Deploying to gh-pages from @ c7c28d9 🚀

.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: 292dc02fd06cfdc97be2832db4ffae7c
+config: eafa99ec19f2fce7bf4d88028139d8ec
 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 7.2.6 and Furo 2023.09.10 -->
-        <title>Overview: module code - SingleCellExperiment 0.4.3 documentation</title>
+    <!-- Generated with Sphinx 7.2.6 and Furo 2024.01.29 -->
+        <title>Overview: module code - SingleCellExperiment 0.4.4 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=135e06be" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo-extensions.css?v=36a5483c" />
@@ -122,7 +122,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../index.html"><div class="brand">SingleCellExperiment 0.4.3 documentation</div></a>
+      <a href="../index.html"><div class="brand">SingleCellExperiment 0.4.4 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -145,7 +145,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../index.html">
 
 
-  <span class="sidebar-brand-text">SingleCellExperiment 0.4.3 documentation</span>
+  <span class="sidebar-brand-text">SingleCellExperiment 0.4.4 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">
@@ -241,7 +241,7 @@ <h1>All modules for which code is available</h1>
 
     </aside>
   </div>
-</div><script src="../_static/documentation_options.js?v=5bfaad31"></script>
+</div><script src="../_static/documentation_options.js?v=90733dfc"></script>
     <script src="../_static/doctools.js?v=888ff710"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/scripts/furo.js?v=32e29ea5"></script>

_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 7.2.6 and Furo 2023.09.10 -->
-        <title>singlecellexperiment.SingleCellExperiment - SingleCellExperiment 0.4.3 documentation</title>
+    <!-- Generated with Sphinx 7.2.6 and Furo 2024.01.29 -->
+        <title>singlecellexperiment.SingleCellExperiment - SingleCellExperiment 0.4.4 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=135e06be" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/furo-extensions.css?v=36a5483c" />
@@ -122,7 +122,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../../index.html"><div class="brand">SingleCellExperiment 0.4.3 documentation</div></a>
+      <a href="../../index.html"><div class="brand">SingleCellExperiment 0.4.4 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -145,7 +145,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../../index.html">
 
 
-  <span class="sidebar-brand-text">SingleCellExperiment 0.4.3 documentation</span>
+  <span class="sidebar-brand-text">SingleCellExperiment 0.4.4 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">
@@ -212,7 +212,6 @@ <h1>Source code for singlecellexperiment.SingleCellExperiment</h1><div class="hi
 
 <span class="kn">import</span> <span class="nn">biocframe</span>
 <span class="kn">import</span> <span class="nn">biocutils</span> <span class="k">as</span> <span class="nn">ut</span>
-<span class="kn">from</span> <span class="nn">genomicranges</span> <span class="kn">import</span> <span class="n">GenomicRanges</span>
 <span class="kn">from</span> <span class="nn">summarizedexperiment._combineutils</span> <span class="kn">import</span> <span class="p">(</span>
     <span class="n">check_assays_are_equal</span><span class="p">,</span>
     <span class="n">merge_assays</span><span class="p">,</span>
@@ -1271,25 +1270,16 @@ <h1>Source code for singlecellexperiment.SingleCellExperiment</h1><div class="hi
 <span class="sd">        Returns:</span>
 <span class="sd">            A tuple with ``AnnData`` main experiment and a list of alternative experiments.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="kn">from</span> <span class="nn">anndata</span> <span class="kn">import</span> <span class="n">AnnData</span>
+        <span class="n">obj</span> <span class="o">=</span> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="n">to_anndata</span><span class="p">()</span>
 
-        <span class="n">layers</span> <span class="o">=</span> <span class="n">OrderedDict</span><span class="p">()</span>
-        <span class="k">for</span> <span class="n">asy</span><span class="p">,</span> <span class="n">mat</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">assays</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
-            <span class="n">layers</span><span class="p">[</span><span class="n">asy</span><span class="p">]</span> <span class="o">=</span> <span class="n">mat</span><span class="o">.</span><span class="n">transpose</span><span class="p">()</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">reduced_dims</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="n">obj</span><span class="o">.</span><span class="n">obsm</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">reduced_dims</span>
 
-        <span class="n">trows</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">row_data</span>
-        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">row_data</span><span class="p">,</span> <span class="n">GenomicRanges</span><span class="p">):</span>
-            <span class="n">trows</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">row_data</span><span class="o">.</span><span class="n">to_pandas</span><span class="p">()</span>
-
-        <span class="n">obj</span> <span class="o">=</span> <span class="n">AnnData</span><span class="p">(</span>
-            <span class="n">obs</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">col_data</span><span class="p">,</span>
-            <span class="n">var</span><span class="o">=</span><span class="n">trows</span><span class="p">,</span>
-            <span class="n">uns</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">metadata</span><span class="p">,</span>
-            <span class="n">obsm</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">reduced_dims</span><span class="p">,</span>
-            <span class="n">layers</span><span class="o">=</span><span class="n">layers</span><span class="p">,</span>
-            <span class="n">varp</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">row_pairs</span><span class="p">,</span>
-            <span class="n">obsp</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">column_pairs</span><span class="p">,</span>
-        <span class="p">)</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">row_pairs</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="n">obj</span><span class="o">.</span><span class="n">varp</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">row_pairs</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">column_pairs</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="n">obj</span><span class="o">.</span><span class="n">obsp</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">column_pairs</span>
 
         <span class="k">if</span> <span class="n">include_alternative_experiments</span> <span class="ow">is</span> <span class="kc">True</span><span class="p">:</span>
             <span class="n">adatas</span> <span class="o">=</span> <span class="kc">None</span>
@@ -1301,8 +1291,6 @@ <h1>Source code for singlecellexperiment.SingleCellExperiment</h1><div class="hi
                 <span class="p">)</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">alternative_experiments</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
                     <span class="n">adatas</span><span class="p">[</span><span class="n">alt_name</span><span class="p">]</span> <span class="o">=</span> <span class="n">alternative_experiment</span><span class="o">.</span><span class="n">to_anndata</span><span class="p">()</span>
 
-            <span class="k">return</span> <span class="n">obj</span><span class="p">,</span> <span class="n">adatas</span>
-
         <span class="k">return</span> <span class="n">obj</span><span class="p">,</span> <span class="kc">None</span></div>
 
 
@@ -1643,7 +1631,7 @@ <h1>Source code for singlecellexperiment.SingleCellExperiment</h1><div class="hi
 
     </aside>
   </div>
-</div><script src="../../_static/documentation_options.js?v=5bfaad31"></script>
+</div><script src="../../_static/documentation_options.js?v=90733dfc"></script>
     <script src="../../_static/doctools.js?v=888ff710"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/scripts/furo.js?v=32e29ea5"></script>

_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 7.2.6 and Furo 2023.09.10 -->
-        <title>singlecellexperiment.io.h5ad - SingleCellExperiment 0.4.3 documentation</title>
+    <!-- Generated with Sphinx 7.2.6 and Furo 2024.01.29 -->
+        <title>singlecellexperiment.io.h5ad - SingleCellExperiment 0.4.4 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=135e06be" />
     <link rel="stylesheet" type="text/css" href="../../../_static/styles/furo-extensions.css?v=36a5483c" />
@@ -122,7 +122,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../../../index.html"><div class="brand">SingleCellExperiment 0.4.3 documentation</div></a>
+      <a href="../../../index.html"><div class="brand">SingleCellExperiment 0.4.4 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -145,7 +145,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../../../index.html">
 
 
-  <span class="sidebar-brand-text">SingleCellExperiment 0.4.3 documentation</span>
+  <span class="sidebar-brand-text">SingleCellExperiment 0.4.4 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">
@@ -262,7 +262,7 @@ <h1>Source code for singlecellexperiment.io.h5ad</h1><div class="highlight"><pre
 
     </aside>
   </div>
-</div><script src="../../../_static/documentation_options.js?v=5bfaad31"></script>
+</div><script src="../../../_static/documentation_options.js?v=90733dfc"></script>
     <script src="../../../_static/doctools.js?v=888ff710"></script>
     <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../../_static/scripts/furo.js?v=32e29ea5"></script>

_modules/singlecellexperiment/io/tenx.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 7.2.6 and Furo 2023.09.10 -->
-        <title>singlecellexperiment.io.tenx - SingleCellExperiment 0.4.3 documentation</title>
+    <!-- Generated with Sphinx 7.2.6 and Furo 2024.01.29 -->
+        <title>singlecellexperiment.io.tenx - SingleCellExperiment 0.4.4 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=135e06be" />
     <link rel="stylesheet" type="text/css" href="../../../_static/styles/furo-extensions.css?v=36a5483c" />
@@ -122,7 +122,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../../../index.html"><div class="brand">SingleCellExperiment 0.4.3 documentation</div></a>
+      <a href="../../../index.html"><div class="brand">SingleCellExperiment 0.4.4 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -145,7 +145,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../../../index.html">
 
 
-  <span class="sidebar-brand-text">SingleCellExperiment 0.4.3 documentation</span>
+  <span class="sidebar-brand-text">SingleCellExperiment 0.4.4 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">
@@ -355,7 +355,7 @@ <h1>Source code for singlecellexperiment.io.tenx</h1><div class="highlight"><pre
 
     </aside>
   </div>
-</div><script src="../../../_static/documentation_options.js?v=5bfaad31"></script>
+</div><script src="../../../_static/documentation_options.js?v=90733dfc"></script>
     <script src="../../../_static/doctools.js?v=888ff710"></script>
     <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../../_static/scripts/furo.js?v=32e29ea5"></script>

_static/documentation_options.js

@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '0.4.3',
+    VERSION: '0.4.4',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

api/modules.html

@@ -5,8 +5,8 @@
     <meta name="color-scheme" content="light dark"><meta name="viewport" content="width=device-width, initial-scale=1" />
 <link rel="index" title="Index" href="../genindex.html" /><link rel="search" title="Search" href="../search.html" /><link rel="next" title="singlecellexperiment package" href="singlecellexperiment.html" /><link rel="prev" title="Tutorial" href="../tutorial.html" />
 
-    <!-- Generated with Sphinx 7.2.6 and Furo 2023.09.10 -->
-        <title>singlecellexperiment - SingleCellExperiment 0.4.3 documentation</title>
+    <!-- Generated with Sphinx 7.2.6 and Furo 2024.01.29 -->
+        <title>singlecellexperiment - SingleCellExperiment 0.4.4 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=135e06be" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo-extensions.css?v=36a5483c" />
@@ -123,7 +123,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../index.html"><div class="brand">SingleCellExperiment 0.4.3 documentation</div></a>
+      <a href="../index.html"><div class="brand">SingleCellExperiment 0.4.4 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -146,7 +146,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../index.html">
 
 
-  <span class="sidebar-brand-text">SingleCellExperiment 0.4.3 documentation</span>
+  <span class="sidebar-brand-text">SingleCellExperiment 0.4.4 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">
@@ -326,7 +326,7 @@ <h1>singlecellexperiment<a class="headerlink" href="#singlecellexperiment" title
 
     </aside>
   </div>
-</div><script src="../_static/documentation_options.js?v=5bfaad31"></script>
+</div><script src="../_static/documentation_options.js?v=90733dfc"></script>
     <script src="../_static/doctools.js?v=888ff710"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/scripts/furo.js?v=32e29ea5"></script>