CI fix #298
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| name: Unit Tests | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| jobs: | |
| main_tests: | |
| name: 'Python ${{ matrix.python-version }} on ${{ matrix.os }}: ${{ matrix.section}})' | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ['ubuntu-latest', 'macos-latest'] | |
| section: ["Tools", "Core"] | |
| python-version: ['3.10'] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| submodules: true | |
| fetch-depth: 0 # full history for setuptools_scm | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| # Don't update conda - performance: | |
| # miniconda-version: 'latest' | |
| # auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| miniforge-variant: Mambaforge | |
| mamba-version: "*" | |
| channels: conda-forge,bioconda | |
| channel-priority: strict | |
| environment-file: environment.yaml | |
| activate-environment: ymp | |
| - name: Install | |
| run: | | |
| pip install --no-deps . | |
| - name: Testing Core | |
| if: matrix.section == 'Core' | |
| run: | | |
| pytest -vv -n auto --junit-xml junit/report.xml --durations=0 | |
| - name: Testing Tools | |
| if: matrix.section == 'Tools' | |
| run: | | |
| pytest -vvvs -n 1 --junit-xml junit-tools/report.xml --run-tools -m runs_tool --timeout=600 --durations=0 | |
| - name: Upload logs | |
| if: failure() | |
| uses: actions/upload-artifact@v1 | |
| with: | |
| name: Test Failure Logs ${{matrix.os}} ${{matrix.section}} | |
| path: test_failures | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v1 | |
| with: | |
| env_vars: OS,PYTHON | |
| verbose: true | |
| files: coverage.xml | |
| flags: ${{matrix.section}} |