Deploying to gh-pages from @ aaca179 🚀

Author: jkanche

.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: 9457f6f4933d9502416d1db4035a8346
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 52a5008e41b72d28c57a6159c9ab24d0
 tags: 645f666f9bcd5a90fca523b33c5a78b7

_modules/index.html

@@ -4,8 +4,8 @@
     <meta name="viewport" content="width=device-width,initial-scale=1"/>
     <meta name="color-scheme" content="light dark"><link rel="index" title="Index" href="../genindex.html" /><link rel="search" title="Search" href="../search.html" />
 
-    <!-- Generated with Sphinx 7.4.7 and Furo 2024.08.06 -->
-        <title>Overview: module code - SingleCellExperiment 0.4.7 documentation</title>
+    <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
+        <title>Overview: module code - SingleCellExperiment 0.5.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo.css?v=354aac6f" />
     <link rel="stylesheet" type="text/css" href="../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
@@ -166,7 +166,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../index.html"><div class="brand">SingleCellExperiment 0.4.7 documentation</div></a>
+      <a href="../index.html"><div class="brand">SingleCellExperiment 0.5.0 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -190,7 +190,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../index.html">
 
 
-  <span class="sidebar-brand-text">SingleCellExperiment 0.4.7 documentation</span>
+  <span class="sidebar-brand-text">SingleCellExperiment 0.5.0 documentation</span>
 
 </a><form class="sidebar-search-container" method="get" action="../search.html" role="search">
   <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -287,8 +287,8 @@ <h1>All modules for which code is available</h1>
 
     </aside>
   </div>
-</div><script src="../_static/documentation_options.js?v=a78bb796"></script>
-    <script src="../_static/doctools.js?v=9a2dae69"></script>
+</div><script src="../_static/documentation_options.js?v=1dd76d02"></script>
+    <script src="../_static/doctools.js?v=9bcbadda"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/scripts/furo.js?v=5fa4622c"></script>
     </body>

_modules/singlecellexperiment/SingleCellExperiment.html

@@ -4,8 +4,8 @@
     <meta name="viewport" content="width=device-width,initial-scale=1"/>
     <meta name="color-scheme" content="light dark"><link rel="index" title="Index" href="../../../genindex.html" /><link rel="search" title="Search" href="../../../search.html" />
 
-    <!-- Generated with Sphinx 7.4.7 and Furo 2024.08.06 -->
-        <title>singlecellexperiment.io.h5ad - SingleCellExperiment 0.4.7 documentation</title>
+    <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
+        <title>singlecellexperiment.io.h5ad - SingleCellExperiment 0.5.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="../../../_static/styles/furo.css?v=354aac6f" />
     <link rel="stylesheet" type="text/css" href="../../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
@@ -166,7 +166,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../../../index.html"><div class="brand">SingleCellExperiment 0.4.7 documentation</div></a>
+      <a href="../../../index.html"><div class="brand">SingleCellExperiment 0.5.0 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -190,7 +190,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../../../index.html">
 
 
-  <span class="sidebar-brand-text">SingleCellExperiment 0.4.7 documentation</span>
+  <span class="sidebar-brand-text">SingleCellExperiment 0.5.0 documentation</span>
 
 </a><form class="sidebar-search-container" method="get" action="../../../search.html" role="search">
   <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -308,8 +308,8 @@ <h1>Source code for singlecellexperiment.io.h5ad</h1><div class="highlight"><pre
 
     </aside>
   </div>
-</div><script src="../../../_static/documentation_options.js?v=a78bb796"></script>
-    <script src="../../../_static/doctools.js?v=9a2dae69"></script>
+</div><script src="../../../_static/documentation_options.js?v=1dd76d02"></script>
+    <script src="../../../_static/doctools.js?v=9bcbadda"></script>
     <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../../_static/scripts/furo.js?v=5fa4622c"></script>
     </body>

_modules/singlecellexperiment/io/h5ad.html

@@ -4,8 +4,8 @@
     <meta name="viewport" content="width=device-width,initial-scale=1"/>
     <meta name="color-scheme" content="light dark"><link rel="index" title="Index" href="../../../genindex.html" /><link rel="search" title="Search" href="../../../search.html" />
 
-    <!-- Generated with Sphinx 7.4.7 and Furo 2024.08.06 -->
-        <title>singlecellexperiment.io.tenx - SingleCellExperiment 0.4.7 documentation</title>
+    <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
+        <title>singlecellexperiment.io.tenx - SingleCellExperiment 0.5.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="../../../_static/styles/furo.css?v=354aac6f" />
     <link rel="stylesheet" type="text/css" href="../../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
@@ -166,7 +166,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../../../index.html"><div class="brand">SingleCellExperiment 0.4.7 documentation</div></a>
+      <a href="../../../index.html"><div class="brand">SingleCellExperiment 0.5.0 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -190,7 +190,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../../../index.html">
 
 
-  <span class="sidebar-brand-text">SingleCellExperiment 0.4.7 documentation</span>
+  <span class="sidebar-brand-text">SingleCellExperiment 0.5.0 documentation</span>
 
 </a><form class="sidebar-search-container" method="get" action="../../../search.html" role="search">
   <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -334,9 +334,7 @@ <h1>Source code for singlecellexperiment.io.tenx</h1><div class="highlight"><pre
     <span class="c1"># read the matrix</span>
     <span class="n">shape</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">h5</span><span class="p">[</span><span class="s2">&quot;matrix&quot;</span><span class="p">][</span><span class="s2">&quot;shape&quot;</span><span class="p">][:])</span>
 
-    <span class="n">counts</span> <span class="o">=</span> <span class="n">Hdf5CompressedSparseMatrix</span><span class="p">(</span>
-        <span class="n">path</span><span class="o">=</span><span class="n">path</span><span class="p">,</span> <span class="n">group_name</span><span class="o">=</span><span class="s2">&quot;matrix&quot;</span><span class="p">,</span> <span class="n">by_column</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">shape</span><span class="o">=</span><span class="n">shape</span>
-    <span class="p">)</span>
+    <span class="n">counts</span> <span class="o">=</span> <span class="n">Hdf5CompressedSparseMatrix</span><span class="p">(</span><span class="n">path</span><span class="o">=</span><span class="n">path</span><span class="p">,</span> <span class="n">group_name</span><span class="o">=</span><span class="s2">&quot;matrix&quot;</span><span class="p">,</span> <span class="n">by_column</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">shape</span><span class="o">=</span><span class="n">shape</span><span class="p">)</span>
 
     <span class="k">if</span> <span class="n">realize_assays</span> <span class="ow">is</span> <span class="kc">True</span><span class="p">:</span>
         <span class="n">counts</span> <span class="o">=</span> <span class="n">da</span><span class="o">.</span><span class="n">to_scipy_sparse_matrix</span><span class="p">(</span><span class="n">counts</span><span class="p">,</span> <span class="s2">&quot;csr&quot;</span><span class="p">)</span>
@@ -370,9 +368,7 @@ <h1>Source code for singlecellexperiment.io.tenx</h1><div class="highlight"><pre
 
     <span class="n">h5</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
 
-    <span class="k">return</span> <span class="n">SingleCellExperiment</span><span class="p">(</span>
-        <span class="n">assays</span><span class="o">=</span><span class="p">{</span><span class="s2">&quot;counts&quot;</span><span class="p">:</span> <span class="n">counts</span><span class="p">},</span> <span class="n">row_data</span><span class="o">=</span><span class="n">features</span><span class="p">,</span> <span class="n">column_data</span><span class="o">=</span><span class="n">barcodes</span>
-    <span class="p">)</span></div>
+    <span class="k">return</span> <span class="n">SingleCellExperiment</span><span class="p">(</span><span class="n">assays</span><span class="o">=</span><span class="p">{</span><span class="s2">&quot;counts&quot;</span><span class="p">:</span> <span class="n">counts</span><span class="p">},</span> <span class="n">row_data</span><span class="o">=</span><span class="n">features</span><span class="p">,</span> <span class="n">column_data</span><span class="o">=</span><span class="n">barcodes</span><span class="p">)</span></div>
 
 </pre></div>
         </article>
@@ -406,8 +402,8 @@ <h1>Source code for singlecellexperiment.io.tenx</h1><div class="highlight"><pre
 
     </aside>
   </div>
-</div><script src="../../../_static/documentation_options.js?v=a78bb796"></script>
-    <script src="../../../_static/doctools.js?v=9a2dae69"></script>
+</div><script src="../../../_static/documentation_options.js?v=1dd76d02"></script>
+    <script src="../../../_static/doctools.js?v=9bcbadda"></script>
     <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../../_static/scripts/furo.js?v=5fa4622c"></script>
     </body>

_modules/singlecellexperiment/io/tenx.html

@@ -1,5 +1,10 @@
 # Changelog
 
+## Version 0.5.0
+
+- chore: Remove Python 3.8 (EOL)
+- precommit: Replace docformatter with ruff's formatter
+
 ## Version 0.4.7
 
 - Fix package version issues to support Python<=3.9. Mostly related to how anndata dependencies are versioned in the MuData package discussed [here](https://github.com/scverse/mudata/issues/82).

_sources/changelog.md.txt

@@ -1,12 +1,5 @@
 /*
- * basic.css
- * ~~~~~~~~~
- *
  * Sphinx stylesheet -- basic theme.
- *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
  */
 
 /* -- main layout ----------------------------------------------------------- */
@@ -115,15 +108,11 @@ img {
 /* -- search page ----------------------------------------------------------- */
 
 ul.search {
-    margin: 10px 0 0 20px;
-    padding: 0;
+    margin-top: 10px;
 }
 
 ul.search li {
-    padding: 5px 0 5px 20px;
-    background-image: url(file.png);
-    background-repeat: no-repeat;
-    background-position: 0 7px;
+    padding: 5px 0;
 }
 
 ul.search li a {

_static/basic.css

@@ -1,12 +1,5 @@
 /*
- * doctools.js
- * ~~~~~~~~~~~
- *
  * Base JavaScript utilities for all Sphinx HTML documentation.
- *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
  */
 "use strict";
 

_static/doctools.js

@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '0.4.7',
+    VERSION: '0.5.0',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

_static/documentation_options.js

@@ -1,13 +1,6 @@
 /*
- * language_data.js
- * ~~~~~~~~~~~~~~~~
- *
  * This script contains the language-specific data used by searchtools.js,
  * namely the list of stopwords, stemmer, scorer and splitter.
- *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
  */
 
 var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"];