Add KEEP, RedDino extractors and fix Gigapath from #159 #325
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| name: CI | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| jobs: | |
| test_extractors: | |
| runs-on: ubuntu-latest | |
| # needs: format_and_lint | |
| strategy: | |
| matrix: | |
| python-version: ["3.11", "3.12"] | |
| extractor: [ | |
| "ctranspath", | |
| "chief-ctranspath", | |
| "conch", | |
| "conch1_5", | |
| "uni", | |
| "uni2", | |
| "dino-bloom", | |
| "gigapath", | |
| "h-optimus-0", | |
| "h-optimus-1", | |
| "mstar", | |
| "plip", | |
| ] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| enable-cache: true | |
| cache-dependency-glob: "uv.lock" | |
| # - name: Set up Python ${{ matrix.python-version }} | |
| # uses: actions/setup-python@v5 | |
| # with: | |
| # python-version: ${{ matrix.python-version }} | |
| - name: Install the project | |
| run: uv sync --extra cpu --dev | |
| - name: Build | |
| run: uv build | |
| - name: Run tests for extractor ${{ matrix.extractor }} | |
| run: uv run pytest -s tests/test_feature_extractors.py -k "${{ matrix.extractor }}" --verbose | |
| env: | |
| HF_TOKEN: ${{ secrets.HF_TOKEN }} | |
| test_others: | |
| runs-on: ubuntu-latest | |
| # needs: format_and_lint | |
| strategy: | |
| matrix: | |
| python-version: ["3.11", "3.12"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| enable-cache: true | |
| cache-dependency-glob: "uv.lock" | |
| # - name: Set up Python ${{ matrix.python-version }} | |
| # uses: actions/setup-python@v5 | |
| # with: | |
| # python-version: ${{ matrix.python-version }} | |
| - name: Install the project | |
| run: uv sync --extra cpu --dev | |
| - name: Build | |
| run: uv build | |
| - name: Run other tests | |
| run: uv run pytest -s tests/ -k "not test_feature_extractors.py" --verbose | |
| env: | |
| HF_TOKEN: ${{ secrets.HF_TOKEN }} | |
| format_and_lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Install the code linting and formatting tool Ruff | |
| run: pipx install ruff | |
| - name: Lint code with Ruff | |
| run: ruff check --output-format=github --target-version=py311 | |
| - name: Check code formatting with Ruff | |
| run: ruff format --diff --target-version=py311 | |
| # continue-on-error: true | |