Remove VCF support #27
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |