feat: Set up comprehensive Python testing infrastructure

[llbbl]

Set up comprehensive Python testing infrastructure

Summary

This PR establishes a complete testing infrastructure for the ChemDFM project using Poetry as the package manager and pytest as the testing framework. The setup provides a ready-to-use testing environment where developers can immediately start writing tests.

Changes Made

Package Management

• Poetry Setup: Created pyproject.toml with Poetry configuration
• Dependencies: Added core dependencies (torch, transformers) and test dependencies (pytest, pytest-cov, pytest-mock)
• Project Structure: Configured project metadata and build settings

Testing Framework

• pytest Configuration: Comprehensive test configuration with:
  • Custom test discovery patterns
  • Coverage reporting (HTML, XML, terminal)
  • 80% coverage threshold requirement
  • Strict options for robust testing
• Custom Markers: Added unit, integration, and slow test markers for test categorization
• Test Directory Structure: Created organized directory structure:

  tests/
  ├── __init__.py
  ├── conftest.py
  ├── unit/
  │   └── __init__.py
  ├── integration/
  │   └── __init__.py
  └── test_infrastructure.py
  

Test Fixtures and Utilities

• Shared Fixtures: Comprehensive conftest.py with reusable fixtures:
  • temp_dir: Temporary directory for test files
  • mock_tokenizer, mock_model: Mock ML model components
  • sample_args: Mock configuration objects
  • capture_stdout, mock_input: Testing utilities
  • clean_environment: Environment isolation

Coverage Configuration

• Source Tracking: Configured to track chemdfm package coverage
• Exclusions: Proper exclusions for test files, migrations, virtual environments
• Reporting: Multiple output formats (HTML, XML, terminal with missing lines)
• Thresholds: 80% coverage requirement with failure on insufficient coverage

Development Environment

• .gitignore: Comprehensive gitignore covering:
  • Testing artifacts (.pytest_cache/, htmlcov/, .coverage)
  • Python artifacts (__pycache__/, *.pyc, dist/)
  • Virtual environments and IDE files
  • Claude Code settings (.claude/*)
• Lock Files: Poetry.lock is preserved for reproducible builds

Testing Instructions

Running Tests

# Install dependencies
poetry install

# Run all tests
poetry run pytest

# Run tests without coverage (faster)
poetry run pytest --no-cov

# Run specific test categories
poetry run pytest -m unit          # Unit tests only
poetry run pytest -m integration   # Integration tests only
poetry run pytest -m "not slow"    # Exclude slow tests

# Run with verbose output
poetry run pytest -v

# Generate coverage report
poetry run pytest --cov-report=html

Coverage Reports

• Terminal: Shows missing lines during test runs
• HTML: Browse htmlcov/index.html for detailed coverage analysis
• XML: coverage.xml for CI/CD integration

Test Organization

• Unit Tests: Place in tests/unit/ for isolated component testing
• Integration Tests: Place in tests/integration/ for end-to-end testing
• Fixtures: Add shared fixtures to tests/conftest.py

Validation

✅ All validation tests pass
✅ Poetry dependency installation successful
✅ pytest configuration working correctly
✅ Custom markers functional
✅ Coverage reporting configured
✅ Fixtures and utilities available

Next Steps

The testing infrastructure is now ready for development:

1. Write Tests: Developers can immediately start writing unit and integration tests
2. Add Source Code: As the codebase grows, coverage reporting will provide meaningful metrics
3. CI/CD Integration: The XML coverage reports and exit codes are CI/CD ready
4. Extend Fixtures: Add project-specific fixtures to conftest.py as needed

Dependencies Added

Production Dependencies

• torch ^2.0.0: PyTorch for ML functionality
• transformers ^4.30.0: Hugging Face transformers library

Test Dependencies

• pytest ^7.4.0: Main testing framework
• pytest-cov ^4.1.0: Coverage reporting
• pytest-mock ^3.11.0: Advanced mocking capabilities

This setup follows Python testing best practices and provides a solid foundation for maintaining high code quality through comprehensive testing.