python_package.yml

name: Pytest
on:
  [push, pull_request]
env:
  SETUP_XVFB: True  # avoid issues if mpl tries to open a GUI window

jobs:
  build:
    runs-on: ubuntu-latest
    # the whole CI pipeline will be skipped if [ci skip] is in the commit msg
    if: "!contains(github.event.head_commit.message, '[ci skip]')"

    timeout-minutes: 60
    strategy:
      matrix:
        python-version: ["3.9"]
        # mpi: ['openmpi']
        # mpi: [ 'mpich', 'openmpi', 'intelmpi']
#    env:   
#      OMP_NUM_THREADS: 1
#      MKL_NUM_THREADS: 1
#      OPENBLAS_NUM_THREADS: 1
#      NUMEXPR_NUM_THREADS: 1
    steps:
    - uses: actions/checkout@master
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@master
      with:
        python-version: ${{ matrix.python-version }}
    # - name: Setup MPI
    #   uses: mpi4py/setup-mpi@v1
    #   with:
    #     mpi: ${{ matrix.mpi }}
    - name: Install dependencies
      run: |
        sudo apt-get -y install libbz2-dev
        python -m pip install --upgrade pip
        pip install wheel flake8 pytest pytest-cov coveralls
        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
    # # TODO: the section below can be removed if the compile step is fixed otherwise
    - name: Reinstall fitsio to ensure the numpy version during compilation matches the one at runtime
      run: |
        pip uninstall fitsio -y
        pip cache purge
        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
    - name: Install lya_2pt
      run: pip install -e .
    - name: Lint with flake8
      run: |
        # stop the build if there are Python syntax errors or undefined names
        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
        # exit-zero treats all errors as warnings
        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=100 --statistics
    - name: Test with pytest and gen report
      timeout-minutes: 30
      run: |
        export NUMBA_DISABLE_JIT=1
        pytest --cov=./ --cov-report=xml
    - name: Upload coverage to Codecov
      uses: codecov/codecov-action@v3
      with:
        env_vars: OS,PYTHON
        fail_ci_if_error: true
        flags: unittests
        verbose: true