Merge branch 'SBU-BMI:main' into main #17
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| name: ci | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.8", "3.9", "3.10", "3.11"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install the package | |
| run: | | |
| sudo apt update | |
| sudo apt install -y libopenslide0 | |
| python -m pip install --upgrade pip setuptools wheel | |
| python -m pip install torch torchvision --extra-index-url https://download.pytorch.org/whl/cpu openslide-python tiffslide | |
| python -m pip install --editable .[dev] | |
| - name: Run tests | |
| run: python -m pytest --verbose tests/ | |
| test-pytorch-nightly: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: Install the package | |
| run: | | |
| sudo apt update | |
| sudo apt install -y libopenslide0 | |
| python -m pip install --upgrade pip setuptools wheel | |
| python -m pip install --pre torch torchvision --extra-index-url https://download.pytorch.org/whl/nightly/cpu openslide-python tiffslide | |
| python -m pip install --editable .[dev] | |
| - name: Check types | |
| run: python -m mypy --install-types --non-interactive wsinfer/ | |
| - name: Run tests | |
| run: python -m pytest --verbose tests/ | |
| test-docker: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Build Docker image | |
| run: docker build -t wsinferimage . | |
| - name: Run pytest in Docker image | |
| run: | | |
| docker run --rm --shm-size=512m --workdir /opt/wsinfer/ --entrypoint bash wsinferimage \ | |
| -c "python -m pip install -e /opt/wsinfer[dev] && python -m pytest -vx /opt/wsinfer/tests/test_all.py" | |
| - name: Run wsinfer on a sample image in Docker | |
| run: | | |
| mkdir slides | |
| cd slides | |
| wget -q https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/JP2K-33003-1.svs | |
| cd .. | |
| docker run --rm --shm-size=512m --volume $HOME:$HOME --volume $(pwd):/work --workdir /work wsinferimage run \ | |
| --wsi-dir slides/ --results-dir results/ --model breast-tumor-resnet34.tcga-brca | |
| test -f results/run_metadata_*.json | |
| test -f results/patches/JP2K-33003-1.h5 | |
| test -f results/model-outputs-csv/JP2K-33003-1.csv | |
| test $(wc -l < results/model-outputs-csv/JP2K-33003-1.csv) -eq 675 | |
| # This is run on multiple operating systems. | |
| test-package: | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, windows-latest, macos-latest] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: Install OpenSlide on Ubuntu | |
| if: matrix.os == 'ubuntu-latest' | |
| run: sudo apt update && sudo apt install -y libopenslide0 | |
| - name: Install OpenSlide on macOS | |
| if: matrix.os == 'macos-latest' | |
| run: brew install openslide | |
| - name: Install the wsinfer python package | |
| run: | | |
| python -m pip install --upgrade pip setuptools wheel | |
| python -m pip install torch torchvision --extra-index-url https://download.pytorch.org/whl/cpu openslide-python tiffslide | |
| python -m pip install . | |
| - name: Run 'wsinfer run' on Unix | |
| if: matrix.os != 'windows-latest' | |
| run: | | |
| mkdir newdir && cd newdir | |
| mkdir slides && cd slides | |
| wget -q https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/JP2K-33003-1.svs | |
| cd .. | |
| WSINFER_FORCE_CPU=1 wsinfer run --wsi-dir slides/ --results-dir results/ --model breast-tumor-resnet34.tcga-brca | |
| test -f results/run_metadata_*.json | |
| test -f results/patches/JP2K-33003-1.h5 | |
| test -f results/model-outputs-csv/JP2K-33003-1.csv | |
| test $(wc -l < results/model-outputs-csv/JP2K-33003-1.csv) -eq 675 | |
| # FIXME: tissue segmentation has different outputs on Windows. The patch sizes | |
| # are the same but the coordinates found are different. | |
| - name: Run 'wsinfer run' on Windows | |
| if: matrix.os == 'windows-latest' | |
| run: | | |
| mkdir newdir && cd newdir | |
| mkdir slides && cd slides | |
| Invoke-WebRequest -URI https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/JP2K-33003-1.svs -OutFile JP2K-33003-1.svs | |
| cd .. | |
| wsinfer run --wsi-dir slides/ --results-dir results/ --model breast-tumor-resnet34.tcga-brca | |
| Test-Path -Path results/run_metadata_*.json -PathType Leaf | |
| Test-Path -Path results/patches/JP2K-33003-1.h5 -PathType Leaf | |
| Test-Path -Path results/model-outputs-csv/JP2K-33003-1.csv -PathType Leaf | |
| # test $(python -c "print(sum(1 for _ in open('results/model-outputs/JP2K-33003-1.csv')))") -eq 675 | |
| style-and-types: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: Install the package | |
| run: | | |
| sudo apt update | |
| sudo apt install -y libopenslide0 | |
| python -m pip install --upgrade pip setuptools wheel | |
| python -m pip install torch torchvision --extra-index-url https://download.pytorch.org/whl/cpu openslide-python tiffslide | |
| python -m pip install .[dev] | |
| - name: Check style (flake8) | |
| run: python -m flake8 wsinfer/ | |
| - name: Check style (black) | |
| run: python -m black --check wsinfer/ | |
| - name: Check types | |
| run: python -m mypy --install-types --non-interactive wsinfer/ | |
| docs: | |
| 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 the package | |
| run: | | |
| sudo apt update | |
| sudo apt install -y libopenslide0 | |
| python -m pip install --upgrade pip setuptools wheel | |
| python -m pip install torch torchvision --extra-index-url https://download.pytorch.org/whl/cpu openslide-python tiffslide | |
| python -m pip install .[docs] | |
| - name: Build docs | |
| run: | | |
| cd docs | |
| make html |