Temp change to run on PR #21
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| name: Cubed | |
| on: | |
| push: | |
| pull_request: | |
| # manual trigger | |
| workflow_dispatch: | |
| 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"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - 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,hwe}.py -k 'test_count_call_alleles or test_hwep or test_sample_stats or (test_count_variant_alleles and not test_count_variant_alleles__chunked[call_genotype]) or (test_variant_stats and not test_variant_stats__chunks[chunks2-False])' --use-cubed |