Validation and refactoring of differential expression analysis #408
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python | |
| name: Build and run tests | |
| on: | |
| push: | |
| branches: [ main, development ] | |
| pull_request: | |
| jobs: | |
| pre-commit: | |
| name: Run all pre-commit hooks | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| - uses: pre-commit/action@v3.0.1 | |
| get-code-review-input: | |
| runs-on: ubuntu-latest | |
| #if: contains(github.event.pull_request.labels.*.name, 'code-review') | |
| steps: | |
| - uses: MannLabs/alphashared/actions/get-code-review-input@v1 | |
| with: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| PR_NUMBER: ${{ github.event.number }} | |
| build-and-test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.8", "3.9", "3.10"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Pip installation | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install . | |
| - name: Install additional dependencies for tests | |
| run: | | |
| pip install -r requirements_dev.txt | |
| - name: Print pip freeze | |
| run: | | |
| pip freeze | |
| - name: Run tests | |
| run: | | |
| coverage run -m pytest | |
| - name: Upload Coverage to Codecov | |
| uses: codecov/codecov-action@v4 | |
| - name: Run notebooks | |
| run: | | |
| python3 -m ipykernel install --user | |
| # TODO add the excluded notebook | |
| TEST_NBS=$(find ./nbs -name "*.ipynb" | grep -v "ramus_2016.ipynb") | |
| python -m pytest --nbmake $(echo $TEST_NBS) |