ci: update workflows (add autoflake and isort)

[cpacker]

Please describe the purpose of this pull request.

Follow-up to #1279

Developers should now use pre-commit to correctly stage the linters (autoflake -> isort -> black):

# install the `dev` package that has precommit/autoflake/isort/black
poetry install --all-extras

# set up pre-commit to run on all git commits
poetry run pre-commit install

To manually trigger pre-commit:

# wipe cache
poetry run pre-commit clean

# run pre-commit hooks across all files
poetry run pre-commit run --all-files

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How to test

See passing workflows.

[sarahwooders]

lgtm!