Update from scikit-bio/scikit-bio@7f944cb

scikit-bio · Jul 8, 2024 · 72eea98 · 72eea98
1 parent 5e7cf8b
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diff --git a/docs/dev/.buildinfo b/docs/dev/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 5c0cd84aba1a0a336252c0910f4d1790
+config: 0cafa89789cf0c2662839a732c1af9d7
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/dev/_sources/generated/skbio.tree.nni.rst.txt b/docs/dev/_sources/generated/skbio.tree.nni.rst.txt
@@ -0,0 +1,6 @@
+skbio.tree.nni
+==============
+
+.. currentmodule:: skbio.tree
+
+.. autofunction:: nni
diff --git a/docs/dev/_static/documentation_options.js b/docs/dev/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '0.6.2-dev',
+    VERSION: '0.6.2',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/docs/dev/alignment.html b/docs/dev/alignment.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Sequence Alignments (skbio.alignment) &#8212; scikit-bio 0.6.2-dev documentation</title>
+    <title>Sequence Alignments (skbio.alignment) &#8212; scikit-bio 0.6.2 documentation</title>
 
 
 
@@ -39,7 +39,7 @@
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   <script src="_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>
 
-    <script src="_static/documentation_options.js?v=be67db09"></script>
+    <script src="_static/documentation_options.js?v=1c28bd9a"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/clipboard.min.js?v=a7894cd8"></script>
@@ -62,7 +62,7 @@
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         DOCUMENTATION_OPTIONS.theme_switcher_json_url = 'https://scikit.bio/versions.json';
-        DOCUMENTATION_OPTIONS.theme_switcher_version_match = 'dev';
+        DOCUMENTATION_OPTIONS.theme_switcher_version_match = '0.6.2';
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@@ -150,8 +150,8 @@
 
 
 
-    <img src="_static/logo.svg" class="logo__image only-light" alt="scikit-bio 0.6.2-dev documentation"/>
-    <script>document.write(`<img src="_static/logo_inv.svg" class="logo__image only-dark" alt="scikit-bio 0.6.2-dev documentation"/>`);</script>
+    <img src="_static/logo.svg" class="logo__image only-light" alt="scikit-bio 0.6.2 documentation"/>
+    <script>document.write(`<img src="_static/logo_inv.svg" class="logo__image only-dark" alt="scikit-bio 0.6.2 documentation"/>`);</script>
 
 
 </a></div>

diff --git a/docs/dev/diversity.html b/docs/dev/diversity.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Community Diversity (skbio.diversity) &#8212; scikit-bio 0.6.2-dev documentation</title>
+    <title>Community Diversity (skbio.diversity) &#8212; scikit-bio 0.6.2 documentation</title>
 
 
 
@@ -39,7 +39,7 @@
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   <script src="_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>
 
-    <script src="_static/documentation_options.js?v=be67db09"></script>
+    <script src="_static/documentation_options.js?v=1c28bd9a"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/clipboard.min.js?v=a7894cd8"></script>
@@ -63,7 +63,7 @@
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         DOCUMENTATION_OPTIONS.theme_switcher_json_url = 'https://scikit.bio/versions.json';
-        DOCUMENTATION_OPTIONS.theme_switcher_version_match = 'dev';
+        DOCUMENTATION_OPTIONS.theme_switcher_version_match = '0.6.2';
         DOCUMENTATION_OPTIONS.show_version_warning_banner = false;
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     <link rel="canonical" href="../../diversity.html" />
@@ -151,8 +151,8 @@
 
 
 
-    <img src="_static/logo.svg" class="logo__image only-light" alt="scikit-bio 0.6.2-dev documentation"/>
-    <script>document.write(`<img src="_static/logo_inv.svg" class="logo__image only-dark" alt="scikit-bio 0.6.2-dev documentation"/>`);</script>
+    <img src="_static/logo.svg" class="logo__image only-light" alt="scikit-bio 0.6.2 documentation"/>
+    <script>document.write(`<img src="_static/logo_inv.svg" class="logo__image only-dark" alt="scikit-bio 0.6.2 documentation"/>`);</script>
 
 
 </a></div>

diff --git a/docs/dev/embedding.html b/docs/dev/embedding.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Biological Embeddings (skbio.embedding) &#8212; scikit-bio 0.6.2-dev documentation</title>
+    <title>Biological Embeddings (skbio.embedding) &#8212; scikit-bio 0.6.2 documentation</title>
 
 
 
@@ -39,7 +39,7 @@
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   <script src="_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>
 
-    <script src="_static/documentation_options.js?v=be67db09"></script>
+    <script src="_static/documentation_options.js?v=1c28bd9a"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
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@@ -62,7 +62,7 @@
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         DOCUMENTATION_OPTIONS.theme_version = '0.15.4';
         DOCUMENTATION_OPTIONS.theme_switcher_json_url = 'https://scikit.bio/versions.json';
-        DOCUMENTATION_OPTIONS.theme_switcher_version_match = 'dev';
+        DOCUMENTATION_OPTIONS.theme_switcher_version_match = '0.6.2';
         DOCUMENTATION_OPTIONS.show_version_warning_banner = false;
         </script>
     <link rel="canonical" href="../../embedding.html" />
@@ -150,8 +150,8 @@
 
 
 
-    <img src="_static/logo.svg" class="logo__image only-light" alt="scikit-bio 0.6.2-dev documentation"/>
-    <script>document.write(`<img src="_static/logo_inv.svg" class="logo__image only-dark" alt="scikit-bio 0.6.2-dev documentation"/>`);</script>
+    <img src="_static/logo.svg" class="logo__image only-light" alt="scikit-bio 0.6.2 documentation"/>
+    <script>document.write(`<img src="_static/logo_inv.svg" class="logo__image only-dark" alt="scikit-bio 0.6.2 documentation"/>`);</script>
 
 
 </a></div>

diff --git a/docs/dev/generated/skbio.alignment.AlignPath.__eq__.html b/docs/dev/generated/skbio.alignment.AlignPath.__eq__.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <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.__eq__ &#8212; scikit-bio 0.6.2-dev documentation</title>
+    <title>skbio.alignment.AlignPath.__eq__ &#8212; scikit-bio 0.6.2 documentation</title>
 
 
 
@@ -39,7 +39,7 @@
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   <script src="../_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>
 
-    <script src="../_static/documentation_options.js?v=be67db09"></script>
+    <script src="../_static/documentation_options.js?v=1c28bd9a"></script>
     <script src="../_static/doctools.js?v=9a2dae69"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -62,7 +62,7 @@
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         DOCUMENTATION_OPTIONS.theme_switcher_json_url = 'https://scikit.bio/versions.json';
-        DOCUMENTATION_OPTIONS.theme_switcher_version_match = 'dev';
+        DOCUMENTATION_OPTIONS.theme_switcher_version_match = '0.6.2';
         DOCUMENTATION_OPTIONS.show_version_warning_banner = false;
         </script>
     <link rel="canonical" href="../../../generated/skbio.alignment.AlignPath.__eq__.html" />
@@ -150,8 +150,8 @@
 
 
 
-    <img src="../_static/logo.svg" class="logo__image only-light" alt="scikit-bio 0.6.2-dev documentation"/>
-    <script>document.write(`<img src="../_static/logo_inv.svg" class="logo__image only-dark" alt="scikit-bio 0.6.2-dev documentation"/>`);</script>
+    <img src="../_static/logo.svg" class="logo__image only-light" alt="scikit-bio 0.6.2 documentation"/>
+    <script>document.write(`<img src="../_static/logo_inv.svg" class="logo__image only-dark" alt="scikit-bio 0.6.2 documentation"/>`);</script>
 
 
 </a></div>

diff --git a/docs/dev/generated/skbio.alignment.AlignPath.__ge__.html b/docs/dev/generated/skbio.alignment.AlignPath.__ge__.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <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.__ge__ &#8212; scikit-bio 0.6.2-dev documentation</title>
+    <title>skbio.alignment.AlignPath.__ge__ &#8212; scikit-bio 0.6.2 documentation</title>
 
 
 
@@ -39,7 +39,7 @@
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   <script src="../_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>
 
-    <script src="../_static/documentation_options.js?v=be67db09"></script>
+    <script src="../_static/documentation_options.js?v=1c28bd9a"></script>
     <script src="../_static/doctools.js?v=9a2dae69"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -62,7 +62,7 @@
     <script>
         DOCUMENTATION_OPTIONS.theme_version = '0.15.4';
         DOCUMENTATION_OPTIONS.theme_switcher_json_url = 'https://scikit.bio/versions.json';
-        DOCUMENTATION_OPTIONS.theme_switcher_version_match = 'dev';
+        DOCUMENTATION_OPTIONS.theme_switcher_version_match = '0.6.2';
         DOCUMENTATION_OPTIONS.show_version_warning_banner = false;
         </script>
     <link rel="canonical" href="../../../generated/skbio.alignment.AlignPath.__ge__.html" />
@@ -150,8 +150,8 @@
 
 
 
-    <img src="../_static/logo.svg" class="logo__image only-light" alt="scikit-bio 0.6.2-dev documentation"/>
-    <script>document.write(`<img src="../_static/logo_inv.svg" class="logo__image only-dark" alt="scikit-bio 0.6.2-dev documentation"/>`);</script>
+    <img src="../_static/logo.svg" class="logo__image only-light" alt="scikit-bio 0.6.2 documentation"/>
+    <script>document.write(`<img src="../_static/logo_inv.svg" class="logo__image only-dark" alt="scikit-bio 0.6.2 documentation"/>`);</script>
 
 
 </a></div>

diff --git a/docs/dev/generated/skbio.alignment.AlignPath.__getstate__.html b/docs/dev/generated/skbio.alignment.AlignPath.__getstate__.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <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.__getstate__ &#8212; scikit-bio 0.6.2-dev documentation</title>
+    <title>skbio.alignment.AlignPath.__getstate__ &#8212; scikit-bio 0.6.2 documentation</title>
 
 
 
@@ -39,7 +39,7 @@
 <link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
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-    <script src="../_static/documentation_options.js?v=be67db09"></script>
+    <script src="../_static/documentation_options.js?v=1c28bd9a"></script>
     <script src="../_static/doctools.js?v=9a2dae69"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -62,7 +62,7 @@
     <script>
         DOCUMENTATION_OPTIONS.theme_version = '0.15.4';
         DOCUMENTATION_OPTIONS.theme_switcher_json_url = 'https://scikit.bio/versions.json';
-        DOCUMENTATION_OPTIONS.theme_switcher_version_match = 'dev';
+        DOCUMENTATION_OPTIONS.theme_switcher_version_match = '0.6.2';
         DOCUMENTATION_OPTIONS.show_version_warning_banner = false;
         </script>
     <link rel="canonical" href="../../../generated/skbio.alignment.AlignPath.__getstate__.html" />
@@ -150,8 +150,8 @@
 
 
 
-    <img src="../_static/logo.svg" class="logo__image only-light" alt="scikit-bio 0.6.2-dev documentation"/>
-    <script>document.write(`<img src="../_static/logo_inv.svg" class="logo__image only-dark" alt="scikit-bio 0.6.2-dev documentation"/>`);</script>
+    <img src="../_static/logo.svg" class="logo__image only-light" alt="scikit-bio 0.6.2 documentation"/>
+    <script>document.write(`<img src="../_static/logo_inv.svg" class="logo__image only-dark" alt="scikit-bio 0.6.2 documentation"/>`);</script>
 
 
 </a></div>

diff --git a/docs/dev/generated/skbio.alignment.AlignPath.__gt__.html b/docs/dev/generated/skbio.alignment.AlignPath.__gt__.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <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.__gt__ &#8212; scikit-bio 0.6.2-dev documentation</title>
+    <title>skbio.alignment.AlignPath.__gt__ &#8212; scikit-bio 0.6.2 documentation</title>
 
 
 
@@ -39,7 +39,7 @@
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-    <script src="../_static/documentation_options.js?v=be67db09"></script>
+    <script src="../_static/documentation_options.js?v=1c28bd9a"></script>
     <script src="../_static/doctools.js?v=9a2dae69"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -62,7 +62,7 @@
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         DOCUMENTATION_OPTIONS.theme_version = '0.15.4';
         DOCUMENTATION_OPTIONS.theme_switcher_json_url = 'https://scikit.bio/versions.json';
-        DOCUMENTATION_OPTIONS.theme_switcher_version_match = 'dev';
+        DOCUMENTATION_OPTIONS.theme_switcher_version_match = '0.6.2';
         DOCUMENTATION_OPTIONS.show_version_warning_banner = false;
         </script>
     <link rel="canonical" href="../../../generated/skbio.alignment.AlignPath.__gt__.html" />
@@ -150,8 +150,8 @@
 
 
 
-    <img src="../_static/logo.svg" class="logo__image only-light" alt="scikit-bio 0.6.2-dev documentation"/>
-    <script>document.write(`<img src="../_static/logo_inv.svg" class="logo__image only-dark" alt="scikit-bio 0.6.2-dev documentation"/>`);</script>
+    <img src="../_static/logo.svg" class="logo__image only-light" alt="scikit-bio 0.6.2 documentation"/>
+    <script>document.write(`<img src="../_static/logo_inv.svg" class="logo__image only-dark" alt="scikit-bio 0.6.2 documentation"/>`);</script>
 
 
 </a></div>

diff --git a/docs/dev/generated/skbio.alignment.AlignPath.__hash__.html b/docs/dev/generated/skbio.alignment.AlignPath.__hash__.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <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.__hash__ &#8212; scikit-bio 0.6.2-dev documentation</title>
+    <title>skbio.alignment.AlignPath.__hash__ &#8212; scikit-bio 0.6.2 documentation</title>
 
 
 
@@ -39,7 +39,7 @@
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-    <script src="../_static/documentation_options.js?v=be67db09"></script>
+    <script src="../_static/documentation_options.js?v=1c28bd9a"></script>
     <script src="../_static/doctools.js?v=9a2dae69"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
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@@ -62,7 +62,7 @@
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         DOCUMENTATION_OPTIONS.theme_switcher_json_url = 'https://scikit.bio/versions.json';
-        DOCUMENTATION_OPTIONS.theme_switcher_version_match = 'dev';
+        DOCUMENTATION_OPTIONS.theme_switcher_version_match = '0.6.2';
         DOCUMENTATION_OPTIONS.show_version_warning_banner = false;
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     <link rel="canonical" href="../../../generated/skbio.alignment.AlignPath.__hash__.html" />
@@ -150,8 +150,8 @@
 
 
 
-    <img src="../_static/logo.svg" class="logo__image only-light" alt="scikit-bio 0.6.2-dev documentation"/>
-    <script>document.write(`<img src="../_static/logo_inv.svg" class="logo__image only-dark" alt="scikit-bio 0.6.2-dev documentation"/>`);</script>
+    <img src="../_static/logo.svg" class="logo__image only-light" alt="scikit-bio 0.6.2 documentation"/>
+    <script>document.write(`<img src="../_static/logo_inv.svg" class="logo__image only-dark" alt="scikit-bio 0.6.2 documentation"/>`);</script>
 
 
 </a></div>

diff --git a/docs/dev/generated/skbio.alignment.AlignPath.__le__.html b/docs/dev/generated/skbio.alignment.AlignPath.__le__.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <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.__le__ &#8212; scikit-bio 0.6.2-dev documentation</title>
+    <title>skbio.alignment.AlignPath.__le__ &#8212; scikit-bio 0.6.2 documentation</title>
 
 
 
@@ -39,7 +39,7 @@
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-    <script src="../_static/documentation_options.js?v=be67db09"></script>
+    <script src="../_static/documentation_options.js?v=1c28bd9a"></script>
     <script src="../_static/doctools.js?v=9a2dae69"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
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@@ -62,7 +62,7 @@
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         DOCUMENTATION_OPTIONS.theme_switcher_json_url = 'https://scikit.bio/versions.json';
-        DOCUMENTATION_OPTIONS.theme_switcher_version_match = 'dev';
+        DOCUMENTATION_OPTIONS.theme_switcher_version_match = '0.6.2';
         DOCUMENTATION_OPTIONS.show_version_warning_banner = false;
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     <link rel="canonical" href="../../../generated/skbio.alignment.AlignPath.__le__.html" />
@@ -150,8 +150,8 @@
 
 
 
-    <img src="../_static/logo.svg" class="logo__image only-light" alt="scikit-bio 0.6.2-dev documentation"/>
-    <script>document.write(`<img src="../_static/logo_inv.svg" class="logo__image only-dark" alt="scikit-bio 0.6.2-dev documentation"/>`);</script>
+    <img src="../_static/logo.svg" class="logo__image only-light" alt="scikit-bio 0.6.2 documentation"/>
+    <script>document.write(`<img src="../_static/logo_inv.svg" class="logo__image only-dark" alt="scikit-bio 0.6.2 documentation"/>`);</script>
 
 
 </a></div>