Change: move black options to pyproject.toml

[ahyangyi]

black supports storing configuration in pyproject.toml. This pull request moves the existing command-line options to the file.

I think this change has a few advantages:

• The current command-line options are duplicated in two places (Makefile and Github Actions), the pyproject.toml is a unified place.
• By putting the configuration in pyproject.toml, running black . anywhere within the repository would produce correct results. This guards against a lot of surprises.
  • Caveat: running black <a file name that's excluded> still formats what should not be formatted. This is a special case that's no worse than before though.

I also included setup.py in the excludes just in case people run black . instead of black nml in the repository root.