auto or manual mode for spark configuration #160
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| name: Tests with Spark | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - dev | |
| pull_request: | |
| branches: | |
| - master | |
| jobs: | |
| test: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: | |
| - ubuntu-latest | |
| - macos-14 | |
| # - windows-latest | |
| python: | |
| - '3.10' | |
| - '3.11' | |
| - '3.12' | |
| spark: | |
| - 3.4.0 | |
| - 3.5.2 | |
| name: ${{ matrix.os }} Python ${{ matrix.python }} Spark ${{ matrix.spark }} | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| - uses: actions/setup-java@v4 | |
| with: | |
| java-version: '17' | |
| distribution: temurin | |
| # Download and install ANTs | |
| - name: Install ANTs | |
| if: startsWith(matrix.os, 'ubuntu') | |
| run: | | |
| wget https://github.com/ANTsX/ANTs/releases/download/v2.5.3/ants-2.5.3-ubuntu-20.04-X64-gcc.zip | |
| unzip ants-2.5.3-ubuntu-20.04-X64-gcc.zip -d $HOME/ | |
| rm ants-2.5.3-ubuntu-20.04-X64-gcc.zip | |
| echo "ANTs installed successfully" | |
| - name: Install ANTs on macOS | |
| if: startsWith(matrix.os, 'macos') | |
| run: | | |
| curl -L -o $HOME/ants-2.5.3-macos-14-ARM64-clang.zip https://github.com/ANTsX/ANTs/releases/download/v2.5.3/ants-2.5.3-macos-14-ARM64-clang.zip | |
| unzip $HOME/ants-2.5.3-macos-14-ARM64-clang.zip -d $HOME/ | |
| rm $HOME/ants-2.5.3-macos-14-ARM64-clang.zip | |
| echo "ANTs installed successfully on macOS" | |
| # - name: Install ANTs on Windows | |
| # if: startsWith(matrix.os, 'windows') | |
| # run: | | |
| # Invoke-WebRequest -Uri https://github.com/ANTsX/ANTs/releases/download/v2.5.3/ants-2.5.3-windows-2022-X64-VS2019.zip -OutFile $env:USERPROFILE\\ants-2.5.3-windows-2022-X64-VS2019.zip | |
| # Expand-Archive -Path $env:USERPROFILE\\ants-2.5.3-windows-2022-X64-VS2019.zip -DestinationPath $env:USERPROFILE\\ants-2.5.3 | |
| # Remove-Item $env:USERPROFILE\\ants-2.5.3-windows-2022-X64-VS2019.zip | |
| # echo "ANTs installed successfully on Windows" | |
| # Install voluseg and dependencies | |
| - name: Install voluseg | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r tests/requirements.txt --no-cache-dir | |
| pip install .[pyspark] --no-cache-dir | |
| # Tests and coverage | |
| - name: Clear previous coverage data | |
| run: coverage erase | |
| - name: Run tests with pytest on Unix-like systems | |
| if: ${{ !startsWith(matrix.os, 'windows') }} | |
| env: | |
| ANTS_PATH: "$HOME/ants-2.5.3/bin" | |
| run: | | |
| coverage run -m pytest -s -v --tb=short | |
| # - name: Run tests with pytest on Windows | |
| # if: startsWith(matrix.os, 'windows') | |
| # env: | |
| # ANTS_PATH: "%USERPROFILE%/ants-2.5.3/bin" | |
| # run: | | |
| # pytest --cov=voluseg --cov-report=term-missing --cov-report=html --cov-report=xml -s -v --tb=short | |
| - name: Generate coverage report | |
| run: coverage report -m | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/codecov-action@v3 | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |