Update latest documentation

sgkit-dev · Sep 17, 2024 · b84fe9f · b84fe9f
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diff --git a/latest/_sources/changelog.rst.txt b/latest/_sources/changelog.rst.txt
@@ -26,8 +26,11 @@ New Features
 .. Bug fixes
 .. ~~~~~~~~~
 
-.. Documentation
-.. ~~~~~~~~~~~~~
+Documentation
+~~~~~~~~~~~~~
+
+- Update GWAS tutorial to use ``vcf2zarr``.
+  (:user:`tomwhite`, :pr:`1258`, :issue:`1257`)
 
 .. _changelog.0.9.0:
 

diff --git a/latest/_sources/examples/gwas_tutorial.ipynb.txt b/latest/_sources/examples/gwas_tutorial.ipynb.txt
diff --git a/latest/about.html b/latest/about.html
@@ -56,13 +56,9 @@
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="News" href="news.html" />
-    <link rel="prev" title="Contributing to sgkit" href="contributing.html" />
-
+    <link rel="prev" title="Contributing to sgkit" href="contributing.html" /> 
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
-  <meta name="docsearch:language" content="en"/>
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+  <meta name="docsearch:language" content="en"/>   
   </head>
 
 
@@ -549,8 +545,7 @@
 
 <div id="searchbox"></div>
                 <article class="bd-article">
-
-<section id="about">
+                   <section id="about">
 <span id="id1"></span><h1>About<a class="headerlink" href="#about" title="Permalink to this heading">#</a></h1>
 <a class="reference external image-reference" href="https://numfocus.org/"><img alt="_images/numfocus_logo.png" src="_images/numfocus_logo.png" style="width: 345.0px; height: 115.0px;" /></a>
 <p>Sgkit is a fiscally sponsored project of <a class="reference external" href="https://numfocus.org">NumFOCUS</a>, a nonprofit dedicated
@@ -564,8 +559,7 @@
 </section>
 
 <div class="section ablog__blog_comments">
-
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                 </article>

diff --git a/latest/api.html b/latest/api.html
@@ -56,13 +56,9 @@
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="sgkit.io.bgen.bgen_to_zarr" href="generated/sgkit.io.bgen.bgen_to_zarr.html" />
-    <link rel="prev" title="Relatedness Tutorial" href="examples/relatedness_tutorial.html" />
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+    <link rel="prev" title="Relatedness Tutorial" href="examples/relatedness_tutorial.html" /> 
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@@ -740,8 +736,7 @@
 
 <div id="searchbox"></div>
                 <article class="bd-article">
-
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+                   <section id="api-reference">
 <h1>API reference<a class="headerlink" href="#api-reference" title="Permalink to this heading">#</a></h1>
 <p>This page provides an auto-generated summary of sgkits’s API.</p>
 <section id="io-imports-and-exports">
@@ -1357,8 +1352,7 @@ <h2>Utilities<a class="headerlink" href="#utilities" title="Permalink to this he
 </section>
 
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 </div>
 
                 </article>

diff --git a/latest/blog.html b/latest/blog.html
@@ -53,20 +53,16 @@
     <script defer="defer" src="_static/docsearch.sbt.js"></script>
     <link rel="author" title="About these documents" href="about.html" />
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   <meta name="viewport" content="width=device-width, initial-scale=1"/>
-  <meta name="docsearch:language" content="en"/>
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+  <meta name="docsearch:language" content="en"/> 
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   title=""
 />
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@@ -542,78 +538,62 @@
 
 <div id="searchbox"></div>
                 <article class="bd-article">
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+
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   <h1>
 
-      <span>All
-
-    Posts
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+    <span
+      >All  Posts 
+    </span>
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+
   <div class="section ablog-post">
     <h2 class="ablog-post-title">
       <a href="news/introducing_sgkit.html">Introducing sgkit</a>
     </h2>
     <ul class="ablog-archive">
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         <i class="fa fa-calendar"></i>
 
         <span>01 August 2022</span>
 
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-  <span>
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+  <li id="ablog-sidebar-item author ablog__author">
+    <span>
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+      <i class="fa-fw fa fa-user"></i>
+
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+    <a href="blog/author/hammer.html">hammer</a>
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+  </li>
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+  <li id="ablog-sidebar-item category ablog__category">
+    <span>
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+      <i class="fa-fw fa fa-folder-open"></i>
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-  <a href="blog/category/releases.html">releases</a>
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+    <a href="blog/category/releases.html">releases</a>
+
+  </li>
+
 </div>
     </ul>
     <p class="ablog-post-excerpt"><p>The sgkit team is pleased to announce the release of <a class="reference external" href="https://github.com/sgkit-dev/sgkit/releases/tag/0.5.0">sgkit 0.5.0</a>! This release adds support for the <a class="reference external" href="https://github.com/sgkit-dev/vcf-zarr-spec">VCF Zarr specification</a>, which describes an encoding of VCF data in chunked-columnar form using the <a class="reference external" href="https://zarr.readthedocs.io/en/stable/">Zarr format</a>.</p>
 </p>
 
-    <p class="ablog-post-expand"><a href="news/introducing_sgkit.html"><em>Read more ...</em></a></p>
-    <hr/>
+    <p class="ablog-post-expand">
+      <a href="news/introducing_sgkit.html"><em>Read more ...</em></a>
+    </p>
+    <hr />
   </div>
-
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+
 </div>
 
                 </article>

diff --git a/latest/blog/2022.html b/latest/blog/2022.html
@@ -53,20 +53,16 @@
     <script defer="defer" src="../_static/docsearch.sbt.js"></script>
     <link rel="author" title="About these documents" href="../about.html" />
     <link rel="index" title="Index" href="../genindex.html" />
-    <link rel="search" title="Search" href="../search.html" />
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   <meta name="viewport" content="width=device-width, initial-scale=1"/>
-  <meta name="docsearch:language" content="en"/>
-
+  <meta name="docsearch:language" content="en"/> 
 <link
   rel="alternate"
   type="application/atom+xml"
   href="../blog/atom.xml"
   title="Posted in 2022"
 />
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@@ -542,78 +538,62 @@
 
 <div id="searchbox"></div>
                 <article class="bd-article">
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   <h1>
 
-      <span>Posted in
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-    2022
-
-  </span>
+    <span
+      >Posted in  2022 
+    </span>
   </h1>
-
-
+
   <div class="section ablog-post">
     <h2 class="ablog-post-title">
       <a href="../news/introducing_sgkit.html">Introducing sgkit</a>
     </h2>
     <ul class="ablog-archive">
       <li>
-
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         <i class="fa fa-calendar"></i>
 
         <span>01 August 2022</span>
 
       </li>
       <div class="ablog-sidebar-item ablog__postcard2">
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-  <span>
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+  <li id="ablog-sidebar-item author ablog__author">
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+    <a href="author/hammer.html">hammer</a>
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+
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-  <a href="category/releases.html">releases</a>
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+
+    <a href="category/releases.html">releases</a>
+
+  </li>
+
 </div>
     </ul>
     <p class="ablog-post-excerpt"><p>The sgkit team is pleased to announce the release of <a class="reference external" href="https://github.com/sgkit-dev/sgkit/releases/tag/0.5.0">sgkit 0.5.0</a>! This release adds support for the <a class="reference external" href="https://github.com/sgkit-dev/vcf-zarr-spec">VCF Zarr specification</a>, which describes an encoding of VCF data in chunked-columnar form using the <a class="reference external" href="https://zarr.readthedocs.io/en/stable/">Zarr format</a>.</p>
 </p>
 
-    <p class="ablog-post-expand"><a href="../news/introducing_sgkit.html"><em>Read more ...</em></a></p>
-    <hr/>
+    <p class="ablog-post-expand">
+      <a href="../news/introducing_sgkit.html"><em>Read more ...</em></a>
+    </p>
+    <hr />
   </div>
-
-
+
 </div>
 
                 </article>