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Test on Python 3.12 - but only on NumPy 2 due to cbgen version constr… #26

Test on Python 3.12 - but only on NumPy 2 due to cbgen version constr…

Test on Python 3.12 - but only on NumPy 2 due to cbgen version constr… #26

Workflow file for this run

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,association,hwe}.py -k 'test_count_call_alleles or test_gwas_linear_regression 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