Improve package structure and code quality

[eleanorfrajka]

Modernize the Python package structure to follow current best practices for scientific software.

Tasks:

• Add init.py with version and main imports
• Include example metadata directory structure
• Add type hints throughout the codebase
• Update pytest configuration in pyproject.toml
• Add coverage reporting setup

References:

• https://learn.scientific-python.org/development/
• See MODERNIZATION_PLAN.md#5-module-architecture

[eleanorfrajka]

Partially addressed with #29

• Added type hints
• Updated pytest configuration
• Gave explanation for coverage reporting