From 903eed90d87b05aea146b5511fda19811bf2a955 Mon Sep 17 00:00:00 2001
From: mataton <62309966+mataton@users.noreply.github.com>
Date: Thu, 28 Mar 2024 20:47:44 +0000
Subject: [PATCH] Update from
 https://github.com/scikit-bio/scikit-bio/commit/df5d62adf2eb7c8e505da5bb20ad043ffde55f05

---
 _sources/index.rst.txt |  2 +-
 about.html             |  4 ++--
 contribute.html        |  4 ++--
 devdoc/code_guide.html |  4 ++--
 devdoc/doc_guide.html  |  6 +++---
 devdoc/new_module.html |  4 ++--
 devdoc/release.html    |  4 ++--
 devdoc/review.html     |  4 ++--
 genindex.html          |  4 ++--
 index.html             | 16 ++++++++--------
 install.html           |  4 ++--
 learn.html             |  4 ++--
 search.html            |  4 ++--
 13 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt
index 87a001987..c1f41dcd3 100644
--- a/_sources/index.rst.txt
+++ b/_sources/index.rst.txt
@@ -74,7 +74,7 @@
 
    Install <install>
    Learn <learn>
-   Documentation <https://scikit.bio/docs/dev/index.html>
+   Documentation <https://scikit.bio/docs/latest/index.html>
    Contribute <contribute>
    Community <https://github.com/scikit-bio/scikit-bio/discussions>
    Releases <https://github.com/scikit-bio/scikit-bio/blob/main/CHANGELOG.md>
diff --git a/about.html b/about.html
index 1611d1f14..c93628461 100644
--- a/about.html
+++ b/about.html
@@ -177,7 +177,7 @@
                 
 
                     <li class="nav-item">
-                      <a class="nav-link nav-external" href="docs/dev/index.html">
+                      <a class="nav-link nav-external" href="docs/latest/index.html">
                         Documentation
                       </a>
                     </li>
@@ -304,7 +304,7 @@
                 
 
                     <li class="nav-item">
-                      <a class="nav-link nav-external" href="docs/dev/index.html">
+                      <a class="nav-link nav-external" href="docs/latest/index.html">
                         Documentation
                       </a>
                     </li>
diff --git a/contribute.html b/contribute.html
index 7e891246d..68f114f36 100644
--- a/contribute.html
+++ b/contribute.html
@@ -178,7 +178,7 @@
                 
 
                     <li class="nav-item">
-                      <a class="nav-link nav-external" href="docs/dev/index.html">
+                      <a class="nav-link nav-external" href="docs/latest/index.html">
                         Documentation
                       </a>
                     </li>
@@ -309,7 +309,7 @@
                 
 
                     <li class="nav-item">
-                      <a class="nav-link nav-external" href="docs/dev/index.html">
+                      <a class="nav-link nav-external" href="docs/latest/index.html">
                         Documentation
                       </a>
                     </li>
diff --git a/devdoc/code_guide.html b/devdoc/code_guide.html
index 16bda845b..cd9b115fe 100644
--- a/devdoc/code_guide.html
+++ b/devdoc/code_guide.html
@@ -178,7 +178,7 @@
                 
 
                     <li class="nav-item">
-                      <a class="nav-link nav-external" href="../docs/dev/index.html">
+                      <a class="nav-link nav-external" href="../docs/latest/index.html">
                         Documentation
                       </a>
                     </li>
@@ -309,7 +309,7 @@
                 
 
                     <li class="nav-item">
-                      <a class="nav-link nav-external" href="../docs/dev/index.html">
+                      <a class="nav-link nav-external" href="../docs/latest/index.html">
                         Documentation
                       </a>
                     </li>
diff --git a/devdoc/doc_guide.html b/devdoc/doc_guide.html
index b478bf5e7..721f323db 100644
--- a/devdoc/doc_guide.html
+++ b/devdoc/doc_guide.html
@@ -178,7 +178,7 @@
                 
 
                     <li class="nav-item">
-                      <a class="nav-link nav-external" href="../docs/dev/index.html">
+                      <a class="nav-link nav-external" href="../docs/latest/index.html">
                         Documentation
                       </a>
                     </li>
@@ -309,7 +309,7 @@
                 
 
                     <li class="nav-item">
-                      <a class="nav-link nav-external" href="../docs/dev/index.html">
+                      <a class="nav-link nav-external" href="../docs/latest/index.html">
                         Documentation
                       </a>
                     </li>
@@ -452,7 +452,7 @@ <h1>Documentation guidelines<a class="headerlink" href="#documentation-guideline
 <p>This guide contains instructions for building the scikit-bio documentation, as well as guidelines for contributing to the documentation. If you would like to contribute to the documentation, whether by adding something entirely new or by modifying existing documentation, please first review <a class="reference internal" href="../contribute.html"><span class="doc">Contribute to scikit-bio</span></a>.</p>
 <div class="admonition note">
 <p class="admonition-title">Note</p>
-<p>If you’re only interested in viewing the scikit-bio documentation, please visit the <a class="reference external" href="https://scikit.bio/docs/latest/index.html">documentation site</a>.</p>
+<p>If you’re only interested in viewing the scikit-bio documentation, please visit the <a class="reference external" href="../docs/latest/index.html">documentation site</a>.</p>
 </div>
 <section id="build-the-documentation">
 <h2>Build the documentation<a class="headerlink" href="#build-the-documentation" title="Link to this heading">#</a></h2>
diff --git a/devdoc/new_module.html b/devdoc/new_module.html
index 36be7976e..39f37e2c7 100644
--- a/devdoc/new_module.html
+++ b/devdoc/new_module.html
@@ -178,7 +178,7 @@
                 
 
                     <li class="nav-item">
-                      <a class="nav-link nav-external" href="../docs/dev/index.html">
+                      <a class="nav-link nav-external" href="../docs/latest/index.html">
                         Documentation
                       </a>
                     </li>
@@ -305,7 +305,7 @@
                 
 
                     <li class="nav-item">
-                      <a class="nav-link nav-external" href="../docs/dev/index.html">
+                      <a class="nav-link nav-external" href="../docs/latest/index.html">
                         Documentation
                       </a>
                     </li>
diff --git a/devdoc/release.html b/devdoc/release.html
index e5a09ca30..4c96c92c8 100644
--- a/devdoc/release.html
+++ b/devdoc/release.html
@@ -178,7 +178,7 @@
                 
 
                     <li class="nav-item">
-                      <a class="nav-link nav-external" href="../docs/dev/index.html">
+                      <a class="nav-link nav-external" href="../docs/latest/index.html">
                         Documentation
                       </a>
                     </li>
@@ -309,7 +309,7 @@
                 
 
                     <li class="nav-item">
-                      <a class="nav-link nav-external" href="../docs/dev/index.html">
+                      <a class="nav-link nav-external" href="../docs/latest/index.html">
                         Documentation
                       </a>
                     </li>
diff --git a/devdoc/review.html b/devdoc/review.html
index 65c0bb17d..77d593ee3 100644
--- a/devdoc/review.html
+++ b/devdoc/review.html
@@ -178,7 +178,7 @@
                 
 
                     <li class="nav-item">
-                      <a class="nav-link nav-external" href="../docs/dev/index.html">
+                      <a class="nav-link nav-external" href="../docs/latest/index.html">
                         Documentation
                       </a>
                     </li>
@@ -309,7 +309,7 @@
                 
 
                     <li class="nav-item">
-                      <a class="nav-link nav-external" href="../docs/dev/index.html">
+                      <a class="nav-link nav-external" href="../docs/latest/index.html">
                         Documentation
                       </a>
                     </li>
diff --git a/genindex.html b/genindex.html
index 43a6d7e80..8b69c3ebd 100644
--- a/genindex.html
+++ b/genindex.html
@@ -175,7 +175,7 @@
                 
 
                     <li class="nav-item">
-                      <a class="nav-link nav-external" href="docs/dev/index.html">
+                      <a class="nav-link nav-external" href="docs/latest/index.html">
                         Documentation
                       </a>
                     </li>
@@ -304,7 +304,7 @@
                 
 
                     <li class="nav-item">
-                      <a class="nav-link nav-external" href="docs/dev/index.html">
+                      <a class="nav-link nav-external" href="docs/latest/index.html">
                         Documentation
                       </a>
                     </li>
diff --git a/index.html b/index.html
index ed53e93d3..27d43d432 100644
--- a/index.html
+++ b/index.html
@@ -177,7 +177,7 @@
                 
 
                     <li class="nav-item">
-                      <a class="nav-link nav-external" href="docs/dev/index.html">
+                      <a class="nav-link nav-external" href="docs/latest/index.html">
                         Documentation
                       </a>
                     </li>
@@ -306,7 +306,7 @@
                 
 
                     <li class="nav-item">
-                      <a class="nav-link nav-external" href="docs/dev/index.html">
+                      <a class="nav-link nav-external" href="docs/latest/index.html">
                         Documentation
                       </a>
                     </li>
@@ -643,7 +643,7 @@
 <div class="sd-card sd-sphinx-override sd-w-100 sd-shadow-sm docutils">
 <div class="sd-card-body docutils">
 <p class="sd-card-text"><span class="fa fa-dna fa-2x sd-text-success"></span></p>
-<p class="sd-card-text"><strong>Biological sequences</strong>: Efficient data structure with a <a class="reference external" href="docs/dev/generated/skbio.sequence.GrammaredSequence.html">flexible grammar</a> for easy manipulation, <a class="reference external" href="docs/dev/generated/skbio.sequence.GrammaredSequence.has_positional_metadata.html">annotation</a>, <a class="reference external" href="docs/dev/generated/skbio.alignment.global_pairwise_align.html">alignment</a>, and conversion into <a class="reference external" href="docs/dev/generated/skbio.sequence.GrammaredSequence.find_motifs.html">motifs</a> or <a class="reference external" href="docs/dev/generated/skbio.sequence.GrammaredSequence.iter_kmers.html">k-mers</a> for in-depth analysis.</p>
+<p class="sd-card-text"><strong>Biological sequences</strong>: Efficient data structure with a <a class="reference external" href="https://scikit.bio/docs/dev/generated/skbio.sequence.GrammaredSequence.html">flexible grammar</a> for easy manipulation, <a class="reference external" href="https://scikit.bio/docs/dev/generated/skbio.sequence.GrammaredSequence.has_positional_metadata.html">annotation</a>, <a class="reference external" href="https://scikit.bio/docs/dev/generated/skbio.alignment.global_pairwise_align.html">alignment</a>, and conversion into <a class="reference external" href="https://scikit.bio/docs/dev/generated/skbio.sequence.GrammaredSequence.find_motifs.html">motifs</a> or <a class="reference external" href="https://scikit.bio/docs/dev/generated/skbio.sequence.GrammaredSequence.iter_kmers.html">k-mers</a> for in-depth analysis.</p>
 </div>
 </div>
 </div>
@@ -651,7 +651,7 @@
 <div class="sd-card sd-sphinx-override sd-w-100 sd-shadow-sm docutils">
 <div class="sd-card-body docutils">
 <p class="sd-card-text"><span class="fa fa-tree fa-2x sd-text-success"></span></p>
-<p class="sd-card-text"><strong>Phylogenetic trees</strong>: Scalable <a class="reference external" href="docs/dev/generated/skbio.tree.TreeNode.html">tree structure</a> tailored for evolutionary biology, supporting diverse operations in <a class="reference external" href="docs/dev/generated/skbio.tree.TreeNode.lca.html">navigation</a>, <a class="reference external" href="docs/dev/generated/skbio.tree.TreeNode.root_at_midpoint.html">manipulation</a>, <a class="reference external" href="docs/dev/generated/skbio.tree.TreeNode.compare_rfd.html">comparison</a>, and <a class="reference external" href="docs/dev/generated/skbio.tree.nj.html">construction</a>.</p>
+<p class="sd-card-text"><strong>Phylogenetic trees</strong>: Scalable <a class="reference external" href="https://scikit.bio/docs/dev/generated/skbio.tree.TreeNode.html">tree structure</a> tailored for evolutionary biology, supporting diverse operations in <a class="reference external" href="https://scikit.bio/docs/dev/generated/skbio.tree.TreeNode.lca.html">navigation</a>, <a class="reference external" href="https://scikit.bio/docs/dev/generated/skbio.tree.TreeNode.root_at_midpoint.html">manipulation</a>, <a class="reference external" href="https://scikit.bio/docs/dev/generated/skbio.tree.TreeNode.compare_rfd.html">comparison</a>, and <a class="reference external" href="https://scikit.bio/docs/dev/generated/skbio.tree.nj.html">construction</a>.</p>
 </div>
 </div>
 </div>
@@ -659,7 +659,7 @@
 <div class="sd-card sd-sphinx-override sd-w-100 sd-shadow-sm docutils">
 <div class="sd-card-body docutils">
 <p class="sd-card-text"><span class="fa fa-chart-column fa-2x sd-text-success"></span></p>
-<p class="sd-card-text"><strong>Community diversity</strong> analysis for ecological studies, with an extensive suite of metrics such as <a class="reference external" href="docs/dev/generated/skbio.diversity.beta.weighted_unifrac.html">UniFrac</a> and <a class="reference external" href="docs/dev/generated/skbio.diversity.alpha.faith_pd.html">PD</a>, optimized to handle large-scale community datasets.</p>
+<p class="sd-card-text"><strong>Community diversity</strong> analysis for ecological studies, with an extensive suite of metrics such as <a class="reference external" href="https://scikit.bio/docs/dev/generated/skbio.diversity.beta.weighted_unifrac.html">UniFrac</a> and <a class="reference external" href="https://scikit.bio/docs/dev/generated/skbio.diversity.alpha.faith_pd.html">PD</a>, optimized to handle large-scale community datasets.</p>
 </div>
 </div>
 </div>
@@ -667,7 +667,7 @@
 <div class="sd-card sd-sphinx-override sd-w-100 sd-shadow-sm docutils">
 <div class="sd-card-body docutils">
 <p class="sd-card-text"><span class="fa fa-compass-drafting fa-2x sd-text-success"></span></p>
-<p class="sd-card-text"><strong>Ordination methods</strong>, such as <a class="reference external" href="docs/dev/generated/skbio.stats.ordination.pcoa.html">PCoA</a>, <a class="reference external" href="docs/dev/generated/skbio.stats.ordination.ca.html">CA</a>, and <a class="reference external" href="docs/dev/generated/skbio.stats.ordination.rda.html">RDA</a>, to uncover patterns underlying high-dimensional data, facilitating insightful visualization.</p>
+<p class="sd-card-text"><strong>Ordination methods</strong>, such as <a class="reference external" href="https://scikit.bio/docs/dev/generated/skbio.stats.ordination.pcoa.html">PCoA</a>, <a class="reference external" href="https://scikit.bio/docs/dev/generated/skbio.stats.ordination.ca.html">CA</a>, and <a class="reference external" href="https://scikit.bio/docs/dev/generated/skbio.stats.ordination.rda.html">RDA</a>, to uncover patterns underlying high-dimensional data, facilitating insightful visualization.</p>
 </div>
 </div>
 </div>
@@ -675,7 +675,7 @@
 <div class="sd-card sd-sphinx-override sd-w-100 sd-shadow-sm docutils">
 <div class="sd-card-body docutils">
 <p class="sd-card-text"><span class="fa fa-arrow-up-right-dots fa-2x sd-text-success"></span></p>
-<p class="sd-card-text"><strong>Multivariate statistical tests</strong>, such as <a class="reference external" href="docs/dev/generated/skbio.stats.distance.permanova.html">PERMANOVA</a>, <a class="reference external" href="docs/dev/generated/skbio.stats.distance.bioenv.html">BIOENV</a>, and <a class="reference external" href="docs/dev/generated/skbio.stats.distance.mantel.html">Mantel</a>, to decode complex relationships across data matrices and sample properties.</p>
+<p class="sd-card-text"><strong>Multivariate statistical tests</strong>, such as <a class="reference external" href="https://scikit.bio/docs/dev/generated/skbio.stats.distance.permanova.html">PERMANOVA</a>, <a class="reference external" href="https://scikit.bio/docs/dev/generated/skbio.stats.distance.bioenv.html">BIOENV</a>, and <a class="reference external" href="https://scikit.bio/docs/dev/generated/skbio.stats.distance.mantel.html">Mantel</a>, to decode complex relationships across data matrices and sample properties.</p>
 </div>
 </div>
 </div>
@@ -683,7 +683,7 @@
 <div class="sd-card sd-sphinx-override sd-w-100 sd-shadow-sm docutils">
 <div class="sd-card-body docutils">
 <p class="sd-card-text"><span class="fa fa-chart-pie fa-2x sd-text-success"></span></p>
-<p class="sd-card-text"><strong>Compositional data</strong> processing and analysis, such as <a class="reference external" href="docs/dev/generated/skbio.stats.composition.clr.html">CLR</a> transform and <a class="reference external" href="docs/dev/generated/skbio.stats.composition.ancom.html">ANCOM</a>, built for various omic data types from high-throughput experiments.</p>
+<p class="sd-card-text"><strong>Compositional data</strong> processing and analysis, such as <a class="reference external" href="https://scikit.bio/docs/dev/generated/skbio.stats.composition.clr.html">CLR</a> transform and <a class="reference external" href="https://scikit.bio/docs/dev/generated/skbio.stats.composition.ancom.html">ANCOM</a>, built for various omic data types from high-throughput experiments.</p>
 </div>
 </div>
 </div>
diff --git a/install.html b/install.html
index e8e0be058..76c3a7986 100644
--- a/install.html
+++ b/install.html
@@ -178,7 +178,7 @@
                 
 
                     <li class="nav-item">
-                      <a class="nav-link nav-external" href="docs/dev/index.html">
+                      <a class="nav-link nav-external" href="docs/latest/index.html">
                         Documentation
                       </a>
                     </li>
@@ -309,7 +309,7 @@
                 
 
                     <li class="nav-item">
-                      <a class="nav-link nav-external" href="docs/dev/index.html">
+                      <a class="nav-link nav-external" href="docs/latest/index.html">
                         Documentation
                       </a>
                     </li>
diff --git a/learn.html b/learn.html
index bc82bfcfe..57bc29e4a 100644
--- a/learn.html
+++ b/learn.html
@@ -178,7 +178,7 @@
                 
 
                     <li class="nav-item">
-                      <a class="nav-link nav-external" href="docs/dev/index.html">
+                      <a class="nav-link nav-external" href="docs/latest/index.html">
                         Documentation
                       </a>
                     </li>
@@ -309,7 +309,7 @@
                 
 
                     <li class="nav-item">
-                      <a class="nav-link nav-external" href="docs/dev/index.html">
+                      <a class="nav-link nav-external" href="docs/latest/index.html">
                         Documentation
                       </a>
                     </li>
diff --git a/search.html b/search.html
index 502f742af..9f4f0c3f0 100644
--- a/search.html
+++ b/search.html
@@ -177,7 +177,7 @@
                 
 
                     <li class="nav-item">
-                      <a class="nav-link nav-external" href="docs/dev/index.html">
+                      <a class="nav-link nav-external" href="docs/latest/index.html">
                         Documentation
                       </a>
                     </li>
@@ -306,7 +306,7 @@
                 
 
                     <li class="nav-item">
-                      <a class="nav-link nav-external" href="docs/dev/index.html">
+                      <a class="nav-link nav-external" href="docs/latest/index.html">
                         Documentation
                       </a>
                     </li>