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Numpy 2 testing (#1237)
* Fix type * Removing the case '0.0005' as it was previously passing by accident. * Fix test_ld on numpy 2 * Fix test_hash_array * Add GitHub Actions workflow to run using NumPy 2 * Restrict to numpy<2.1 for numba compatibility * Don't run NumPy 2 on Python 3.9 due to scikit-allel incompatibility
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name: Build NumPy 2 | ||
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on: | ||
push: | ||
pull_request: | ||
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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"] | ||
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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/[email protected] | ||
- 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 |
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