pythonpackage.yml

name: Python package

on:
  push:
    branches: [main]
  pull_request:
    branches: [main]
  schedule:
    - cron: "0 5 1,15 * *"

jobs:
  build:

    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.10", "3.12"]

    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 dependencies
      run: |
        python -m pip install --upgrade pip
        python -m pip install uv
        uv venv
        source .venv/bin/activate
        uv pip install ruff pytest
        uv pip install .[dev,test,atac]
    - name: Install dev dependencies
      run: >
        uv pip install
        git+https://github.com/bioFAM/mofapy2
        git+https://github.com/scverse/mudata
    - name: Ruff check
      run: |
        source .venv/bin/activate
        ruff check src/muon
    - name: Test with pytest
      run: |
        source .venv/bin/activate
        python -m pytest