feat: Add comprehensive Python testing infrastructure with Poetry

[llbbl]

Add Python Testing Infrastructure

Summary

This PR sets up a complete testing infrastructure for the CGCNN Python project using Poetry for dependency management and pytest for testing. The infrastructure provides a foundation for writing comprehensive unit and integration tests.

Changes Made

1. Package Management

• ✅ Created pyproject.toml with Poetry configuration
• ✅ Migrated dependencies from project imports (PyTorch, NumPy, scikit-learn, pymatgen)
• ✅ Added development dependencies for testing (pytest, pytest-cov, pytest-mock)

2. Testing Configuration

• ✅ Configured pytest with:
  • Test discovery patterns for test_*.py and *_test.py files
  • Custom markers: unit, integration, and slow
  • Coverage reporting with HTML and XML outputs
  • Strict mode with verbose output
• ✅ Configured coverage with:
  • Source directory targeting cgcnn module
  • Exclusion patterns for test files and boilerplate code
  • Coverage threshold set to 0% (with note to increase to 80% when writing actual tests)

3. Directory Structure

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

4. Testing Fixtures

Created comprehensive fixtures in conftest.py:

• temp_dir: Temporary directory for test files
• sample_data_dir: Sample data directory with test files
• mock_crystal_data: Mock crystal structure data
• sample_model_config: Model configuration for testing
• sample_training_config: Training configuration
• mock_torch_model: Simple PyTorch model for testing
• sample_checkpoint: Model checkpoint file
• capture_stdout: Stdout capture utility
• reset_random_seeds: Reproducible test runs
• disable_cuda: CPU-only testing
• mock_args: Command line argument mocking

5. Development Commands

Added Poetry script commands:

• poetry run test - Run all tests
• poetry run tests - Alternative command (both work)

6. Additional Setup

• ✅ Updated .gitignore with:
  • Testing artifacts (.pytest_cache/, htmlcov/, coverage.xml)
  • Claude settings (.claude/*)
  • IDE files and OS artifacts
• ✅ Created validation tests to verify the infrastructure works correctly

Instructions for Running Tests

1. Install dependencies:

   poetry install

2. Run all tests:

   poetry run test
   # or
   poetry run tests

3. Run specific test markers:

   poetry run pytest -m unit        # Run only unit tests
   poetry run pytest -m integration # Run only integration tests
   poetry run pytest -m "not slow"  # Skip slow tests

4. View coverage report:

   • HTML report: Open htmlcov/index.html in a browser
   • Terminal report: Automatically shown when running tests
   • XML report: Available at coverage.xml for CI integration

Notes

• Coverage Threshold: Currently set to 0% to allow infrastructure setup without actual unit tests. Should be increased to 80% when implementing real tests.
• Python Version: Configured for Python 3.8+ to match PyTorch requirements
• Dependencies: All existing dependencies from the project have been properly migrated to Poetry
• Poetry Lock: The poetry.lock file is intentionally NOT gitignored to ensure reproducible builds

Validation

The infrastructure has been validated with 9 passing tests that verify:

• ✅ Pytest installation and configuration
• ✅ Project structure integrity
• ✅ Module importability
• ✅ Fixture availability
• ✅ Coverage configuration
• ✅ Custom marker functionality

All validation tests pass successfully, confirming the testing infrastructure is ready for use.