Merge pull request #36 from andreped/google-colab #13
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| name: Integration Tests | |
| on: | |
| push: | |
| branches: 'main' | |
| pull_request: | |
| branches: 'main' | |
| workflow_dispatch: | |
| jobs: | |
| build: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v1 | |
| - name: Set up Python 3.6 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.6' | |
| - name: Install dependencies | |
| run: pip install wheel setuptools | |
| - name: Build package | |
| run: python setup.py bdist_wheel | |
| - name: Upload Python wheel | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: "Python wheel" | |
| path: ./dist/* | |
| if-no-files-found: error | |
| integration-tests: | |
| needs: build | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [macos-latest] | |
| python: ["3.10"] | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v1 | |
| - name: Set up Python ${{ matrix.python }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| - name: Install dependencies | |
| run: pip install wheel setuptools | |
| - name: Download artifact | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: "Python wheel" | |
| - name: Install wheel | |
| run: pip install --find-links=. vsi2tif-* | |
| shell: bash | |
| - name: Install vips | |
| run: | | |
| brew install --cask zulu@8 | |
| brew install vips | |
| - name: Install bftools | |
| run: | | |
| wget http://downloads.openmicroscopy.org/latest/bio-formats5.6/artifacts/bftools.zip | |
| unzip bftools.zip | |
| - name: Download test data | |
| run: | | |
| wget https://openslide.cs.cmu.edu/download/openslide-testdata/Olympus/OS-1.zip | |
| wget https://openslide.cs.cmu.edu/download/openslide-testdata/Olympus/OS-2.zip | |
| unzip OS-1.zip | |
| unzip OS-2.zip | |
| mkdir WSI/ | |
| mv OS-* WSI/ | |
| - name: Test single conversion | |
| run: vsi2tif -i ./WSI/OS-2.vsi -o ./OS-2.tif -b bftools/bfconvert -v 0 | |
| shell: bash | |
| - name: Test batch conversion | |
| run: vsi2tif -i ./WSI -o ./converted/ -b bftools/bfconvert -v 0 | |
| shell: bash |