feat: run pdb2pqr in python (no CLI)

[kiyoon]

Closes #405

Usage:

from pdb2pqr import run_pdb2pqr

run_pdb2pqr(["-h"])

Changes:

• There already is run_pdb2pqr in tests/common.py function for tests. To make the naming consistent and not confusing, I changed it to run_pdb2pqr_for_tests just like another function in the module called run_propka_for_tests.
• main_driver() doesn't include io.setup_logger() call anymore. It's moved to main() instead for maximum flexibility.

[kiyoon]

1. I don't know why some tests failed? -> Fixed.
2. Once you approve this, I will apply ruff formatting following ci: ruff format, isort, and lint #409 , so don't merge just yet please. -> DONE

[kiyoon]

In this case, from __future__ import annotations is used because of def run_pdb2pqr(args: Sequence[str | PathLike]):

[sobolevnrm]

Thanks for the PR!