Dev fpo (#125) #591
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| name: testing | |
| on: [push, pull_request] | |
| jobs: | |
| pytest: | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| matrix: | |
| python-version: ["3.11", "3.12"] | |
| os: [ubuntu-22.04, macos-latest] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: ConorMacBride/install-package@v1 | |
| with: | |
| brew: bowtie2 freebayes | |
| apt: bowtie2 freebayes | |
| - name: Install Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install poetry | |
| uses: abatilo/actions-poetry@v2 | |
| - name: Install the project dependencies | |
| run: poetry install --only test | |
| - name: Run the automated tests (for example) | |
| run: poetry run pytest --deselect meteor/tests/test_variantcalling.py::test_execute --deselect meteor/tests/test_strain.py::test_execute --log-level=DEBUG --cache-clear -s -vv --cov=meteor --cov-report xml | |
| timeout-minutes: 15 | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/codecov-action@v4.0.1 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| slug: metagenopolis/meteor |