feat: Set up comprehensive Python testing infrastructure with Poetry

[llbbl]

Add Complete Python Testing Infrastructure

Summary

This PR sets up a comprehensive testing infrastructure for the Restore RWKV medical imaging project using Poetry as the package manager and pytest as the testing framework.

Changes Made

Package Management

• Poetry Configuration: Created pyproject.toml with complete project metadata and dependency management
• Dependencies: Added all required project dependencies including:
  • Core: torch, torchvision, numpy, pandas, einops, simpleitk
  • Testing: pytest, pytest-cov, pytest-mock, pytest-xdist
  • Development: black, isort, flake8, mypy, pre-commit

Testing Configuration

• pytest Settings: Configured comprehensive pytest options including:

  • Coverage reporting with HTML and XML output
  • Custom markers for unit, integration, and slow tests
  • Strict mode with verbose output
  • Test discovery patterns

• Coverage Settings: Set up coverage configuration with:

  • Source code coverage tracking
  • Exclusion patterns for test files and generated code
  • HTML and XML report generation
  • Branch coverage analysis

Directory Structure

tests/
├── __init__.py
├── conftest.py                    # Shared fixtures
├── test_infrastructure_validation.py # Validation tests
├── unit/
│   └── __init__.py
└── integration/
    └── __init__.py

Test Fixtures

Created comprehensive fixtures in conftest.py:

• Temporary Resources: temp_dir, isolated_filesystem
• Configuration: mock_config with model/training/data settings
• Data Fixtures: sample tensors, numpy arrays, PIL images, medical data
• Model Mocks: mock_model, mock_dataloader, mock_optimizer, mock_scheduler
• Testing Utilities: random_seed, capture_stdout, mock_tqdm
• CUDA Management: cleanup_cuda fixture for memory management

Additional Setup

• Git Ignore: Updated .gitignore with Python, testing, and Claude-specific patterns
• Test Runner: Created run_tests.sh helper script for easy test execution
• Validation Suite: Comprehensive test suite to verify all infrastructure components work

How to Use

Install Dependencies

poetry install --with dev

Run Tests

# Run all tests
poetry run pytest

# Run with coverage
poetry run pytest --cov

# Run specific test file
poetry run pytest tests/test_infrastructure_validation.py

# Run tests by marker
poetry run pytest -m unit
poetry run pytest -m integration
poetry run pytest -m "not slow"

# Using the helper script
./run_tests.sh

View Coverage Reports

• Terminal: Coverage summary is shown after each test run
• HTML Report: Open htmlcov/index.html in a browser
• XML Report: Available at coverage.xml for CI/CD integration

Testing Infrastructure Validation

The PR includes a validation test suite that verifies:

• All dependencies are properly installed
• Test markers work correctly
• All fixtures function as expected
• Project modules can be imported
• Coverage reporting generates properly

All validation tests pass successfully (33 passed, 1 skipped due to CUDA compilation requirement).

Notes

• Coverage threshold is currently set to 0% as this PR only sets up infrastructure
• Once actual unit tests are written, update the threshold in pyproject.toml (line 47)
• The model import test is skipped as it requires CUDA kernel compilation
• Poetry lock file is included and should be committed for reproducible builds

Next Steps

Developers can now immediately start writing tests using this infrastructure:

1. Create test files in tests/unit/ or tests/integration/
2. Use the provided fixtures from conftest.py
3. Run tests with poetry run pytest
4. Monitor coverage to ensure code quality