ONT support #137
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| # 786 | |
| # https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: aldy-test | |
| on: | |
| push: | |
| branches: [ master ] | |
| tags: | |
| - '*' | |
| pull_request: | |
| branches: [ master ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-20.04 | |
| strategy: | |
| matrix: | |
| python-version: ['3.7', '3.8', '3.9', '3.10'] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get install libgfortran4 samtools | |
| python -m pip install --upgrade pip | |
| python -m pip install flake8 pytest pytest-cov codecov black | |
| python -m pip install setuptools wheel twine numpy cython | |
| python -m pip install . | |
| - name: Format with black | |
| run: black aldy | |
| - name: Lint with flake8 | |
| run: flake8 aldy | |
| - name: Run Aldy tests | |
| run: | | |
| mkdir -p tmp | |
| cd tmp | |
| aldy test | |
| cd .. | |
| - name: Run code coverage tests | |
| run: | | |
| python setup.py build_ext --inplace | |
| pytest --cov=./ -v aldy | |
| - name: Upload code coverage data | |
| uses: codecov/codecov-action@v1 | |
| - name: Build package | |
| run: | | |
| python setup.py sdist | |
| - name: Publish on TestPyPI | |
| if: matrix.python-version == '3.7' | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_TEST_TOKEN }} | |
| repository_url: https://test.pypi.org/legacy/ | |
| skip_existing: true | |
| - name: Publish package | |
| if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') && matrix.python-version == '3.7' | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: ${{ secrets.PYPI_USERNAME }} | |
| password: ${{ secrets.PYPI_PASSWORD }} | |