Rename package to SpinPath #19
Workflow file for this run
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| name: Test CLI | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| jobs: | |
| Linux: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| # python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"] | |
| python-version: ["3.12"] | |
| steps: | |
| - name: Cache sample WSI | |
| id: cache-wsi | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/wsi/ | |
| key: sample-wsi | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install SpinPath CLI | |
| run: | | |
| python -m pip install --upgrade pip setuptools wheel | |
| python -m pip install torch torchvision --extra-index-url https://download.pytorch.org/whl/cpu | |
| python -m pip install . | |
| - name: Download sample WSI | |
| if: steps.cache-wsi.outputs.cache-hit != 'true' | |
| run: | | |
| mkdir -p ~/wsi | |
| cd ~/wsi | |
| wget -nc -q https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/CMU-1.svs | |
| cd - | |
| - name: Run tests | |
| # Go to a different directory to test that SpinPath still finds everything it needs. | |
| # Test it twice so the second time we get cache hits. | |
| run: | | |
| cd /tmp | |
| SPINPATH_FORCE_CPU=1 spinpath run -m kaczmarj/pancancer-tissue-classifier.tcga -i ~/wsi/CMU-1.svs | |
| SPINPATH_FORCE_CPU=1 spinpath run -m kaczmarj/pancancer-tissue-classifier.tcga -i ~/wsi/CMU-1.svs | |
| macOS: | |
| runs-on: macos-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.12"] | |
| steps: | |
| - name: Cache sample WSI | |
| id: cache-wsi | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/wsi/ | |
| key: sample-wsi | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install SpinPath CLI | |
| run: | | |
| python -m pip install --upgrade pip setuptools wheel | |
| python -m pip install torch torchvision --extra-index-url https://download.pytorch.org/whl/cpu | |
| python -m pip install . | |
| - name: Download sample WSI | |
| if: steps.cache-wsi.outputs.cache-hit != 'true' | |
| run: | | |
| mkdir -p ~/wsi | |
| cd ~/wsi | |
| wget -nc -q https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/CMU-1.svs | |
| cd - | |
| - name: Run tests | |
| # Go to a different directory to test that SpinPath still finds everything it needs. | |
| # Test it twice so the second time we get cache hits. | |
| run: | | |
| cd /tmp | |
| SPINPATH_FORCE_CPU=1 spinpath run -m kaczmarj/pancancer-tissue-classifier.tcga -i ~/wsi/CMU-1.svs | |
| SPINPATH_FORCE_CPU=1 spinpath run -m kaczmarj/pancancer-tissue-classifier.tcga -i ~/wsi/CMU-1.svs | |
| Windows: | |
| runs-on: windows-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.12"] | |
| steps: | |
| - name: Cache sample WSI | |
| id: cache-wsi | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/wsi/ | |
| key: sample-wsi | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install SpinPath CLI | |
| run: | | |
| python -m pip install --upgrade pip setuptools wheel | |
| python -m pip install torch torchvision --extra-index-url https://download.pytorch.org/whl/cpu | |
| python -m pip install . | |
| - name: Download sample WSI | |
| if: steps.cache-wsi.outputs.cache-hit != 'true' | |
| run: | | |
| mkdir -p ~/wsi | |
| cd ~/wsi | |
| Invoke-WebRequest -URI https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/CMU-1.svs -OutFile CMU-1.svs | |
| cd - | |
| - name: Run tests | |
| # Go to a different directory to test that SpinPath still finds everything it needs. | |
| # Test it twice so the second time we get cache hits. | |
| run: | | |
| mkdir -p ~/foobar | |
| cd ~/foobar | |
| set SPINPATH_FORCE_CPU=1 | |
| spinpath run -m kaczmarj/pancancer-tissue-classifier.tcga -i ~/wsi/CMU-1.svs | |
| spinpath run -m kaczmarj/pancancer-tissue-classifier.tcga -i ~/wsi/CMU-1.svs |