Use sgkit.distarray for sample_stats and hardy_weinberg_test #3237
Workflow file for this run
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name: Build | |
on: | |
push: | |
pull_request: | |
schedule: | |
# Run at the end of every day | |
- cron: "0 0 * * *" | |
jobs: | |
build: | |
# Scheduled runs only on the origin org | |
if: (github.event_name == 'schedule' && github.repository_owner == 'sgkit-dev') || (github.event_name != 'schedule') | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
python-version: ["3.9", "3.10", "3.11"] | |
steps: | |
- uses: actions/checkout@v2 | |
- name: Set up Python ${{ matrix.python-version }} | |
uses: actions/setup-python@v2 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Install dependencies | |
run: | | |
python -m pip install --upgrade pip | |
pip install -r requirements.txt -r requirements-dev.txt | |
- name: Run pre-commit | |
uses: pre-commit/action@v2.0.0 | |
- name: Test with pytest (numba jit disabled) | |
env: | |
NUMBA_DISABLE_JIT: 1 | |
run: | | |
# avoid guvectorized functions #1194 | |
pytest -v sgkit/tests/test_pedigree.py | |
pytest -v sgkit/tests/io/vcf/test_vcf_writer_utils.py | |
- name: Test with pytest and coverage | |
run: | | |
pytest -v --cov=sgkit --cov-report=term-missing | |
- name: Upload coverage to Codecov | |
uses: codecov/codecov-action@v3 | |
with: | |
token: ${{ secrets.CODECOV_TOKEN }} |