pytest_and_coveralls.yml

name: pytests
on:
  push:
    paths-ignore:
      - "CHANGELOG.rst"
      - "docs/**"
  pull_request:
    paths-ignore:
      - "CHANGELOG.rst"
      - "docs/**"
jobs:
  pytest_coveralls:
    name: run PyTest
    runs-on: ubuntu-20.04
    steps:
      # Checkout BALSAMIC
      - name: Git checkout
        id: git_checkout
        uses: actions/checkout@v3
      # Get branch name
      - name: Get branch name
        id: get_branch_name
        shell: bash
        run: echo "##[set-output name=branch;]$(echo ${GITHUB_REF##*/})"
      # Conda env create
      - name: setup conda
        id: setup_conda
        uses: conda-incubator/setup-miniconda@v2
        with:
          activate-environment: balsamic
          environment-file: BALSAMIC/conda/balsamic.yaml
      # Install BALSAMIC
      - name: Install BALSAMIC
        id: install_balsamic
        shell: bash -l {0}
        run: |
          conda activate balsamic
          pip install --no-cache-dir .
      # Install pytest coveralls dependencies
      - name: Install PyTest and Coveralls
        id: install_pytest
        shell: bash -l {0}
        run: |
          conda activate balsamic
          pip install --no-cache-dir -r requirements-dev.txt
      # Run PyTest
      - name: Run PyTest
        id: pytest
        shell: bash -l {0}
        run: |
          conda activate balsamic
          py.test --cov-report=xml --cov=BALSAMIC -rsxv tests/*
        env:
          SENTIEON_LICENSE: dummy_license
          SENTIEON_INSTALL_DIR: dummy_install_dir
      # Run Codecov
      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v3
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          file: ./coverage.xml
          flags: unittests
          fail_ci_if_error: true
          verbose: true