Fix ruff documentation violations in existing BioNeMo v2 code

[pstjohn]

We should go back and fix ignored noqa: D*** violations in our code base to make our docstrings more consistent, and parseable by eventual documentation machinery.

Missing docstrings for functions / classes:

• D101 public class docstring
• D102 public method docstring
• D103 public function docstring
• D107 missing init docstring
• D105 Missing docstring for magic method (i.e., __len__ or __getitem__). I could be convinced to ignore this 🤷

Mis-formatted docstrings:

• D205 Needs a single-line summary, then blank line.
• D415 first line needs to end in punctionation.
• D417 Parameter missing from docstring