[#161] refactoring multiple small files

[angeloprobst]

Progress on ticket #161

Refactors multiple files:

hyperon_das_atomdb/__init__.py
hyperon_das_atomdb/adapters/ram_only.py
hyperon_das_atomdb/adapters/__init__.py
hyperon_das_atomdb/exceptions.py
hyperon_das_atomdb/index.py
hyperon_das_atomdb/logger.py
hyperon_das_atomdb/utils/expression_hasher.py
hyperon_das_atomdb/utils/patterns.py
hyperon_das_atomdb/utils/settings.py

1. Applies black formatting.
2. Ensures lines width at max 100 chars.
3. Adds and fixes type annotations, mainly returns.
4. Applies new standard of type annotations (i.e. dict[A, B] | None instead of Optional[Dict[A, B]].
5. Adds and/or fixes docstrings.
6. Ensures the files pass green through pylint.
7. Fixes some typos.
8. Left some TODO comments for future evaluation.