Add nextflow script #102
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| name: CI | |
| on: | |
| push: | |
| paths: | |
| - '.github/**' | |
| - 'lazyslide/**' | |
| - 'tests/**' | |
| - 'pyproject.toml' | |
| pull_request: | |
| paths: | |
| - '.github/**' | |
| - 'lazyslide/**' | |
| - 'tests/**' | |
| - 'pyproject.toml' | |
| jobs: | |
| Test: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, windows-latest, macos-latest] | |
| python-version: ['3.8', '3.11'] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install Linux dependencies | |
| if: ${{ matrix.os == 'ubuntu-latest' }} | |
| run: | | |
| sudo apt-get install -y openslide-tools | |
| - name: Install MacOS dependencies | |
| if: ${{ matrix.os == 'macos-latest' }} | |
| run: | | |
| brew install openslide | |
| - name: Install Project dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install .[all,dev] | |
| - name: Test with pytest | |
| run: | | |
| pytest tests/ | |
| # Upload_to_test_pypi: | |
| # runs-on: ubuntu-latest | |
| # steps: | |
| # - uses: actions/checkout@v3 | |
| # - name: Set up Python | |
| # uses: actions/setup-python@v4 | |
| # with: | |
| # python-version: '3.10' | |
| # | |
| # - name: Install dependencies | |
| # run: | | |
| # python -m pip install --upgrade pip | |
| # pip install flit | |
| # pip install . | |
| # - name: Publish to test.ipynb pypi | |
| # env: | |
| # FLIT_INDEX_URL: https://test.ipynb.pypi.org/legacy/ | |
| # FLIT_USERNAME: ${{ secrets.PYPI_USERNAME }} | |
| # FLIT_PASSWORD: ${{ secrets.PYPI_PASSWORD }} | |
| # run: flit publish || exit 0 | |
| # | |
| # - name: Publish to pypi | |
| # if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v') | |
| # env: | |
| # FLIT_INDEX_URL: https://upload.pypi.org/legacy/ | |
| # FLIT_USERNAME: ${{ secrets.PYPI_USERNAME }} | |
| # FLIT_PASSWORD: ${{ secrets.PYPI_PASSWORD }} | |
| # run: flit publish |