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Python cellxgene_census package full unit tests #3

Python cellxgene_census package full unit tests

Python cellxgene_census package full unit tests #3

name: Python cellxgene_census package full unit tests
# Run all Python unit tets, including those that are too expensive to run frequently.
on:
workflow_dispatch: # used for debugging or manual validation
jobs:
all_unit_tests:
runs-on: single-cell-1tb-runner
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v4
with:
python-version: 3.11
- name: Install OS dependencies
run: |
sudo apt update
sudo apt install -y build-essential
- name: Install dependencies (including experimental)
run: |
python -m pip install -U pip setuptools wheel
# pip install --use-pep517 accumulation-tree # Geneformer dependency needs --use-pep517 for Cython
pip install -r ./api/python/cellxgene_census/scripts/requirements-dev.txt
pip install -e './api/python/cellxgene_census/[experimental]'
- name: Log debugging info
run: |
python -c 'import tiledbsoma; tiledbsoma.show_package_versions()'
- name: Pytest (--expensive --experimental)
run: |
PYTHONPATH=. pytest -v --durations=0 -rP --experimental --expensive ./api/python/cellxgene_census/tests/ -k test_incremental_read_obs