Merge branch 'rc/0.4.0'

AllenInstitute · Dec 18, 2024 · 52c073b · 52c073b
2 parents e4a6696 + 474f8b8
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diff --git a/.github/workflows/abc_atlas_access_ci.yaml b/.github/workflows/abc_atlas_access_ci.yaml
@@ -21,6 +21,6 @@ jobs:
       - name: Install
         run: |
           python -m pip install --upgrade pip
-          pip install .
+          pip install ".[test]"
       - name: Test
         run: pytest tests
diff --git a/.github/workflows/deploy_book.yaml b/.github/workflows/deploy_book.yaml
@@ -4,7 +4,7 @@ name: deploy-book
 on:
   push:
     branches:
-    - main 
+    - main
 
 # This job installs dependencies, builds the book, and pushes it to `gh-pages`
 jobs:
@@ -21,7 +21,7 @@ jobs:
 
     - name: Install dependencies
       run: |
-        pip install -r requirements.txt
+        pip install ".[jupyter-book]"
 
     # Build the book
     - name: Build the book

diff --git a/README.md b/README.md
@@ -19,10 +19,30 @@ Note: for scientific questions regarding the data this repository is accessing,
 please use the
 [Allen Institute's community forum](https://community.brain-map.org/).
 If you are having an issue with the code or notebooks not running properly
-please open an issue on this Github respoitory. However, please see below.
+please open an issue on this Github repository. However, please see below.
 
 ## Level of support
 We are not currently supporting this code, but simply releasing it to the
 community AS IS but are not able to provide any guarantees of support. The
 community is welcome to submit issues, but you should not expect an active
 response.
+
+## Installation
+
+To install base package with the cache object in your python environment, use
+pip with the following command:
+
+```console
+pip install git+https://github.com/alleninstitute/abc_atlas_access.git
+```
+
+To install the package with all optional dependencies, specifically those needed
+to re-run the notebooks, you can use the following command:
+
+```console
+pip install "abc_atlas_access[notebooks] @ git+https://github.com/alleninstitute/abc_atlas_access.git"
+```
+
+We assume that you already have Jupyter installed if you are re-running the
+notebooks. Running the [getting_started notebook](https://alleninstitute.github.io/abc_atlas_access/notebooks/getting_started.html)
+will also help you install the package.
diff --git a/_static/WMB-taxonomy/20231215/class.html b/_static/WMB-taxonomy/20231215/class.html
@@ -0,0 +1,119 @@
+
+    <html>
+    <head><title>WMB-taxonmy: cell type classes</title></head>
+    <link rel="stylesheet" type="text/css" href="../../simple_style.css"/>
+    <body>
+    <table border="1" class="dataframe mystyle">
+  <thead>
+    <tr style="text-align: right;">
+      <th>class</th>
+    </tr>
+  </thead>
+  <tbody>
+    <tr>
+      <td><div id="CS20230722_CLAS_01"></div><div class="circle" style="background-color:#FA0087"></div><div class="celltext">01 IT-ET Glut</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_001">[+]</a></div></td>
+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_02"></div><div class="circle" style="background-color:#61e2a4"></div><div class="celltext">02 NP-CT-L6b Glut</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_027">[+]</a></div></td>
+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_03"></div><div class="circle" style="background-color:#D00000"></div><div class="celltext">03 OB-CR Glut</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_035">[+]</a></div></td>
+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_04"></div><div class="circle" style="background-color:#16f2f2"></div><div class="celltext">04 DG-IMN Glut</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_037">[+]</a></div></td>
+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_05"></div><div class="circle" style="background-color:#1b4332"></div><div class="celltext">05 OB-IMN GABA</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_039">[+]</a></div></td>
+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_06"></div><div class="circle" style="background-color:#CCFF33"></div><div class="celltext">06 CTX-CGE GABA</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_046">[+]</a></div></td>
+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_07"></div><div class="circle" style="background-color:#f954ee"></div><div class="celltext">07 CTX-MGE GABA</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_050">[+]</a></div></td>
+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_08"></div><div class="circle" style="background-color:#70E000"></div><div class="celltext">08 CNU-MGE GABA</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_054">[+]</a></div></td>
+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_09"></div><div class="circle" style="background-color:#B199FF"></div><div class="celltext">09 CNU-LGE GABA</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_059">[+]</a></div></td>
+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_10"></div><div class="circle" style="background-color:#3283FE"></div><div class="celltext">10 LSX GABA</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_067">[+]</a></div></td>
+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_11"></div><div class="circle" style="background-color:#450099"></div><div class="celltext">11 CNU-HYa GABA</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_066">[+]</a></div></td>
+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_12"></div><div class="circle" style="background-color:#FF6600"></div><div class="celltext">12 HY GABA</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_091">[+]</a></div></td>
+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_13"></div><div class="circle" style="background-color:#90E0EF"></div><div class="celltext">13 CNU-HYa Glut</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_110">[+]</a></div></td>
+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_14"></div><div class="circle" style="background-color:#AA0DFE"></div><div class="celltext">14 HY Glut</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_123">[+]</a></div></td>
+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_15"></div><div class="circle" style="background-color:#F28266"></div><div class="celltext">15 HY Gnrh1 Glut</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_142">[+]</a></div></td>
+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_16"></div><div class="circle" style="background-color:#01d669"></div><div class="celltext">16 HY MM Glut</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_143">[+]</a></div></td>
+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_17"></div><div class="circle" style="background-color:#FAA307"></div><div class="celltext">17 MH-LH Glut</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_145">[+]</a></div></td>
+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_18"></div><div class="circle" style="background-color:#0D47A1"></div><div class="celltext">18 TH Glut</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_147">[+]</a></div></td>
+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_19"></div><div class="circle" style="background-color:#007200"></div><div class="celltext">19 MB Glut</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_155">[+]</a></div></td>
+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_20"></div><div class="circle" style="background-color:#9EF01A"></div><div class="celltext">20 MB GABA</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_191">[+]</a></div></td>
+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_21"></div><div class="circle" style="background-color:#38B000"></div><div class="celltext">21 MB Dopa</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_215">[+]</a></div></td>
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+      <td><div id="CS20230722_CLAS_22"></div><div class="circle" style="background-color:#EC4067"></div><div class="celltext">22 MB-HB Sero</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_216">[+]</a></div></td>
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+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_24"></div><div class="circle" style="background-color:#F0A0FF"></div><div class="celltext">24 MY Glut</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_236">[+]</a></div></td>
+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_25"></div><div class="circle" style="background-color:#086375"></div><div class="celltext">25 Pineal Glut</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_262">[+]</a></div></td>
+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_26"></div><div class="circle" style="background-color:#72195a"></div><div class="celltext">26 P GABA</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_263">[+]</a></div></td>
+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_27"></div><div class="circle" style="background-color:#0096C7"></div><div class="celltext">27 MY GABA</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_283">[+]</a></div></td>
+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_28"></div><div class="circle" style="background-color:#FFFB46"></div><div class="celltext">28 CB GABA</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_308">[+]</a></div></td>
+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_29"></div><div class="circle" style="background-color:#9D0208"></div><div class="celltext">29 CB Glut</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_314">[+]</a></div></td>
+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_30"></div><div class="circle" style="background-color:#594a26"></div><div class="celltext">30 Astro-Epen</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_316">[+]</a></div></td>
+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_31"></div><div class="circle" style="background-color:#03045E"></div><div class="celltext">31 OPC-Oligo</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_326">[+]</a></div></td>
+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_32"></div><div class="circle" style="background-color:#996B2E"></div><div class="celltext">32 OEC</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_328">[+]</a></div></td>
+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_33"></div><div class="circle" style="background-color:#858881"></div><div class="celltext">33 Vascular</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_329">[+]</a></div></td>
+    </tr>
+    <tr>
+      <td><div id="CS20230722_CLAS_34"></div><div class="circle" style="background-color:#825f45"></div><div class="celltext">34 Immune</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_334">[+]</a></div></td>
+    </tr>
+  </tbody>
+</table>
+    </body>
+    </html>.
+