Update from scikit-bio/scikit-bio@df5d62a

scikit-bio · Mar 28, 2024 · 903eed9 · 903eed9
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diff --git 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
@@ -177,7 +177,7 @@
 
 
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-                      <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
@@ -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
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                     <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
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diff --git 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
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@@ -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
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diff --git a/devdoc/doc_guide.html b/devdoc/doc_guide.html
@@ -178,7 +178,7 @@
 
 
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-                      <a class="nav-link nav-external" href="../docs/dev/index.html">
+                      <a class="nav-link nav-external" href="../docs/latest/index.html">
                         Documentation
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@@ -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
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@@ -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
@@ -178,7 +178,7 @@
 
 
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+                      <a class="nav-link nav-external" href="../docs/latest/index.html">
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@@ -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>
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diff --git 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">
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@@ -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
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diff --git 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">
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@@ -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
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diff --git a/genindex.html b/genindex.html
@@ -175,7 +175,7 @@
 
 
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@@ -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
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diff --git a/index.html b/index.html
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                     <li class="nav-item">
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                     <li class="nav-item">
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@@ -643,47 +643,47 @@
 <div class="sd-card sd-sphinx-override sd-w-100 sd-shadow-sm docutils">
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 <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>
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-<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>
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-<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>
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-<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>
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-<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>
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-<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>
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diff --git a/install.html b/install.html
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