Invalid pylint options

[lilyminium]

There's a lot of pylint warnings in CI.

In general pylint is a bit of a headache. Not sure how other alternatives stack up -- flake8 or black?

[RMeli]

Black doesn’t do linting, but I also find out that pylint is a bit too annoying with respect to flake8. I use black for automated formatting and flak8 for linting (with settings to work well with black).

[lilyminium]

That seems like a good workflow @RMeli, I wonder if having some kind of opt-in/out for the black/flake8 options would be the best solution here. Since the core library is moving in this direction especially, IMO the cookiecutter should keep pace.

I'll fix pylint in the interim but unless anyone disagrees I'll follow whatever MDA core does.

[IAlibay]

One of the biggest issues with the MolSSI cookiecutter is that is just tries to do too many things.

My suggestion is to keep it simple - in many ways not providing anything is better than trying to provide everything.
Right now flake8 and isort are available via precommit but there's no real docummentation for it (at least nothing I can see in the rtd builds). Similar thing for pylint.

Switching to flake8/black is reasonable, as long as we are ok keeping up to date & having it well documented, otherwise we fall in the same cookiecutter issue of having things that new users are going to not be too sure what to do with it.