conda-pytest.yml

---
name: Pytest
on: [pull_request,workflow_dispatch]

jobs:
  build-linux:
    runs-on: ubuntu-latest
    strategy:
      max-parallel: 5
    defaults:
      run:
        shell: bash -el {0}

    steps:
      - name: Remove docs before testing
        run: rm -rf /github/workspace/docs

      - name: Remove tutorials before testing
        run: rm -rf /github/workspace/tutorials

      - name: Remove archived code before testing
        run: rm -rf /github/workspace/src/archive
      
      - name: Fetch actions (v2)
        uses: actions/checkout@v2

      - name: Setup Conda
        uses: conda-incubator/setup-miniconda@v2
        with:
          environment-file: requirements/testing.yml
          activate-environment: test
          auto-activate-base: false
          
      - name: Conda info
        run: |
          conda info
          conda list

      - name: Lint with flake8
        run: |
          # activate the test environment
          conda activate test
          # 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. The GitHub editor 
          # is 127 chars wide
          flake8 . --count --exit-zero --max-complexity=10 \
            --max-line-length=127 --statistics

      - name: Test with pytest
        run: |
          conda activate test
          pytest --cov-config=.coveragerc \
              --cov=src --cov-report xml \
              src/
        
      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v3
        with:
            token: ${{ secrets.CODECOV_TOKEN }}
            env_vars: OS,PYTHON
            verbose: true