From 6c3c66dfef7da9d8779b679aadc2cc2f7ade728e Mon Sep 17 00:00:00 2001
From: morriscb <morriscb@users.noreply.github.com>
Date: Wed, 20 Mar 2024 17:40:06 +0000
Subject: [PATCH] deploy: 2fee9ffa4c00615e7782cc81f5240c484249bd15

---
 .../notebooks/general_accessing_10x_snRNASeq_tutorial.ipynb     | 2 +-
 _sources/notebooks/getting_started.ipynb                        | 2 +-
 notebooks/general_accessing_10x_snRNASeq_tutorial.html          | 2 +-
 notebooks/getting_started.html                                  | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/_sources/notebooks/general_accessing_10x_snRNASeq_tutorial.ipynb b/_sources/notebooks/general_accessing_10x_snRNASeq_tutorial.ipynb
index c5830d8..c7a38c0 100644
--- a/_sources/notebooks/general_accessing_10x_snRNASeq_tutorial.ipynb
+++ b/_sources/notebooks/general_accessing_10x_snRNASeq_tutorial.ipynb
@@ -623,7 +623,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Below is a function that can be used to load specific genes from the from the full set of data in the WHB dataset. Adjust the chunk size down if you find your system still running out of memory. Additionally, reduce the number of genes if you still have issues. Note that the funciton can load either the raw expression data or the log2 data. The full code of this function can be found [here](https://github.com/AllenInstitute/abc_atlas_access/blob/4c4a7dfb124971b543de2cb737d059e7cabd620a/src/abc_atlas_access/abc_atlas_cache/anndata_utils.py#L9)"
+    "Below is a function that can be used to load specific genes from the from the full set of data in the WHB dataset. Adjust the chunk size down if you find your system still running out of memory. Additionally, reduce the number of genes if you still have issues. Note that the funciton can load either the raw expression data or the log2 data. The full code of this function can be found [here](https://github.com/AllenInstitute/abc_atlas_access/blob/7a53a08cff0f07e9b67911c0db04fa6932fa6e9d/src/abc_atlas_access/abc_atlas_cache/anndata_utils.py#L9)"
    ]
   },
   {
diff --git a/_sources/notebooks/getting_started.ipynb b/_sources/notebooks/getting_started.ipynb
index 94b75d1..df30b21 100644
--- a/_sources/notebooks/getting_started.ipynb
+++ b/_sources/notebooks/getting_started.ipynb
@@ -105,7 +105,7 @@
     }
    ],
    "source": [
-    "pip install -U git+https://github.com/alleninstitute/abc_atlas_access@u/morriscb/updateJupyterBook"
+    "pip install -U git+https://github.com/alleninstitute/abc_atlas_access"
    ]
   },
   {
diff --git a/notebooks/general_accessing_10x_snRNASeq_tutorial.html b/notebooks/general_accessing_10x_snRNASeq_tutorial.html
index 40ee665..e2dee45 100644
--- a/notebooks/general_accessing_10x_snRNASeq_tutorial.html
+++ b/notebooks/general_accessing_10x_snRNASeq_tutorial.html
@@ -884,7 +884,7 @@ <h3>Loading specific genes from the data<a class="headerlink" href="#loading-spe
 </div>
 </div>
 </div>
-<p>Below is a function that can be used to load specific genes from the from the full set of data in the WHB dataset. Adjust the chunk size down if you find your system still running out of memory. Additionally, reduce the number of genes if you still have issues. Note that the funciton can load either the raw expression data or the log2 data. The full code of this function can be found <a class="reference external" href="https://github.com/AllenInstitute/abc_atlas_access/blob/4c4a7dfb124971b543de2cb737d059e7cabd620a/src/abc_atlas_access/abc_atlas_cache/anndata_utils.py#L9">here</a></p>
+<p>Below is a function that can be used to load specific genes from the from the full set of data in the WHB dataset. Adjust the chunk size down if you find your system still running out of memory. Additionally, reduce the number of genes if you still have issues. Note that the funciton can load either the raw expression data or the log2 data. The full code of this function can be found <a class="reference external" href="https://github.com/AllenInstitute/abc_atlas_access/blob/7a53a08cff0f07e9b67911c0db04fa6932fa6e9d/src/abc_atlas_access/abc_atlas_cache/anndata_utils.py#L9">here</a></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="o">?</span>get_gene_data
diff --git a/notebooks/getting_started.html b/notebooks/getting_started.html
index db65dbb..1ed191f 100644
--- a/notebooks/getting_started.html
+++ b/notebooks/getting_started.html
@@ -474,7 +474,7 @@ <h1>Getting started<a class="headerlink" href="#getting-started" title="Permalin
 <p>Below we install the python library we will be using throughout to this python enviroment.</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="n">pip</span> <span class="n">install</span> <span class="o">-</span><span class="n">U</span> <span class="n">git</span><span class="o">+</span><span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">alleninstitute</span><span class="o">/</span><span class="n">abc_atlas_access</span><span class="nd">@u</span><span class="o">/</span><span class="n">morriscb</span><span class="o">/</span><span class="n">updateJupyterBook</span>
+<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="o">-</span><span class="n">U</span> <span class="n">git</span><span class="o">+</span><span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">alleninstitute</span><span class="o">/</span><span class="n">abc_atlas_access</span>
 </pre></div>
 </div>
 </div>