Refactor: Unify tool configurations under pyproject.toml

[zwimer]

Most python tools provide support for putting their configurations in pyproject.toml. For example:

https://github.com/pytest-dev/pytest/blob/main/pyproject.toml

Just search for [tool. Tools that support pyproject.toml include black, flake8, bandit, pytest, among others. I might be able to make a PR for this later, though I will do so after addressing #694 as it will hit merge conflicts.