Deploying to gh-pages from @ 3daf3d8 🚀

.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: 94da59e4e46aab1f6778842c9a99d1a0
+config: 06d591b5f178db149daf8d6f046e5480
 tags: 645f666f9bcd5a90fca523b33c5a78b7

_modules/index.html

@@ -5,7 +5,7 @@
     <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 7.3.7 and Furo 2024.05.06 -->
-        <title>Overview: module code - scrnaseq 0.1.0 documentation</title>
+        <title>Overview: module code - scrnaseq 0.1.1 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=387cc868" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo-extensions.css?v=36a5483c" />
@@ -178,7 +178,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../index.html"><div class="brand">scrnaseq 0.1.0 documentation</div></a>
+      <a href="../index.html"><div class="brand">scrnaseq 0.1.1 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -202,7 +202,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../index.html">
 
 
-  <span class="sidebar-brand-text">scrnaseq 0.1.0 documentation</span>
+  <span class="sidebar-brand-text">scrnaseq 0.1.1 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">
@@ -295,7 +295,7 @@ <h1>All modules for which code is available</h1>
 
     </aside>
   </div>
-</div><script src="../_static/documentation_options.js?v=01f34227"></script>
+</div><script src="../_static/documentation_options.js?v=a58bc63e"></script>
     <script src="../_static/doctools.js?v=9a2dae69"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/scripts/furo.js?v=4e2eecee"></script>

_modules/scrnaseq/fetch_dataset.html

@@ -5,7 +5,7 @@
     <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 7.3.7 and Furo 2024.05.06 -->
-        <title>scrnaseq.fetch_dataset - scrnaseq 0.1.0 documentation</title>
+        <title>scrnaseq.fetch_dataset - scrnaseq 0.1.1 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=387cc868" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/furo-extensions.css?v=36a5483c" />
@@ -178,7 +178,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../../index.html"><div class="brand">scrnaseq 0.1.0 documentation</div></a>
+      <a href="../../index.html"><div class="brand">scrnaseq 0.1.1 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -202,7 +202,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../../index.html">
 
 
-  <span class="sidebar-brand-text">scrnaseq 0.1.0 documentation</span>
+  <span class="sidebar-brand-text">scrnaseq 0.1.1 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">
@@ -455,7 +455,7 @@ <h1>Source code for scrnaseq.fetch_dataset</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../../_static/documentation_options.js?v=01f34227"></script>
+</div><script src="../../_static/documentation_options.js?v=a58bc63e"></script>
     <script src="../../_static/doctools.js?v=9a2dae69"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/scripts/furo.js?v=4e2eecee"></script>

_modules/scrnaseq/list_datasets.html

@@ -5,7 +5,7 @@
     <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 7.3.7 and Furo 2024.05.06 -->
-        <title>scrnaseq.list_datasets - scrnaseq 0.1.0 documentation</title>
+        <title>scrnaseq.list_datasets - scrnaseq 0.1.1 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=387cc868" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/furo-extensions.css?v=36a5483c" />
@@ -178,7 +178,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../../index.html"><div class="brand">scrnaseq 0.1.0 documentation</div></a>
+      <a href="../../index.html"><div class="brand">scrnaseq 0.1.1 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -202,7 +202,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../../index.html">
 
 
-  <span class="sidebar-brand-text">scrnaseq 0.1.0 documentation</span>
+  <span class="sidebar-brand-text">scrnaseq 0.1.1 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">
@@ -327,7 +327,7 @@ <h1>Source code for scrnaseq.list_datasets</h1><div class="highlight"><pre>
 
 
 <span class="k">def</span> <span class="nf">_format_query_results</span><span class="p">(</span><span class="n">results</span><span class="p">:</span> <span class="nb">list</span><span class="p">,</span> <span class="n">key_names</span><span class="p">:</span> <span class="nb">list</span><span class="p">):</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;Format the results from sqlite as a pandas dataframe</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Format the results from sqlite as a pandas dataframe.</span>
 
 <span class="sd">    Key names must be in the exact same order as the query.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
@@ -485,7 +485,7 @@ <h1>Source code for scrnaseq.list_datasets</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../../_static/documentation_options.js?v=01f34227"></script>
+</div><script src="../../_static/documentation_options.js?v=a58bc63e"></script>
     <script src="../../_static/doctools.js?v=9a2dae69"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/scripts/furo.js?v=4e2eecee"></script>

_modules/scrnaseq/list_versions.html

@@ -5,7 +5,7 @@
     <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 7.3.7 and Furo 2024.05.06 -->
-        <title>scrnaseq.list_versions - scrnaseq 0.1.0 documentation</title>
+        <title>scrnaseq.list_versions - scrnaseq 0.1.1 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=387cc868" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/furo-extensions.css?v=36a5483c" />
@@ -178,7 +178,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../../index.html"><div class="brand">scrnaseq 0.1.0 documentation</div></a>
+      <a href="../../index.html"><div class="brand">scrnaseq 0.1.1 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -202,7 +202,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../../index.html">
 
 
-  <span class="sidebar-brand-text">scrnaseq 0.1.0 documentation</span>
+  <span class="sidebar-brand-text">scrnaseq 0.1.1 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">
@@ -338,7 +338,7 @@ <h1>Source code for scrnaseq.list_versions</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../../_static/documentation_options.js?v=01f34227"></script>
+</div><script src="../../_static/documentation_options.js?v=a58bc63e"></script>
     <script src="../../_static/doctools.js?v=9a2dae69"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/scripts/furo.js?v=4e2eecee"></script>

_modules/scrnaseq/polish_dataset.html

@@ -5,7 +5,7 @@
     <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 7.3.7 and Furo 2024.05.06 -->
-        <title>scrnaseq.polish_dataset - scrnaseq 0.1.0 documentation</title>
+        <title>scrnaseq.polish_dataset - scrnaseq 0.1.1 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=387cc868" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/furo-extensions.css?v=36a5483c" />
@@ -178,7 +178,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../../index.html"><div class="brand">scrnaseq 0.1.0 documentation</div></a>
+      <a href="../../index.html"><div class="brand">scrnaseq 0.1.1 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -202,7 +202,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../../index.html">
 
 
-  <span class="sidebar-brand-text">scrnaseq 0.1.0 documentation</span>
+  <span class="sidebar-brand-text">scrnaseq 0.1.1 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">
@@ -256,10 +256,8 @@
         <article role="main" id="furo-main-content">
           <h1>Source code for scrnaseq.polish_dataset</h1><div class="highlight"><pre>
 <span></span><span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Type</span>
-<span class="kn">from</span> <span class="nn">warnings</span> <span class="kn">import</span> <span class="n">warn</span>
 
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
-<span class="kn">from</span> <span class="nn">delayedarray</span> <span class="kn">import</span> <span class="n">DelayedArray</span>
 <span class="kn">from</span> <span class="nn">scipy</span> <span class="kn">import</span> <span class="n">sparse</span> <span class="k">as</span> <span class="n">sp</span>
 <span class="kn">from</span> <span class="nn">singlecellexperiment</span> <span class="kn">import</span> <span class="n">SingleCellExperiment</span>
 <span class="kn">from</span> <span class="nn">summarizedexperiment</span> <span class="kn">import</span> <span class="n">SummarizedExperiment</span>
@@ -421,7 +419,7 @@ <h1>Source code for scrnaseq.polish_dataset</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../../_static/documentation_options.js?v=01f34227"></script>
+</div><script src="../../_static/documentation_options.js?v=a58bc63e"></script>
     <script src="../../_static/doctools.js?v=9a2dae69"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/scripts/furo.js?v=4e2eecee"></script>

_modules/scrnaseq/save_dataset.html

@@ -5,7 +5,7 @@
     <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 7.3.7 and Furo 2024.05.06 -->
-        <title>scrnaseq.save_dataset - scrnaseq 0.1.0 documentation</title>
+        <title>scrnaseq.save_dataset - scrnaseq 0.1.1 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=387cc868" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/furo-extensions.css?v=36a5483c" />
@@ -178,7 +178,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../../index.html"><div class="brand">scrnaseq 0.1.0 documentation</div></a>
+      <a href="../../index.html"><div class="brand">scrnaseq 0.1.1 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -202,7 +202,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../../index.html">
 
 
-  <span class="sidebar-brand-text">scrnaseq 0.1.0 documentation</span>
+  <span class="sidebar-brand-text">scrnaseq 0.1.1 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">
@@ -288,7 +288,7 @@ <h1>Source code for scrnaseq.save_dataset</h1><div class="highlight"><pre>
 
 <span class="sd">        metadata:</span>
 <span class="sd">            Dictionary containing the metadata for this dataset.</span>
-<span class="sd">            see the schema returned by </span>
+<span class="sd">            see the schema returned by</span>
 <span class="sd">            :py:func:`~gypsum_client.fetch_metadata_schema.fetch_metadata_schema`.</span>
 
 <span class="sd">            Note that the ``applications.takane`` property will be automatically</span>
@@ -425,7 +425,7 @@ <h1>Source code for scrnaseq.save_dataset</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../../_static/documentation_options.js?v=01f34227"></script>
+</div><script src="../../_static/documentation_options.js?v=a58bc63e"></script>
     <script src="../../_static/doctools.js?v=9a2dae69"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/scripts/furo.js?v=4e2eecee"></script>

_modules/scrnaseq/search_datasets.html

@@ -5,7 +5,7 @@
     <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 7.3.7 and Furo 2024.05.06 -->
-        <title>scrnaseq.search_datasets - scrnaseq 0.1.0 documentation</title>
+        <title>scrnaseq.search_datasets - scrnaseq 0.1.1 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=387cc868" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/furo-extensions.css?v=36a5483c" />
@@ -178,7 +178,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../../index.html"><div class="brand">scrnaseq 0.1.0 documentation</div></a>
+      <a href="../../index.html"><div class="brand">scrnaseq 0.1.1 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -202,7 +202,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../../index.html">
 
 
-  <span class="sidebar-brand-text">scrnaseq 0.1.0 documentation</span>
+  <span class="sidebar-brand-text">scrnaseq 0.1.1 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">
@@ -256,14 +256,13 @@
         <article role="main" id="furo-main-content">
           <h1>Source code for scrnaseq.search_datasets</h1><div class="highlight"><pre>
 <span></span><span class="kn">import</span> <span class="nn">sqlite3</span>
+<span class="kn">from</span> <span class="nn">functools</span> <span class="kn">import</span> <span class="n">lru_cache</span>
 <span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Union</span>
 
 <span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
 <span class="kn">from</span> <span class="nn">gypsum_client</span> <span class="kn">import</span> <span class="n">cache_directory</span><span class="p">,</span> <span class="n">fetch_metadata_database</span>
 <span class="kn">from</span> <span class="nn">gypsum_client.search_metadata</span> <span class="kn">import</span> <span class="p">(</span>
     <span class="n">GypsumSearchClause</span><span class="p">,</span>
-    <span class="n">define_text_query</span><span class="p">,</span>
-    <span class="n">search_metadata_text</span><span class="p">,</span>
     <span class="n">search_metadata_text_filter</span><span class="p">,</span>
 <span class="p">)</span>
 
@@ -276,14 +275,14 @@ <h1>Source code for scrnaseq.search_datasets</h1><div class="highlight"><pre>
 
 <div class="viewcode-block" id="search_datasets">
 <a class="viewcode-back" href="../../api/scrnaseq.html#scrnaseq.search_datasets.search_datasets">[docs]</a>
+<span class="nd">@lru_cache</span>
 <span class="k">def</span> <span class="nf">search_datasets</span><span class="p">(</span>
     <span class="n">query</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">GypsumSearchClause</span><span class="p">],</span>
     <span class="n">cache_dir</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">cache_directory</span><span class="p">(),</span>
     <span class="n">overwrite</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
     <span class="n">latest</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">:</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;Search for datasets of interest based on matching text in the</span>
-<span class="sd">    associated metadata.</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Search for datasets of interest based on matching text in the associated metadata.</span>
 
 <span class="sd">    This is a wrapper around</span>
 <span class="sd">    :py:func:`~gypsum_client.search_metadata.search_metadata_text`.</span>
@@ -404,7 +403,7 @@ <h1>Source code for scrnaseq.search_datasets</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../../_static/documentation_options.js?v=01f34227"></script>
+</div><script src="../../_static/documentation_options.js?v=a58bc63e"></script>
     <script src="../../_static/doctools.js?v=9a2dae69"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/scripts/furo.js?v=4e2eecee"></script>