Deploying to gh-pages from @ bcad34d 🚀

.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: 2b0adff3c8bf010f7feabb9f9c1e7ac1
+config: c4511841f97a030af4792e6187835bb8
 tags: 645f666f9bcd5a90fca523b33c5a78b7

_modules/index.html

@@ -13,7 +13,7 @@
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
         <script src="../_static/documentation_options.js?v=360bc84d"></script>
-        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/doctools.js?v=9a2dae69"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />

_modules/pandasaurus_cxg/anndata_analyzer.html

@@ -13,7 +13,7 @@
         <script src="../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
         <script src="../../_static/documentation_options.js?v=360bc84d"></script>
-        <script src="../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />

_modules/pandasaurus_cxg/anndata_enricher.html

@@ -13,7 +13,7 @@
         <script src="../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
         <script src="../../_static/documentation_options.js?v=360bc84d"></script>
-        <script src="../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
@@ -122,10 +122,14 @@ <h1>Source code for pandasaurus_cxg.anndata_enricher</h1><div class="highlight">
         <span class="c1"># TODO Do we need to keep whole anndata? Would it be enough to keep the obs only?</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">anndata</span> <span class="o">=</span> <span class="n">anndata</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">seed_dict</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">anndata</span><span class="o">.</span><span class="n">obs</span><span class="o">.</span><span class="n">drop_duplicates</span><span class="p">(</span><span class="n">subset</span><span class="o">=</span><span class="p">[</span><span class="n">cell_type_field</span><span class="p">,</span> <span class="s2">&quot;cell_type&quot;</span><span class="p">])</span><span class="o">.</span><span class="n">dropna</span><span class="p">()[</span>
-                <span class="p">[</span><span class="n">cell_type_field</span><span class="p">,</span> <span class="s2">&quot;cell_type&quot;</span><span class="p">]</span>
-            <span class="p">]</span><span class="o">.</span><span class="n">values</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">anndata</span><span class="o">.</span><span class="n">obs</span><span class="o">.</span><span class="n">drop_duplicates</span><span class="p">(</span><span class="n">subset</span><span class="o">=</span><span class="p">[</span><span class="n">cell_type_field</span><span class="p">,</span> <span class="s2">&quot;cell_type&quot;</span><span class="p">])</span>
+            <span class="o">.</span><span class="n">dropna</span><span class="p">()[[</span><span class="n">cell_type_field</span><span class="p">,</span> <span class="s2">&quot;cell_type&quot;</span><span class="p">]]</span>
+            <span class="o">.</span><span class="n">values</span>
         <span class="p">)</span>
+        <span class="c1"># &quot;unknown&quot; patch</span>
+        <span class="k">if</span> <span class="s2">&quot;unknown&quot;</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">seed_dict</span><span class="p">:</span>
+            <span class="k">del</span> <span class="bp">self</span><span class="o">.</span><span class="n">seed_dict</span><span class="p">[</span><span class="s2">&quot;unknown&quot;</span><span class="p">]</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">seed_dict</span><span class="p">[</span><span class="s2">&quot;CL:0000000&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="s2">&quot;cell&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">enricher</span> <span class="o">=</span> <span class="n">Query</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">seed_dict</span><span class="o">.</span><span class="n">keys</span><span class="p">()))</span>
         <span class="k">try</span><span class="p">:</span>
             <span class="n">unique_context</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">anndata</span><span class="o">.</span><span class="n">obs</span><span class="p">[</span>

_modules/pandasaurus_cxg/enrichment_analysis.html

@@ -13,7 +13,7 @@
         <script src="../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
         <script src="../../_static/documentation_options.js?v=360bc84d"></script>
-        <script src="../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />

_modules/pandasaurus_cxg/graph_generator/graph_generator.html

@@ -13,7 +13,7 @@
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
         <script src="../../../_static/documentation_options.js?v=360bc84d"></script>
-        <script src="../../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../../genindex.html" />

_modules/pandasaurus_cxg/graph_generator/graph_generator_utils.html

@@ -13,7 +13,7 @@
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
         <script src="../../../_static/documentation_options.js?v=360bc84d"></script>
-        <script src="../../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../../genindex.html" />

_modules/pandasaurus_cxg/utils/anndata_loader.html

@@ -13,7 +13,7 @@
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
         <script src="../../../_static/documentation_options.js?v=360bc84d"></script>
-        <script src="../../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../../genindex.html" />

_modules/pandasaurus_cxg/utils/exceptions.html

@@ -13,7 +13,7 @@
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
         <script src="../../../_static/documentation_options.js?v=360bc84d"></script>
-        <script src="../../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../../genindex.html" />

_static/basic.css

@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

_static/doctools.js

@@ -4,7 +4,7 @@
  *
  * Base JavaScript utilities for all Sphinx HTML documentation.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

_static/language_data.js

@@ -5,15 +5,15 @@
  * This script contains the language-specific data used by searchtools.js,
  * namely the list of stopwords, stemmer, scorer and splitter.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :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"];
 
 
-/* Non-minified version is copied as a separate JS file, is available */
+/* Non-minified version is copied as a separate JS file, if available */
 
 /**
  * Porter Stemmer