start Github Action to build native shared libs #17
Workflow file for this run
This file contains hidden or 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: 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: 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: [windows-latest, 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: 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: Check if documentation can be built | |
| run: poetry run mkdocs build -s |