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Add GH actions workflow to test on Cubed
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name: Cubed | ||
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on: | ||
push: | ||
pull_request: | ||
# manual trigger | ||
workflow_dispatch: | ||
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jobs: | ||
build: | ||
# This workflow only runs on the origin org | ||
# if: github.repository_owner == 'sgkit-dev' | ||
runs-on: ubuntu-latest | ||
strategy: | ||
matrix: | ||
python-version: ["3.11"] | ||
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steps: | ||
- uses: actions/checkout@v4 | ||
- name: Set up Python ${{ matrix.python-version }} | ||
uses: actions/setup-python@v5 | ||
with: | ||
python-version: ${{ matrix.python-version }} | ||
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- name: Install deps and sgkit | ||
run: | | ||
python -m pip install --upgrade pip | ||
python -m pip install -r requirements.txt -r requirements-dev.txt | ||
python -m pip install -U git+https://github.com/cubed-dev/cubed.git -U git+https://github.com/cubed-dev/cubed-xarray.git -U git+https://github.com/pydata/xarray.git | ||
- name: Test with pytest | ||
run: | | ||
pytest -v sgkit/tests/test_aggregation.py -k "test_count_call_alleles" --use-cubed |