Implement FHIR type interoperability and client helpers #62
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| name: CI | |
| on: | |
| push: | |
| branches: [main, master, develop] | |
| pull_request: | |
| branches: [main, master, develop] | |
| workflow_dispatch: # Allow manual triggering | |
| jobs: | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v6 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install ruff mypy | |
| pip install -e ".[dev]" | |
| - name: Run Ruff linter | |
| run: ruff check src/ | |
| - name: Run Ruff formatter check | |
| run: ruff format --check src/ | |
| - name: Run MyPy | |
| run: mypy src/omophub | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.10", "3.11", "3.12", "3.13"] | |
| steps: | |
| - uses: actions/checkout@v6 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -e ".[dev]" | |
| - name: Run unit tests with coverage | |
| run: | | |
| pytest tests/unit --cov=omophub --cov-report=xml --cov-report=term-missing | |
| - name: Upload coverage to Codecov | |
| if: matrix.python-version == '3.12' | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| files: ./coverage.xml | |
| fail_ci_if_error: false | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| integration: | |
| # Only run on push to main/develop, not on PRs (saves ~7-8 min per PR) | |
| if: github.event_name == 'push' || github.event_name == 'workflow_dispatch' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v6 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -e ".[dev]" | |
| - name: Run integration tests | |
| env: | |
| TEST_API_KEY: ${{ secrets.TEST_API_KEY }} | |
| run: | | |
| pytest tests/integration -v |