Use native config files for coverage, flake8, and yapf

[eirrgang]

The cookiecutter template puts the configuration for coverage, flake8, and yapf in setup.cfg.

However, setup.cfg is traditionally the setuptools config file. setuptools traditionally provided setuptools.config.read_configuration(), but the project is abandoning setup.cfg, and the tool is deprecated.

I haven't checked whether these specific tools have their own parsing or not. But, to avoid confusion or deprecation warnings (or ultimately errors), we should probably move the configuration for these tools to their own native config files.

• coverage: https://coverage.readthedocs.io/en/6.4.4/config.html#configuration-reference; Note also https://pytest-cov.readthedocs.io/en/latest/config.html#caveats
• flake8: https://flake8.pycqa.org/en/latest/user/configuration.html#configuration-locations
• yapf supports several alternatives: https://github.com/google/yapf#formatting-style (I thought MolSSI advocated Black. Is yapf in use?)
• https://docs.codecov.com/docs/codecov-yaml

[janash]

Hi @eirrgang - yes, I think these are good ideas. You're also correct that we use black these days, so that should also be updated.