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combine linux/macos/windows tests into one file (#3)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,120 @@ | ||
| name: Test CLI | ||
| on: | ||
| push: | ||
| branches: [ main ] | ||
| pull_request: | ||
| branches: [ main ] | ||
|
|
||
| jobs: | ||
|
|
||
| Linux: | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| python-version: ["3.8", "3.9", "3.10", "3.11", "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 WSInfer-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 WSInfer-MIL still finds everything it needs. | ||
| # Test it twice so the second time we get cache hits. | ||
| run: | | ||
| cd /tmp | ||
| wsinfer-mil run -m kaczmarj/pancancer-tissue-classifier.tcga -i ~/wsi/CMU-1.svs | ||
| wsinfer-mil run -m kaczmarj/pancancer-tissue-classifier.tcga -i ~/wsi/CMU-1.svs | ||
| macOS: | ||
| runs-on: macos-latest | ||
| strategy: | ||
| matrix: | ||
| python-version: ["3.10"] | ||
| 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 WSInfer-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 WSInfer-MIL still finds everything it needs. | ||
| # Test it twice so the second time we get cache hits. | ||
| run: | | ||
| cd /tmp | ||
| wsinfer-mil run -m kaczmarj/pancancer-tissue-classifier.tcga -i ~/wsi/CMU-1.svs | ||
| wsinfer-mil run -m kaczmarj/pancancer-tissue-classifier.tcga -i ~/wsi/CMU-1.svs | ||
| Windows: | ||
| runs-on: windows-latest | ||
| strategy: | ||
| matrix: | ||
| python-version: ["3.10"] | ||
| 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 WSInfer-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 WSInfer-MIL still finds everything it needs. | ||
| # Test it twice so the second time we get cache hits. | ||
| run: | | ||
| mkdir -p ~/foobar | ||
| cd ~/foobar | ||
| wsinfer-mil run -m kaczmarj/pancancer-tissue-classifier.tcga -i ~/wsi/CMU-1.svs | ||
| wsinfer-mil run -m kaczmarj/pancancer-tissue-classifier.tcga -i ~/wsi/CMU-1.svs |