debug

.github/workflows/compatibility_tests.yml

@@ -7,9 +7,9 @@ on:
     branches:
       - main
 
-  # For debug - uncomment below to run on all PRs
+  ### For debugging purposes - uncomment below to run on all PRs
-  # pull_request:
+  pull_request:
-  #   branches: "*"
+    branches: "*"
 
 env:
   JEST_ENV: prod
@@ -34,12 +34,12 @@ jobs:
       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"]
+        python-version: ["3.10", "3.11", "3.12"]
         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: 3.11
+          - python-version: 3.12
             cellxgene_build: latest
             # TODO: dynamically use the literal version in requirements.txt,
             # to avoid having to update this in manually in the future

.github/workflows/push_tests.yml

@@ -17,10 +17,10 @@ jobs:
       - uses: actions/checkout@v4
       - run: |
           git fetch --depth=1 origin +${{github.base_ref}}
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v5
         with:
-          python-version: 3.11
+          python-version: 3.12
       - name: Node cache
         uses: actions/cache@v4
         with:
@@ -28,11 +28,14 @@ jobs:
           key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
           restore-keys: |
             ${{ runner.os }}-node-
-      - name: Install dependencies
+      - name: Install dependencies now
         run: |
           pip install flake8
           pip install black
-          cd client
+          pip install setuptools
+      - name: Install client dependencies
+        run: |
+          cd client 
           npm install
       - name: Format with black and lint with flake8
         run: |
@@ -46,10 +49,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.11 (pyenv) # pyenv needed for mlflow in cli annotate tests
+      - name: Set up Python 3.12 (pyenv) # pyenv needed for mlflow in cli annotate tests
         uses: gabrielfalcao/pyenv-action@v9
         with:
-          default: 3.11
+          default: 3.12
           command: pip install -U pip # upgrade pip after installing python
       - run: pip install virtualenv # virtualenv needed for mlflow in cli annotate tests
       - name: Python cache
@@ -79,10 +82,10 @@ jobs:
     timeout-minutes: 20
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v5
         with:
-          python-version: 3.11
+          python-version: 3.12
       - name: Python cache
         uses: actions/cache@v4
         with:

server/requirements.txt

@@ -7,7 +7,7 @@ Flask-Cors>=3.0.9
 Flask-RESTful>=0.3.6
 flask-server-timing>=0.1.2
 flask-talisman>=0.7.0
-flatbuffers>=1.11.0,<2.0.0 # cellxgene is not compatible with 2.0.0. Requires migration
+flatbuffers==2.0.7
 flatten-dict>=0.2.0
 fsspec>0.8.0
 gunicorn>=20.0.4
@@ -19,4 +19,5 @@ pandas>=2.2.2
 PyYAML>=5.4  # CVE-2020-14343
 requests>=2.22.0
 s3fs==0.4.2
-scipy>=1.4
+scipy>=1.4
+setuptools

setup.py

@@ -24,7 +24,7 @@ setup(
     long_description=long_description,
     long_description_content_type="text/markdown",
     install_requires=requirements,
-    python_requires=">=3.6",
+    python_requires=">=3.10",
     include_package_data=True,
     zip_safe=False,
     classifiers=[