Merge pull request #434 from Dana-Farber-AIOS/dev_graph #1
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Tests windows | |
| on: | |
| workflow_dispatch: | |
| pull_request: | |
| branches: | |
| - dev | |
| - master | |
| push: | |
| branches: | |
| - dev | |
| - master | |
| jobs: | |
| build: | |
| runs-on: windows-latest | |
| strategy: | |
| max-parallel: 5 | |
| matrix: | |
| python-version: ["3.8", "3.9", "3.10"] | |
| timeout-minutes: 120 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up JDK 17 | |
| uses: actions/setup-java@v2 | |
| with: | |
| java-version: '17' | |
| distribution: 'temurin' | |
| - name: Print JAVA_HOME and PATH | |
| run: | | |
| echo "JAVA_HOME: $env:JAVA_HOME" | |
| echo "PATH: $env:PATH" | |
| shell: pwsh | |
| - name: Set JDK_HOME environment variable | |
| run: echo "JDK_HOME=${JAVA_HOME}" >> $GITHUB_ENV | |
| shell: bash | |
| - name: Setup Miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-activate-base: false | |
| activate-environment: pathml | |
| environment-file: environment.yml | |
| # environment-file: '.github/ci-environments/env-py39.yml' | |
| # environment-file: .github/ci-environments/env-py${{ matrix.python-version == '3.10' && '310' || matrix.python-version == '3.9' && '39' || '38' }}.yml | |
| mamba-version: "*" | |
| python-version: ${{ matrix.python-version }} | |
| # - name: Install JavaBridge and other dependencies | |
| # shell: bash -l {0} | |
| # run: | | |
| # pip install python-javabridge | |
| - name: Run Python script to find JVM path | |
| shell: bash -l {0} | |
| run: | | |
| python -c "import javabridge; print('javabridge.locate.find_javahome():', javabridge.locate.find_javahome()); print('javabridge.jutil._find_jvm_windows():', javabridge.jutil._find_jvm_windows())" | |
| - name: Print JAVA_HOME and PATH Second | |
| run: | | |
| echo "JAVA_HOME: $env:JAVA_HOME" | |
| echo "PATH: $env:PATH" | |
| shell: pwsh | |
| - name: Download and Setup OpenSlide | |
| run: | | |
| # $zipFile = "openslide-win64-20231011.zip" | |
| $zipFile = "openslide-win64-20230414.zip" | |
| $extractPath = Join-Path $env:GITHUB_WORKSPACE "openslide-binaries" | |
| # Invoke-WebRequest -Uri "https://github.com/openslide/openslide-bin/releases/download/v20231011/$zipFile" -OutFile $zipFile | |
| Invoke-WebRequest -Uri "https://github.com/openslide/openslide-bin/releases/download/v20230414/$zipFile" -OutFile $zipFile | |
| Expand-Archive -Path $zipFile -DestinationPath $extractPath | |
| # $binPath = Join-Path $extractPath "openslide-win64-20231011/bin" | |
| $binPath = Join-Path $extractPath "openslide-win64-20230414/bin" | |
| Write-Host "Adding to PATH: $binPath" | |
| echo "OPENSLIDE_PATH=$binPath" | Out-File -Append -FilePath $env:GITHUB_ENV | |
| # echo "$binPath" | Out-File -Append -FilePath $env:GITHUB_PATH | |
| shell: pwsh | |
| # Optional: List files in OpenSlide bin directory to verify | |
| - name: List files in OpenSlide bin directory | |
| run: | | |
| Get-ChildItem -Path $env:OPENSLIDE_PATH | |
| shell: pwsh | |
| env: | |
| OPENSLIDE_PATH: ${{ env.OPENSLIDE_PATH }} | |
| - name: Conda info | |
| shell: bash -l {0} | |
| run: | | |
| conda info | |
| conda list | |
| - name: Install PathML | |
| shell: bash -l {0} | |
| run: pip install -e . | |
| - name: Install torchvision | |
| shell: bash -l {0} | |
| run: pip install torchvision==0.14.1 | |
| - name: Set OPENSLIDE_PATH | |
| run: echo "OPENSLIDE_PATH=D:\a\pathml\pathml\openslide-binaries\openslide-win64-20231011\bin" >> $GITHUB_ENV | |
| shell: pwsh | |
| - name: Test other modules with pytest and generate coverage | |
| shell: bash -l {0} | |
| run: | | |
| coverage run --data-file=.coverage_others -m pytest -m "not slow and not exclude" | |
| - name: Test tile_stitcher with pytest and generate coverage | |
| shell: bash -l {0} | |
| run: | | |
| coverage run --data-file=.coverage_tilestitcher -m pytest tests/preprocessing_tests/test_tilestitcher.py |