Updating the segmentation to use Cellpose SAM #534
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| name: pull-request-ci | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| jobs: | |
| style: | |
| name: Check Style | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - uses: psf/black@stable | |
| with: | |
| src: "biahub" | |
| options: "--check --verbose" | |
| use_pyproject: true # Requires python >3.11 | |
| - uses: py-actions/flake8@v2 | |
| with: | |
| path: "biahub" | |
| flake8-version: "7.2.0" # Duplicates the version in pyproject.toml | |
| - uses: isort/isort-action@v1 | |
| with: | |
| isort-version: "6.0.1" # Duplicates the version in pyproject.toml | |
| test: | |
| name: Run Tests | |
| needs: [style] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Install the biahub package | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install torch torchvision ".[all]" --extra-index-url https://download.pytorch.org/whl/cpu | |
| - name: Test with pytest | |
| run: pytest -v |