python-package-conda.yml

name: Unit tests

on: [push]

jobs:
  build-linux:
    runs-on: ubuntu-latest
    strategy:
      max-parallel: 5
      matrix:
        python-version: ["3.7"]

    steps:
    - uses: actions/checkout@v4

    - name: Set up Miniconda
      uses: conda-incubator/setup-miniconda@v2
      with:
        python-version: ${{ matrix.python-version }}
        activate-environment: lameg
        auto-activate-base: false

    - name: Install dependencies and build package
      run: |
        conda activate lameg
        pip install -v .
        lameg-postinstall
      shell: bash -l {0}

    - name: Lint with pylint
      run: |
        conda activate lameg
        pip install -r dev_requirements.txt
        pylint --rcfile=${{ github.workspace }}/.pylintrc $(git ls-files '*.py')
      shell: bash -l {0}

    - name: Test with pytest
      env:
        SUBJECTS_DIR: ${{ github.workspace }}/test_data/fs
        MALLOC_TRIM_THRESHOLD_: 0
        PYTHONUNBUFFERED: 1
      run: |
        set +e
        conda activate lameg
        wget -q -c https://osf.io/x4zd3/download -O "${{ github.workspace }}/test_data.tar.gz"
        tar -xzf ${{ github.workspace }}/test_data.tar.gz -C ${{ github.workspace }}
        rm ${{ github.workspace }}/test_data.tar.gz
        stdbuf -oL -eL pytest -v -s --color=yes --cov=lameg --cov-report=xml
        code=$?
        # Fail only on nonzero codes other than segfault (139)
        if [ $code -ne 0 ] && [ $code -ne 139 ]; then
          exit $code
        fi
      shell: bash -l {0}

    - name: Upload coverage to Codecov
      uses: codecov/codecov-action@v3
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        files: ./coverage.xml