lint: update pre-commit and run on all files

[maximlt]

• pre-commit config file updated
• flake8 args moved from the pre-commit config file to setup.cfg
• isort config fixed to be compatible with black (new param required for isort >= 5)
• pre-commit ran over all the files (add a missing module docstring and reformatted a long string)
• flake8 tox env replaced by a linters env that runs pre-commit

[maximlt]

#159 requires this PR to be merged to add the pre-commit action.

All the tests ran file locally with this new pre-commit config.