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| name: Pytest | |
| # This workflow is triggered on pushes and PRs to the repository. | |
| # It runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
| on: [push, pull_request] | |
| jobs: | |
| test: | |
| env: | |
| NXF_VER: ${{ matrix.nxf_ver }} | |
| NXF_ANSI_LOG: false | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| # Nextflow versions: check pipeline minimum and current latest | |
| python-version: ['3.6', '3.7'] | |
| os: ['ubuntu-latest', 'macos-latest'] | |
| steps: | |
| - name: Run tests with coverage | |
| shell: bash -l {0} | |
| run: | | |
| pip install -r requirements_testing.txt | |
| coverage run -m unittest discover -s detection -p "*_test.py" | |
| - name: Send coverage to codecov.io | |
| shell: bash -l {0} | |
| run: | | |
| pip install codecov | |
| codecov |