Replace flake8 with ruff

[jsstevenson]

Side note: this repo is getting pretty big -- that would make it a good candidate for Ruff imo. Not sure how flake8/etc checks feel in others' editors but flake8 alone is taking me almost 5 seconds to cover variation/ and tests/ whereas Ruff is almost instant.

[jsstevenson]

...and, as I keep reading, it looks like this should be addressed in #474

[korikuzma]

I added it in #474 but it wasn’t getting everything. I was wondering why sometimes flake8 (both GH actions and local) wouldn’t catch missing docstrings. Flake8 passed locally on my machine, so I’ll switch to ruff in #474.

[korikuzma]

The annotation warnings we ignore in flake8. It looks like we do this in therapy but not disease/gene

[korikuzma]

@jsstevenson this is what i have in my ruff.toml. Let me know if I should modify

select = ["E", "W", "F", "ANN", "Q", "D"]

line-length = 88

ignore = ["D205", "D400", "D415", "ANN101"]

[flake8-quotes]
inline-quotes = "double"

[per-file-ignores]
"tests/*" = ["ANN001", "ANN2", "ANN102"]
"setup.py" = ["F821"]
"*__init__.py" = ["F401"]

[jsstevenson]

👍 my vote would also be to ignore ANN003 (https://beta.ruff.rs/docs/rules/missing-type-kwargs/)

[github-actions]

Closed by #494.