Merge pull request #1 from virtualcell/add-java-to-ci #24
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| name: Main | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| types: [opened, synchronize, reopened, ready_for_review] | |
| jobs: | |
| quality: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out | |
| uses: actions/checkout@v4 | |
| - uses: actions/cache@v4 | |
| with: | |
| path: ~/.cache/pre-commit | |
| key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }} | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - uses: abatilo/actions-poetry@v3 | |
| - name: Install python dependencies | |
| run: poetry install --no-interaction | |
| - name: Run checks | |
| run: make check | |
| tests-and-type-check: | |
| strategy: | |
| matrix: # python-version: ["3.9", "3.10", "3.11", "3.12"] | |
| python-version: ["3.11", "3.12"] | |
| # os: [macos-13, windows-latest, ubuntu-latest, macos-14] | |
| os: [ubuntu-latest, macos-14] | |
| fail-fast: false | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - name: Check out | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| fetch-depth: 2 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - uses: abatilo/actions-poetry@v3 | |
| - name: setup graalvm for static native build | |
| uses: graalvm/setup-graalvm@v1 | |
| with: | |
| java-version: "23" | |
| distribution: "graalvm-community" | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| components: "native-image" | |
| # native-image-musl: 'true' # Now semi-static by not including libc | |
| native-image-job-reports: "true" | |
| cache: "maven" | |
| - name: build entire project | |
| working-directory: vcell_submodule | |
| run: | | |
| mvn --batch-mode clean install dependency:copy-dependencies -DskipTests=true | |
| - name: test, record, and build/install native library (ubuntu) | |
| working-directory: vcell-native | |
| run: | | |
| mvn --batch-mode clean install | |
| java -agentlib:native-image-agent=config-output-dir=target/recording \ | |
| -jar target/vcell-native-1.0-SNAPSHOT.jar \ | |
| "src/test/resources/TinySpacialProject_Application0.xml" \ | |
| "target/sbml-input" | |
| mvn --batch-mode -P shared-dll package | |
| cp target/libvcell.so ../libvcell/_internal/libs | |
| if: ${{ startsWith(matrix.os, 'ubuntu') }} | |
| - name: test, record, and build/install native library (macos) | |
| working-directory: vcell-native | |
| run: | | |
| mvn --batch-mode clean install | |
| java -agentlib:native-image-agent=config-output-dir=target/recording \ | |
| -jar target/vcell-native-1.0-SNAPSHOT.jar \ | |
| "src/test/resources/TinySpacialProject_Application0.xml" \ | |
| "target/sbml-input" | |
| mvn --batch-mode -P shared-dll package | |
| cp target/libvcell.dylib ../libvcell/_internal/libs | |
| if: ${{ startsWith(matrix.os, 'macos') }} | |
| - name: test, record, and build/install native library (windows) | |
| working-directory: vcell-native | |
| run: | | |
| mvn --batch-mode clean install | |
| java -agentlib:native-image-agent=config-output-dir=target\recording -jar "target\vcell-native-1.0-SNAPSHOT.jar" "src\test\resources\TinySpacialProject_Application0.xml" "target\sbml-input" | |
| mvn --batch-mode -P shared-dll package | |
| cp target/libvcell.dll ../libvcell/_internal/libs | |
| if: ${{ startsWith(matrix.os, 'windows') }} | |
| - name: Install python dependencies | |
| run: poetry install --no-interaction | |
| - name: Run tests | |
| run: poetry run pytest tests --cov --cov-config=pyproject.toml --cov-report=xml | |
| - name: Check typing | |
| run: poetry run mypy | |
| - name: Upload coverage reports to Codecov with GitHub Action on Python 3.11 | |
| uses: codecov/codecov-action@v4 | |
| if: ${{ matrix.python-version == '3.11' }} | |
| - name: Setup tmate | |
| if: failure() | |
| uses: mxschmitt/action-tmate@v3 | |
| with: | |
| limit-access-to-actor: true | |
| check-docs: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out | |
| uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - uses: abatilo/actions-poetry@v3 | |
| - name: Install python dependencies | |
| run: poetry install --no-interaction | |
| - name: Check if documentation can be built | |
| run: poetry run mkdocs build -s |