pythonpackage.yml

name: Python package

on: [push, pull_request]

jobs:
  build:

    runs-on: ubuntu-latest
    strategy:
      max-parallel: 4
      matrix:
        python-version: [3.7, 3.8, 3.9, "3.10"]
        r-version: ['release']
        os: [ubuntu-latest, macOS-latest]
    steps:
    - uses: actions/checkout@v3
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v4
      with:
        python-version: ${{ matrix.python-version }}
    - name: Set up R ${{ matrix.config.r }}
      uses: r-lib/actions/setup-r@v2
      with:
        r-version: ${{ matrix.config.r }}
    - name: Install dependencies
      run: |
        sudo apt-get update
        python -m pip install --upgrade pip
    - name: Lint with flake8
      run: |
        pip install flake8
        ./run_linting.sh
    - name: Install Python dependencies
      run: |
        pip install flake8 pytest codecov pytest-cov
        pip install ipython scipy
	pip install rpy2
    - name: Install R dependencies
      run: |
        Rscript -e 'install.packages(c("dplyr", "ggplot2", "tidyr"))'
    - name: Install package
      run: |
        pip install .
    - name: Test with pytest
      run: |
        export LD_LIBRARY_PATH=$(python -m rpy2.situation LD_LIBRARY_PATH):${LD_LIBRARY_PATH}
        pip install pytest codecov pytest-cov ipython
        ./run_tests.sh