Skip to content

Commit 52c073b

Browse files
morriscbmorriscb
committed
Merge branch 'rc/0.4.0'
2 parents e4a6696 + 474f8b8 commit 52c073b

File tree

53 files changed

+63756
-424
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

53 files changed

+63756
-424
lines changed

‎.github/workflows/abc_atlas_access_ci.yaml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -21,6 +21,6 @@ jobs:
2121
- name: Install
2222
run: |
2323
python -m pip install --upgrade pip
24-
pip install .
24+
pip install ".[test]"
2525
- name: Test
2626
run: pytest tests

‎.github/workflows/deploy_book.yaml‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@ name: deploy-book
44
on:
55
push:
66
branches:
7-
- main
7+
- main
88

99
# This job installs dependencies, builds the book, and pushes it to `gh-pages`
1010
jobs:
@@ -21,7 +21,7 @@ jobs:
2121

2222
- name: Install dependencies
2323
run: |
24-
pip install -r requirements.txt
24+
pip install ".[jupyter-book]"
2525
2626
# Build the book
2727
- name: Build the book

‎README.md‎

Lines changed: 21 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -19,10 +19,30 @@ Note: for scientific questions regarding the data this repository is accessing,
1919
please use the
2020
[Allen Institute's community forum](https://community.brain-map.org/).
2121
If you are having an issue with the code or notebooks not running properly
22-
please open an issue on this Github respoitory. However, please see below.
22+
please open an issue on this Github repository. However, please see below.
2323

2424
## Level of support
2525
We are not currently supporting this code, but simply releasing it to the
2626
community AS IS but are not able to provide any guarantees of support. The
2727
community is welcome to submit issues, but you should not expect an active
2828
response.
29+
30+
## Installation
31+
32+
To install base package with the cache object in your python environment, use
33+
pip with the following command:
34+
35+
```console
36+
pip install git+https://github.com/alleninstitute/abc_atlas_access.git
37+
```
38+
39+
To install the package with all optional dependencies, specifically those needed
40+
to re-run the notebooks, you can use the following command:
41+
42+
```console
43+
pip install "abc_atlas_access[notebooks] @ git+https://github.com/alleninstitute/abc_atlas_access.git"
44+
```
45+
46+
We assume that you already have Jupyter installed if you are re-running the
47+
notebooks. Running the [getting_started notebook](https://alleninstitute.github.io/abc_atlas_access/notebooks/getting_started.html)
48+
will also help you install the package.

‎_static/WMB-taxonomy/20231215/class.html‎

Lines changed: 119 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,119 @@
1+
2+
<html>
3+
<head><title>WMB-taxonmy: cell type classes</title></head>
4+
<link rel="stylesheet" type="text/css" href="../../simple_style.css"/>
5+
<body>
6+
<table border="1" class="dataframe mystyle">
7+
<thead>
8+
<tr style="text-align: right;">
9+
<th>class</th>
10+
</tr>
11+
</thead>
12+
<tbody>
13+
<tr>
14+
<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>
15+
</tr>
16+
<tr>
17+
<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>
18+
</tr>
19+
<tr>
20+
<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>
21+
</tr>
22+
<tr>
23+
<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>
24+
</tr>
25+
<tr>
26+
<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>
27+
</tr>
28+
<tr>
29+
<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>
30+
</tr>
31+
<tr>
32+
<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>
33+
</tr>
34+
<tr>
35+
<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>
36+
</tr>
37+
<tr>
38+
<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>
39+
</tr>
40+
<tr>
41+
<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>
42+
</tr>
43+
<tr>
44+
<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>
45+
</tr>
46+
<tr>
47+
<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>
48+
</tr>
49+
<tr>
50+
<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>
51+
</tr>
52+
<tr>
53+
<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>
54+
</tr>
55+
<tr>
56+
<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>
57+
</tr>
58+
<tr>
59+
<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>
60+
</tr>
61+
<tr>
62+
<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>
63+
</tr>
64+
<tr>
65+
<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>
66+
</tr>
67+
<tr>
68+
<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>
69+
</tr>
70+
<tr>
71+
<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>
72+
</tr>
73+
<tr>
74+
<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>
75+
</tr>
76+
<tr>
77+
<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>
78+
</tr>
79+
<tr>
80+
<td><div id="CS20230722_CLAS_23"></div><div class="circle" style="background-color:#6b5ca5"></div><div class="celltext">23 P Glut</div><div class="celltext"><a href="subclass.html#CS20230722_SUBC_217">[+]</a></div></td>
81+
</tr>
82+
<tr>
83+
<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>
84+
</tr>
85+
<tr>
86+
<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>
87+
</tr>
88+
<tr>
89+
<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>
90+
</tr>
91+
<tr>
92+
<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>
93+
</tr>
94+
<tr>
95+
<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>
96+
</tr>
97+
<tr>
98+
<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>
99+
</tr>
100+
<tr>
101+
<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>
102+
</tr>
103+
<tr>
104+
<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>
105+
</tr>
106+
<tr>
107+
<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>
108+
</tr>
109+
<tr>
110+
<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>
111+
</tr>
112+
<tr>
113+
<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>
114+
</tr>
115+
</tbody>
116+
</table>
117+
</body>
118+
</html>.
119+

0 commit comments

Comments
 (0)