-  <meta name="docsearch:version" content="0.6.3" />
+  <meta name="docsearch:version" content="0.6.4-dev" />
   </head>
 
 
@@ -144,8 +144,8 @@
 
 
 
-    <img src="../_static/logo.svg" class="logo__image only-light" alt="scikit-bio 0.6.3 documentation"/>
-    <img src="../_static/logo_inv.svg" class="logo__image only-dark pst-js-only" alt="scikit-bio 0.6.3 documentation"/>
+    <img src="../_static/logo.svg" class="logo__image only-light" alt="scikit-bio 0.6.4-dev documentation"/>
+    <img src="../_static/logo_inv.svg" class="logo__image only-dark pst-js-only" alt="scikit-bio 0.6.4-dev documentation"/>
 
 
 </a></div>
@@ -692,7 +692,7 @@
 <h1>skbio.alignment.AlignPath.from_bits<a class="headerlink" href="#skbio-alignment-alignpath-from-bits" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.alignment.AlignPath.from_bits">
-<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">AlignPath.</span></span><span class="sig-name descname"><span class="pre">from_bits</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">bits</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">starts</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/0.6.3/skbio/alignment/_path.py#L200"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.alignment.AlignPath.from_bits" title="Link to this definition">#</a></dt>
+<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">AlignPath.</span></span><span class="sig-name descname"><span class="pre">from_bits</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">bits</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">starts</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/alignment/_path.py#L200"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.alignment.AlignPath.from_bits" title="Link to this definition">#</a></dt>
 <dd><p>Create an alignment path from a bit array (0 - character, 1 - gap).</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>

diff --git a/docs/dev/generated/skbio.alignment.AlignPath.from_coordinates.html b/docs/dev/generated/skbio.alignment.AlignPath.from_coordinates.html
@@ -9,7 +9,7 @@
     <meta name="description" content="Generate an alignment path from an array of segment coordinates." />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>skbio.alignment.AlignPath.from_coordinates &#8212; scikit-bio 0.6.3 documentation</title>
+    <title>skbio.alignment.AlignPath.from_coordinates &#8212; scikit-bio 0.6.4-dev documentation</title>
 
 
 
@@ -43,7 +43,7 @@
   <link rel="preload" as="script" href="../_static/scripts/bootstrap.js?digest=8878045cc6db502f8baf" />
 <link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=8878045cc6db502f8baf" />
 
-    <script src="../_static/documentation_options.js?v=b8503983"></script>
+    <script src="../_static/documentation_options.js?v=dcd4525e"></script>
     <script src="../_static/doctools.js?v=9bcbadda"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -66,7 +66,7 @@
     <script>
         DOCUMENTATION_OPTIONS.theme_version = '0.16.1';
         DOCUMENTATION_OPTIONS.theme_switcher_json_url = 'https://scikit.bio/versions.json';
-        DOCUMENTATION_OPTIONS.theme_switcher_version_match = '0.6.3';
+        DOCUMENTATION_OPTIONS.theme_switcher_version_match = 'dev';
         DOCUMENTATION_OPTIONS.show_version_warning_banner =
             false;
         </script>
@@ -78,7 +78,7 @@
     <link rel="prev" title="skbio.alignment.AlignPath.from_bits" href="skbio.alignment.AlignPath.from_bits.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-  <meta name="docsearch:version" content="0.6.3" />
+  <meta name="docsearch:version" content="0.6.4-dev" />
   </head>
 
 
@@ -144,8 +144,8 @@
 
 
 
-    <img src="../_static/logo.svg" class="logo__image only-light" alt="scikit-bio 0.6.3 documentation"/>
-    <img src="../_static/logo_inv.svg" class="logo__image only-dark pst-js-only" alt="scikit-bio 0.6.3 documentation"/>
+    <img src="../_static/logo.svg" class="logo__image only-light" alt="scikit-bio 0.6.4-dev documentation"/>
+    <img src="../_static/logo_inv.svg" class="logo__image only-dark pst-js-only" alt="scikit-bio 0.6.4-dev documentation"/>
 
 
 </a></div>
@@ -692,7 +692,7 @@
 <h1>skbio.alignment.AlignPath.from_coordinates<a class="headerlink" href="#skbio-alignment-alignpath-from-coordinates" title="Link to this heading">#</a></h1>
 <dl class="py method">
 <dt class="sig sig-object py" id="skbio.alignment.AlignPath.from_coordinates">
-<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">AlignPath.</span></span><span class="sig-name descname"><span class="pre">from_coordinates</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">coords</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/0.6.3/skbio/alignment/_path.py#L441"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.alignment.AlignPath.from_coordinates" title="Link to this definition">#</a></dt>
+<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">AlignPath.</span></span><span class="sig-name descname"><span class="pre">from_coordinates</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">coords</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/scikit-bio/scikit-bio/blob/main/skbio/alignment/_path.py#L441"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#skbio.alignment.AlignPath.from_coordinates" title="Link to this definition">#</a></dt>
 <dd><p>Generate an alignment path from an array of segment coordinates.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>