Don't run NumPy 2 on Python 3.9 due to scikit-allel incompatibility #5
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: Build NumPy 2 | |
on: | |
push: | |
pull_request: | |
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: ["3.10", "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 | |
pip install -U 'numpy<2.1' | |
- 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 |