feat: Set up comprehensive Python testing infrastructure

[llbbl]

Set up Python Testing Infrastructure

Summary

This PR establishes a comprehensive testing infrastructure for the SV-callers project using Poetry as the package manager and pytest as the testing framework. The setup provides a solid foundation for developers to immediately start writing and running tests.

Changes Made

Package Management

• Added Poetry configuration (pyproject.toml) with proper project metadata
• Migrated dependencies from test-requirements.txt and environment.yaml
• Set up development dependencies including pytest, pytest-cov, pytest-mock, and codacy-coverage

Testing Configuration

• Configured pytest with comprehensive settings in pyproject.toml:
  • Test discovery patterns for files, classes, and functions
  • Coverage reporting with 50% threshold (HTML, XML, terminal)
  • Custom markers: unit, integration, slow
  • Strict configuration for markers and config validation

Directory Structure

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

Shared Testing Utilities

• Comprehensive fixtures in conftest.py:
  • temp_dir: Temporary directory management
  • sample_config: Mock configuration objects
  • File fixtures: sample_fasta_file, sample_bed_file, etc.
  • mock_config_object: Structured mock for workflow configuration

Infrastructure Validation

• Validation tests verify the entire setup:
  • pytest functionality and markers
  • Project structure validation
  • Package imports and coverage integration
  • Python version compatibility

Development Environment

• Updated .gitignore with testing artifacts, IDE files, and Claude Code settings
• Coverage configuration excluding test files, build artifacts, and virtual environments

Testing Instructions

Running Tests

# Activate virtual environment and run tests
source .venv/bin/activate
python -m pytest tests/ --no-cov  # Without coverage
python -m pytest tests/ -v        # With coverage and verbose output

# Run specific test types
python -m pytest -m unit tests/           # Unit tests only
python -m pytest -m integration tests/    # Integration tests only
python -m pytest -m slow tests/          # Slow tests only

Coverage Reports

• Terminal output: Shows coverage summary with missing lines
• HTML report: Generated in htmlcov/ directory
• XML report: Generated as coverage.xml for CI integration

Dependencies Added

Production Dependencies

• snakemake==6.15.3
• tabulate==0.8.10
• yatiml==0.7

Development Dependencies

• pytest>=4.6 - Main testing framework
• pytest-cov - Coverage reporting
• pytest-mock - Mocking utilities
• codacy-coverage - Code quality reporting

Configuration Notes

• Coverage threshold: Set to 50% to allow gradual improvement
• Python version: Requires Python 3.8+ (defined in pyproject.toml)
• Virtual environment: Poetry creates .venv/ in project root
• Poetry lock file: Generated automatically, should be committed

Next Steps

With this infrastructure in place, developers can:

1. Start writing unit tests for workflow/helper_functions.py
2. Add integration tests for the complete workflow
3. Gradually increase coverage threshold as tests are added
4. Use the provided fixtures to mock file system operations and configurations

🤖 Generated with Claude Code