Bump tqdm from 4.66.1 to 4.66.3 #66
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| 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}" >> $GITHUB_ENV | |
| shell: bash | |
| - name: Setup Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| micromamba-version: '1.5.6-0' | |
| environment-name: pathml | |
| environment-file: environment.yml | |
| init-shell: >- | |
| bash | |
| create-args: >- | |
| python=${{ matrix.python-version }} | |
| - 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: Mamba info | |
| shell: bash -l {0} | |
| run: | | |
| micromamba info | |
| micromamba config | |
| micromamba 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 |