From caf591ef288c92681b778bf97ca757fbe35ec604 Mon Sep 17 00:00:00 2001
From: kaloster <rkalo@contractor.chanzuckerberg.com>
Date: Mon, 9 Sep 2024 16:16:03 -0400
Subject: [PATCH] chore: add support for python 3.12

---
 .github/workflows/compatibility_tests.yml | 11 +++++------
 .github/workflows/push_tests.yml          | 16 +++++++++-------
 client/jest-puppeteer.config.js           |  4 ++--
 server/requirements.txt                   |  5 +++--
 setup.py                                  |  7 ++++---
 5 files changed, 23 insertions(+), 20 deletions(-)

diff --git a/.github/workflows/compatibility_tests.yml b/.github/workflows/compatibility_tests.yml
index 72edc0465..da1a28138 100644
--- a/.github/workflows/compatibility_tests.yml
+++ b/.github/workflows/compatibility_tests.yml
@@ -7,9 +7,9 @@ on:
     branches:
       - main
 
-  # For debug - uncomment below to run on all PRs
-  # pull_request:
-  #   branches: "*"
+  ### For debugging purposes - uncomment below to run on all PRs
+  pull_request:
+    branches: "*"
 
 env:
   JEST_ENV: prod
@@ -32,14 +32,13 @@ 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"]
+        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
diff --git a/.github/workflows/push_tests.yml b/.github/workflows/push_tests.yml
index 5de6038b1..20a77be5c 100644
--- a/.github/workflows/push_tests.yml
+++ b/.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:
@@ -46,10 +46,10 @@ 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 +79,10 @@ 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:
@@ -98,7 +98,9 @@ jobs:
           restore-keys: |
             ${{ runner.os }}-node-
       - name: Install dependencies
-        run: make pydist install-dist
+        run: |
+          pip install setuptools
+          make pydist install-dist
       - name: Smoke tests (without annotations feature)
         run: |
           cd client && make smoke-test
diff --git a/client/jest-puppeteer.config.js b/client/jest-puppeteer.config.js
index a3391a6fd..0512e6260 100644
--- a/client/jest-puppeteer.config.js
+++ b/client/jest-puppeteer.config.js
@@ -23,7 +23,7 @@ const DEFAULT_LAUNCH_CONFIG = {
 const LAUNCH_CONFIG_BY_ENV = {
   [ENV_DEFAULT.DEBUG]: {
     ...DEFAULT_LAUNCH_CONFIG,
-    headless: false,
+    headless: true,
     slowMo: 100,
     devtools: true,
     defaultViewport: {
@@ -33,7 +33,7 @@ const LAUNCH_CONFIG_BY_ENV = {
   },
   [ENV_DEFAULT.DEV]: {
     ...DEFAULT_LAUNCH_CONFIG,
-    headless: false,
+    headless: true,
     slowMo: 5,
   },
 };
diff --git a/server/requirements.txt b/server/requirements.txt
index ddbdb3f3d..2af0df3eb 100644
--- a/server/requirements.txt
+++ b/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
\ No newline at end of file
+scipy>=1.4
+setuptools
diff --git a/setup.py b/setup.py
index 53b2c1b4b..38c187c94 100644
--- a/setup.py
+++ b/setup.py
@@ -24,7 +24,7 @@
     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=[
@@ -37,8 +37,9 @@
         "Operating System :: MacOS :: MacOS X",
         "Programming Language :: JavaScript",
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.6",
-        "Programming Language :: Python :: 3.7",
+        "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
         "Programming Language :: Python :: 3 :: Only",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
     ],