Bug fix, improvement on security, path, documentation

[monodera]

This pull request includes bug fixes, improvements on security, path, and documentation.

• add ruff and black for dev dependency
• insecure options (lists) are changed to None and fillled with the default values in the functions
• import sorter are changed from isort to ruff in the init.py
• if statements in the foreign key references are clarified
• other minor fixes