CI #815
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| name: CI | |
| on: | |
| push: | |
| branches: [main, "feature/**"] | |
| pull_request: | |
| branches: [main] | |
| schedule: | |
| - cron: "0 8 * * *" | |
| workflow_dispatch: | |
| jobs: | |
| quality: | |
| name: Quality (ruff + mypy) | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - run: pip install -e ".[dev]" | |
| - run: ruff format --check . | |
| - run: ruff check . | |
| - name: mypy (core modules only) | |
| run: mypy src/omega_pbpk/core src/omega_pbpk/drugs src/omega_pbpk/config.py | |
| continue-on-error: true | |
| test: | |
| name: Test (Python ${{ matrix.python-version }}) | |
| runs-on: ubuntu-latest | |
| needs: quality | |
| strategy: | |
| matrix: | |
| python-version: ["3.10", "3.11", "3.12"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - run: pip install pandas && pip install -e ".[dev,api,auth,viz]" | |
| - name: Check test count | |
| run: | | |
| pytest tests/ --collect-only -q 2>&1 | tail -3 | |
| - name: Run tests with coverage | |
| run: | | |
| pytest tests/ -m "not slow and not benchmark" \ | |
| --cov=src/omega_pbpk \ | |
| --cov-report=term-missing \ | |
| --cov-fail-under=70 \ | |
| -q | |
| - name: Upload coverage | |
| if: matrix.python-version == '3.11' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-report | |
| path: .coverage | |
| smoke: | |
| name: Smoke Test | |
| runs-on: ubuntu-latest | |
| needs: test | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - run: pip install pandas && pip install -e ".[dev,api,viz]" | |
| - name: CLI smoke | |
| run: omega --help | |
| - name: Import smoke | |
| run: python -c "import omega_pbpk; print('OK')" | |
| slow-tests: | |
| name: Slow Tests (nightly) | |
| runs-on: ubuntu-latest | |
| if: github.event_name == 'schedule' || github.event_name == 'workflow_dispatch' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - run: pip install pandas && pip install -e ".[all]" | |
| - name: Run slow tests | |
| run: PYTHONPATH=src python3 -m pytest tests/ -m "slow" --timeout=600 -v |