debug

.github/workflows/compatibility_tests.yml

@@ -7,6 +7,10 @@ on:
     branches:
       - main
 
+  # For debug - uncomment below to run on all PRs
+  pull_request:
+    branches: "*"
+
 env:
   JEST_ENV: prod
 
@@ -28,13 +32,14 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
+        # note: The `macos-latest` is latest Catalina version, and not Big Sur. So we explicitly ask for Big Sur (`macos-11`)
         os: [ubuntu-latest, macos-latest, macos-13]
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11"]
         cellxgene_build: [main, latest]
         # add anndata pinned version test for subset of matrix configurations,
         # in order to reduce matrix cross-product explosion
         include:
-          - python-version: 3.12
+          - python-version: 3.11
             cellxgene_build: latest
             # TODO: dynamically use the literal version in requirements.txt,
             # to avoid having to update this in manually in the future
@@ -95,7 +100,7 @@ jobs:
           # keep same pip pkg versions as in the cxg release
           sed -i'' -e 's/-r requirements.txt//' server/requirements-dev.txt
           pip install -r server/requirements-dev.txt
-          pip install --force-reinstall numpy==2.0.1 numba>=0.60.0 pandas flatbuffers==2.0.7
+          pip install --force-reinstall numpy==2.0.1 numba>=0.60.0 pandas
       - name: Install anndata version per matrix variable
         run: pip install anndata${{ matrix.anndata_version }}
       - name: Install node

LICENSE

@@ -1,20 +0,0 @@
-The MIT License (MIT)
-
-Copyright (c) 2017-2023 Chan Zuckerberg Initiative
-
-Permission is hereby granted, free of charge, to any person obtaining a copy of
-this software and associated documentation files (the "Software"), to deal in
-the Software without restriction, including without limitation the rights to
-use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
-the Software, and to permit persons to whom the Software is furnished to do so,
-subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
-FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
-COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
-IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
-CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

README.md

@@ -1,4 +1,4 @@
-<img src="./docs/cellxgene-logo.png" width="300">
+![](https://github.com/chanzuckerberg/cellxgene/raw/main/docs/cellxgene-logo.png)
 
 _an interactive explorer for single-cell transcriptomics data_
 
@@ -11,7 +11,8 @@ CZ CELLxGENE Annotate (pronounced "cell-by-gene") is an interactive data explore
 
 Whether you need to visualize one thousand cells or one million, CELLxGENE Annotate helps you gain insight into your single-cell data.
 
-<img src="https://github.com/chanzuckerberg/cellxgene/raw/main/docs/images/crossfilter.gif" width="350" height="200" hspace="30"><img src="https://github.com/chanzuckerberg/cellxgene/raw/main/docs/images/category-breakdown.gif" width="350" height="200" hspace="30">
+![](https://github.com/chanzuckerberg/cellxgene/raw/main/docs/images/crossfilter.gif)
+![](https://github.com/chanzuckerberg/cellxgene/raw/main/docs/images/category-breakdown.gif)
 
 # Getting started
 
@@ -27,7 +28,7 @@ Whether you need to visualize one thousand cells or one million, CELLxGENE Annot
 
 ### Quick start
 
-To install CELLxGENE Annotate you need Python 3.10+. We recommend [installing Annotate into a conda or virtual environment.](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/desktop/install.md)
+_To install CELLxGENE Annotate you need Python 3.10+_. We recommend [installing Annotate into a conda or virtual environment.](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/desktop/install.md)
 
 Install the package.
 
@@ -82,13 +83,6 @@ extension could be directly contributed, which would make it available for a wid
 
 See the [CELLxGENE extensions](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/community-extensions.md) section of our documentation for examples of community use and CELLxGENE extensions.
 
-### Trademarks
-
-CZ CELLXGENE, CZ CELLXGENE DISCOVER, and CZ CELLXGENE ANNOTATE are trademarks of the Chan Zuckerberg Initiative. All rights reserved.
-
-Use, reuse, modification, and re-distribution of the source code in this repository is subject to the terms of the applicable open source [license](LICENSE.txt). However, that license does not grant permission to use the trademarks without separate, express permission from the Chan Zuckerberg Initiative.
-
-
 ### Security
 
 If you believe you have found a security issue, we would appreciate notification. Please send email to <security@chanzuckerberg.com>.

SECURITY.md

@@ -1,2 +0,0 @@
-## Reporting Security Issues
-If you believe you have found a security issue, please responsibly disclose by contacting us at [security@chanzuckerberg.com](mailto:security@chanzuckerberg.com).