From dda7e6bb7152b80cbc26d8961b5b479c2432ca20 Mon Sep 17 00:00:00 2001
From: morriscb <morriscb@users.noreply.github.com>
Date: Thu, 20 Jun 2024 21:20:30 +0000
Subject: [PATCH] deploy: bb3f4c95be992e6535d8bc7c2d974cd78db95148

---
 _sources/intro.md                                            | 2 ++
 .../notebooks/general_accessing_10x_snRNASeq_tutorial.ipynb  | 2 +-
 _sources/notebooks/getting_started.ipynb                     | 4 ++--
 intro.html                                                   | 5 +++++
 notebooks/getting_started.html                               | 2 +-
 searchindex.js                                               | 2 +-
 6 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/_sources/intro.md b/_sources/intro.md
index 18e3092..ecdc192 100644
--- a/_sources/intro.md
+++ b/_sources/intro.md
@@ -58,6 +58,8 @@ Available notebooks:
   (Kimberly Siletti)**
 
 ## Release Notes
+* **[abc_atlas_access (v0.1.0)]**
+  * Fixed issue with loading 10X mouse data with the `get_gene_data` function.
 * **[Spring 2024 Public Beta (version 20240330)]**
   * Added Whole Human Brain transcriptomic, taxonomy and clustering datasets
     from Siletti et al. 2023 to the ABC Atlas.
diff --git a/_sources/notebooks/general_accessing_10x_snRNASeq_tutorial.ipynb b/_sources/notebooks/general_accessing_10x_snRNASeq_tutorial.ipynb
index c7a38c0..d4df1d5 100644
--- a/_sources/notebooks/general_accessing_10x_snRNASeq_tutorial.ipynb
+++ b/_sources/notebooks/general_accessing_10x_snRNASeq_tutorial.ipynb
@@ -983,7 +983,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.8"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,
diff --git a/_sources/notebooks/getting_started.ipynb b/_sources/notebooks/getting_started.ipynb
index df30b21..efb2930 100644
--- a/_sources/notebooks/getting_started.ipynb
+++ b/_sources/notebooks/getting_started.ipynb
@@ -121,7 +121,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# get_ipython().kernel.do_shutdown()"
+    "get_ipython().kernel.do_shutdown(restart=True)"
    ]
   },
   {
@@ -1321,7 +1321,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.8"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,
diff --git a/intro.html b/intro.html
index 49e3f5b..b9325a6 100644
--- a/intro.html
+++ b/intro.html
@@ -508,6 +508,11 @@ <h1>Allen Brain Cell Atlas - Data Access<a class="headerlink" href="#allen-brain
 <section id="release-notes">
 <h2>Release Notes<a class="headerlink" href="#release-notes" title="Permalink to this heading">#</a></h2>
 <ul class="simple">
+<li><p><strong>[abc_atlas_access (v0.1.0)]</strong></p>
+<ul>
+<li><p>Fixed issue with loading 10X mouse data with the <code class="docutils literal notranslate"><span class="pre">get_gene_data</span></code> function.</p></li>
+</ul>
+</li>
 <li><p><strong>[Spring 2024 Public Beta (version 20240330)]</strong></p>
 <ul>
 <li><p>Added Whole Human Brain transcriptomic, taxonomy and clustering datasets
diff --git a/notebooks/getting_started.html b/notebooks/getting_started.html
index 1ed191f..5827040 100644
--- a/notebooks/getting_started.html
+++ b/notebooks/getting_started.html
@@ -556,7 +556,7 @@ <h1>Getting started<a class="headerlink" href="#getting-started" title="Permalin
 <p>After installing these new packages we need to restart the python kernel in this notebook. This can either be done by selecting <code class="docutils literal notranslate"><span class="pre">Restart</span> <span class="pre">Kernel...</span></code> under the <code class="docutils literal notranslate"><span class="pre">Kernel</span></code> drop down menu above or uncommenting and running the cell below.</p>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
-<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># get_ipython().kernel.do_shutdown()</span>
+<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">get_ipython</span><span class="p">()</span><span class="o">.</span><span class="n">kernel</span><span class="o">.</span><span class="n">do_shutdown</span><span class="p">(</span><span class="n">restart</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
 </pre></div>
 </div>
 </div>
diff --git a/searchindex.js b/searchindex.js
index edae1c8..8529fbf 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["descriptions/Allen-CCF-2020", "descriptions/MERFISH-C57BL6J-638850", "descriptions/MERFISH-C57BL6J-638850-CCF", "descriptions/WHB-10X-clustering", "descriptions/WHB-10Xv3", "descriptions/WHB-taxonomy", "descriptions/WHB_dataset", "descriptions/WHB_notebooks", "descriptions/WMB-10X", "descriptions/WMB-10XMulti", "descriptions/WMB-10Xv2", "descriptions/WMB-10Xv3", "descriptions/WMB-neighborhoods", "descriptions/WMB-taxonomy", "descriptions/WMB_dataset", "descriptions/Zhuang-ABCA-1", "descriptions/Zhuang-ABCA-2", "descriptions/Zhuang-ABCA-3", "descriptions/Zhuang-ABCA-4", "descriptions/Zhuang_dataset", "descriptions/notebook_subtitle1", "descriptions/notebook_subtitle2", "descriptions/notebook_subtitle3", "descriptions/notebook_subtitle4", "docs/README", "docs/cluster_annotations/README", "docs/gene_lists/README", "docs/parcellation_annotations/README", "intro", "notebooks/10x_snRNASeq_tutorial_part_1", "notebooks/10x_snRNASeq_tutorial_part_2a", "notebooks/10x_snRNASeq_tutorial_part_2b", "notebooks/WHB-10x_snRNASeq_tutorial_part_1", "notebooks/WHB-10x_snRNASeq_tutorial_part_2", "notebooks/WHB_cluster_annotation_tutorial", "notebooks/ccf_and_parcellation_annotation_tutorial", "notebooks/cluster_annotation_tutorial", "notebooks/cluster_groups_and_embeddings_tutorial", "notebooks/cluster_neighborhood_gallery", "notebooks/general_accessing_10x_snRNASeq_tutorial", "notebooks/getting_started", "notebooks/merfish_ccf_registration_tutorial", "notebooks/merfish_tutorial_part_1", "notebooks/merfish_tutorial_part_2a", "notebooks/merfish_tutorial_part_2b", "notebooks/zhuang_merfish_tutorial"], "filenames": ["descriptions/Allen-CCF-2020.md", "descriptions/MERFISH-C57BL6J-638850.md", "descriptions/MERFISH-C57BL6J-638850-CCF.md", "descriptions/WHB-10X-clustering.md", "descriptions/WHB-10Xv3.md", "descriptions/WHB-taxonomy.md", "descriptions/WHB_dataset.md", "descriptions/WHB_notebooks.md", "descriptions/WMB-10X.md", "descriptions/WMB-10XMulti.md", "descriptions/WMB-10Xv2.md", "descriptions/WMB-10Xv3.md", "descriptions/WMB-neighborhoods.md", "descriptions/WMB-taxonomy.md", "descriptions/WMB_dataset.md", "descriptions/Zhuang-ABCA-1.md", "descriptions/Zhuang-ABCA-2.md", "descriptions/Zhuang-ABCA-3.md", "descriptions/Zhuang-ABCA-4.md", "descriptions/Zhuang_dataset.md", "descriptions/notebook_subtitle1.md", "descriptions/notebook_subtitle2.md", "descriptions/notebook_subtitle3.md", "descriptions/notebook_subtitle4.md", "docs/README.md", "docs/cluster_annotations/README.md", "docs/gene_lists/README.md", "docs/parcellation_annotations/README.md", "intro.md", "notebooks/10x_snRNASeq_tutorial_part_1.ipynb", "notebooks/10x_snRNASeq_tutorial_part_2a.ipynb", "notebooks/10x_snRNASeq_tutorial_part_2b.ipynb", "notebooks/WHB-10x_snRNASeq_tutorial_part_1.ipynb", "notebooks/WHB-10x_snRNASeq_tutorial_part_2.ipynb", "notebooks/WHB_cluster_annotation_tutorial.ipynb", "notebooks/ccf_and_parcellation_annotation_tutorial.ipynb", "notebooks/cluster_annotation_tutorial.ipynb", "notebooks/cluster_groups_and_embeddings_tutorial.ipynb", "notebooks/cluster_neighborhood_gallery.ipynb", "notebooks/general_accessing_10x_snRNASeq_tutorial.ipynb", "notebooks/getting_started.ipynb", "notebooks/merfish_ccf_registration_tutorial.ipynb", "notebooks/merfish_tutorial_part_1.ipynb", "notebooks/merfish_tutorial_part_2a.ipynb", "notebooks/merfish_tutorial_part_2b.ipynb", "notebooks/zhuang_merfish_tutorial.ipynb"], "titles": ["Allen Mouse Common Coordinate Framework (2020 version)", "MERFISH spatial transcriptomics dataset of a single adult mouse brain", "MERFISH CCF mapped coordinates", "Clustering analysis of whole human brain 10X single nucleus transcriptomes", "Human brain 10Xv3 single nucleus transcriptomes", "Human brain taxonomy of cell types", "Human whole-brain transcriptomic cell type atlas (Kimberly Siletti)", "Whole Human Brain 10x scRNA-seq gene expression data", "Clustering analysis of whole adult mouse brain 10X single cell transcriptomes", "Whole mouse brain 10XMulti single cell transcriptomes", "Whole mouse brain 10Xv2 single cell transcriptomes", "Whole mouse brain 10Xv3 single cell transcriptomes", "Cluster groups and neighborhood specific UMAP embeddings", "Whole adult mouse brain taxonomy of cell types", "Mouse whole-brain transcriptomic cell type atlas (Hongkui Zeng)", "MERFISH spatial transcriptomics dataset of a single adult mouse brain (Zhuang-ABCA-1)", "MERFISH spatial transcriptomics dataset of a single adult mouse brain (Zhuang-ABCA-2)", "MERFISH spatial transcriptomics dataset of a single adult mouse brain (Zhuang-ABCA-3)", "MERFISH spatial transcriptomics dataset of a single adult mouse brain (Zhuang-ABCA-4)", "A molecularly defined and spatially resolved cell atlas of the whole mouse brain (Xiaowei Zhuang)", "Mouse whole-brain transcriptomic cell type atlas (Hongkui Zeng)", "10x scRNA-seq gene expression data", "MERFISH 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\ No newline at end of file