cubed.yml

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.py -k 'test_count_call_alleles 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