Tests Cross-Platform #152
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 Cross-Platform | |
| 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: [3.9] | |
| timeout-minutes: 60 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up JDK 17 | |
| uses: actions/setup-java@v2 | |
| with: | |
| java-version: '17' | |
| distribution: 'temurin' | |
| id: setup-java | |
| - name: Debug JAVA_HOME | |
| run: | | |
| echo $env:JAVA_HOME | |
| echo $env:PATH | |
| shell: pwsh | |
| - name: Set JDK_HOME environment variable | |
| run: echo "JDK_HOME=${JAVA_HOME}" >> $GITHUB_ENV | |
| shell: bash | |
| - name: Print JAVA_HOME and JDK_HOME | |
| run: | | |
| echo "JAVA_HOME: $env:JAVA_HOME" | |
| echo "JDK_HOME: $env:JDK_HOME" | |
| shell: pwsh | |
| - name: Download and Setup OpenSlide | |
| run: | | |
| $zipFile = "openslide-win64-20231011.zip" | |
| $extractPath = Join-Path $env:GITHUB_WORKSPACE "openslide-binaries" | |
| Invoke-WebRequest -Uri "https://github.com/openslide/openslide-bin/releases/download/v20231011/$zipFile" -OutFile $zipFile | |
| Expand-Archive -Path $zipFile -DestinationPath $extractPath | |
| $binPath = Join-Path $extractPath "openslide-win64-20231011/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: ${{ env.OPENSLIDE_PATH }} | |
| # - name: Download and Setup OpenSlide | |
| # run: | | |
| # Invoke-WebRequest -Uri "https://github.com/openslide/openslide-bin/releases/download/v20231011/openslide-win64-20231011.zip" -OutFile "openslide-win64-20231011.zip" | |
| # # Expand-Archive -Path "openslide-win64-20231011.zip" -DestinationPath "${{ github.workspace }}/openslide-binaries" | |
| # # echo "${{ github.workspace }}/openslide-binaries/openslide-win64-20231011" | Out-File -Append -FilePath $env:GITHUB_PATH -Encoding utf8 | |
| # shell: pwsh | |
| # - name: Extract OpenSlide Binaries | |
| # run: | | |
| # Expand-Archive -Path "openslide-win64-20231011.zip" -DestinationPath "${{ github.workspace }}/openslide-binaries" | |
| # $binPath = Join-Path ${{ github.workspace }} "openslide-binaries/openslide-win64-20231011/bin" | |
| # Write-Host "Adding to PATH: $binPath" | |
| # echo "$binPath" | Out-File -Append -FilePath $env:GITHUB_PATH -Encoding utf8 | |
| # shell: pwsh | |
| # - name: List files in OpenSlide bin directory | |
| # run: | | |
| # $binPath = Join-Path ${{ github.workspace }} "openslide-binaries/openslide-win64-20231011/bin" | |
| # Get-ChildItem -Path $binPath | |
| # shell: pwsh | |
| - name: Check PATH | |
| run: | | |
| # echo $env:JAVA_HOME | |
| echo $env:PATH | |
| shell: pwsh | |
| - name: Setup Miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-activate-base: false | |
| activate-environment: pathml | |
| environment-file: '.github/ci-environments/env-py39.yml' | |
| mamba-version: "*" | |
| python-version: ${{ matrix.python-version }} | |
| - name: Debugging | |
| shell: bash -l {0} | |
| run: | | |
| echo "Checking the status of mamba..." | |
| mamba --version | |
| echo "Checking the available disk space..." | |
| df -h | |
| - name: Conda info | |
| shell: bash -l {0} | |
| run: | | |
| conda info | |
| conda list | |
| - name: Install PathML | |
| shell: bash -l {0} | |
| run: pip install -e . | |
| - name: Install torchvision | |
| shell: bash -l {0} | |
| run: pip install torchvision==0.14.1 | |
| # - name: Download and Setup OpenSlide | |
| # run: | | |
| # Invoke-WebRequest -Uri "https://github.com/openslide/openslide-bin/releases/download/v20231011/openslide-win64-20231011.zip" -OutFile "openslide-win64-20231011.zip" | |
| # Expand-Archive -Path "openslide-win64-20231011.zip" -DestinationPath "${{ github.workspace }}/openslide-binaries" | |
| # echo "${{ github.workspace }}/openslide-binaries/openslide-win64-20231011" | Out-File -Append -FilePath $env:GITHUB_PATH -Encoding utf8 | |
| # shell: pwsh | |
| - name: Set OPENSLIDE_PATH | |
| run: echo "OPENSLIDE_PATH=D:\a\pathml\pathml\openslide-binaries\openslide-win64-20231011\bin" >> $GITHUB_ENV | |
| shell: pwsh | |
| - name: Check PATH | |
| run: | | |
| # echo $env:JAVA_HOME | |
| echo $env:PATH | |
| shell: pwsh | |
| - 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 | |
| continue-on-error: true | |
| - 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" | |
| continue-on-error: true | |
| # name: Tests Cross-Platform | |
| # on: | |
| # workflow_dispatch: | |
| # pull_request: | |
| # branches: | |
| # - dev | |
| # - master | |
| # push: | |
| # branches: | |
| # - dev | |
| # - master | |
| # jobs: | |
| # build: | |
| # runs-on: windows-latest # Use Ubuntu if you're building on Linux, or keep windows-latest if you're targeting Windows. | |
| # strategy: | |
| # max-parallel: 5 | |
| # matrix: | |
| # python-version: [3.9] | |
| # timeout-minutes: 60 | |
| # steps: | |
| # - uses: actions/checkout@v2 | |
| # - name: Set up JDK 17 | |
| # uses: actions/setup-java@v2 | |
| # with: | |
| # java-version: '17' | |
| # distribution: 'temurin' # Use 'temurin' for Eclipse Temurin distribution | |
| # id: setup-java | |
| # - name: Debug JAVA_HOME | |
| # run: | | |
| # echo $env:JAVA_HOME | |
| # echo $env:PATH | |
| # shell: pwsh | |
| # - name: Set JDK_HOME environment variable | |
| # shell: bash | |
| # run: echo "JDK_HOME=${JAVA_HOME}" >> $GITHUB_ENV | |
| # - name: Print JAVA_HOME and JDK_HOME | |
| # run: | | |
| # echo "JAVA_HOME: $env:JAVA_HOME" | |
| # echo "JDK_HOME: $env:JDK_HOME" | |
| # shell: pwsh | |
| # - name: vcpkg build | |
| # uses: johnwason/vcpkg-action@v6 | |
| # id: vcpkg | |
| # with: | |
| # pkgs: openslide | |
| # triplet: x64-windows | |
| # token: ${{ github.token }} | |
| # github-binarycache: true | |
| # - name: Setup Miniconda | |
| # uses: conda-incubator/setup-miniconda@v2 | |
| # with: | |
| # auto-activate-base: false | |
| # activate-environment: pathml | |
| # environment-file: '.github/ci-environments/env-py39.yml' # Directly specify the env-py39.yml file | |
| # mamba-version: "*" | |
| # python-version: ${{ matrix.python-version }} | |
| # - name: Debugging | |
| # shell: bash -l {0} | |
| # run: | | |
| # echo "Checking the status of mamba..." | |
| # mamba --version | |
| # echo "Checking the available disk space..." | |
| # df -h | |
| # - name: Conda info | |
| # shell: bash -l {0} | |
| # run: | | |
| # conda info | |
| # conda list | |
| # - name: Install PathML | |
| # shell: bash -l {0} | |
| # run: pip install -e . | |
| # # - name: Install python-spams | |
| # # shell: bash -l {0} | |
| # # run: pip install spams | |
| # - name: Install torchvision | |
| # shell: bash -l {0} | |
| # run: pip install torchvision==0.14.1 | |
| # - name: Set up vcpkg | |
| # uses: lukka/run-vcpkg@v10 | |
| # with: | |
| # # Setup vcpkg directory | |
| # vcpkgDirectory: '${{ github.workspace }}/vcpkg' | |
| # # Clone vcpkg repo | |
| # setupOnly: true | |
| # - name: Install OpenSlide with vcpkg | |
| # run: | | |
| # ./vcpkg/vcpkg install openslide | |
| # working-directory: ${{ github.workspace }} | |
| # - name: Test tile_stitcher with pytest and generate coverage | |
| # shell: bash -l {0} | |
| # run: | | |
| # # COVERAGE_FILE=.coverage_tilestitcher coverage run -m pytest tests/preprocessing_tests/test_tilestitcher.py | |
| # coverage run --data-file=.coverage_tilestitcher -m pytest tests/preprocessing_tests/test_tilestitcher.py | |
| # - 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" | |
| # # COVERAGE_FILE=.coverage_others coverage run -m pytest -m "not slow and not exclude" | |