test.yaml

name: Test

on:
    push:
        branches: [master]
    pull_request:
        branches: [master, devel]

jobs:
    test:
        runs-on: ${{ matrix.os }}
        defaults:
            run:
                shell: bash -e {0} # -e to fail on error

        strategy:
            fail-fast: false
            matrix:
                python: ["3.8", "3.10"]
                os: [ubuntu-latest]

        env:
            OS: ${{ matrix.os }}
            PYTHON: ${{ matrix.python }}

        steps:
            - uses: actions/checkout@v2
            - uses: r-lib/actions/setup-r@v2
            - name: Set up Python ${{ matrix.python }}
              uses: actions/setup-python@v2
              with:
                  python-version: ${{ matrix.python }}

            - name: Get pip cache dir
              id: pip-cache-dir
              run: |
                  echo "::set-output name=dir::$(pip cache dir)"
            - name: Restore pip cache
              uses: actions/cache@v2
              with:
                  path: ${{ steps.pip-cache-dir.outputs.dir }}
                  key: pip-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/pyproject.toml') }}
                  restore-keys: |
                      pip-${{ runner.os }}-${{ env.pythonLocation }}-
            - name: Install test dependencies
              run: |
                  python -m pip install --upgrade pip wheel
                  pip install codecov
            - name: Install dependencies
              run: |
                  pip install ".[dev,test]"
            - name: Install R package dependencies
              run: |
                  Rscript --vanilla -e "install.packages(c('BiocManager', 'statmod'), repos='http://cran.us.r-project.org'); library('BiocManager'); BiocManager::install('edgeR')"
            - name: Test
              env:
                  MPLBACKEND: agg
                  PLATFORM: ${{ matrix.os }}
                  DISPLAY: :42
              run: |
                  pytest -v --cov --color=yes
            - name: Upload coverage
              env:
                  CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
              #   run: |
              #       codecov --required --flags=unittests
              uses: codecov/codecov-action@v3
              with:
                  token: ${{secrets.CODECOV_TOKEN}}