tests #8
Workflow file for this run
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| name: Tests with Spark | |
| on: | |
| push: | |
| branches: | |
| - dev-tests | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python: | |
| - '3.10' | |
| - '3.11' | |
| spark: | |
| - 3.4.0 | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| - uses: actions/setup-java@v4 | |
| with: | |
| java-version: '21' | |
| distribution: temurin | |
| # https://github.com/marketplace/actions/setup-apache-spark | |
| - uses: vemonet/setup-spark@v1 | |
| with: | |
| spark-version: ${{ matrix.spark }} | |
| hadoop-version: '3' | |
| - run: spark-submit --version | |
| # Download and install ANTs | |
| - name: Install ANTs | |
| 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 test dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r tests/requirements.txt --no-cache-dir | |
| - name: Install voluseg | |
| run: | | |
| pip install -r requirements.txt --no-cache-dir | |
| pip install . --no-cache-dir | |
| - name: Run tests with pytest | |
| env: | |
| ANTS_PATH: $HOME/ants-2.5.3/bin | |
| INPUT_PATH: /path/to/input # Set this to the actual input path | |
| run: | | |
| pytest --cov=voluseg --cov-report=term-missing | |
| - name: Upload coverage report | |
| if: success() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: coverage-report | |
| path: htmlcov/ |