Make pre-commit functional

[ekatef]

The current pre-commit hook is not quite functional. In particular, it gives the following error even for the update of the pre-commit itself #56:

snakefmt.exceptions.InvalidPython: Black error:

Cannot parse for target version Python 3.12: 2:0: EOF in multi-line statement

(Note reported line number may be incorrect, as snakefmt could not determine the true line number)

The high-level reason may be the fact that pre-commit currently contains plenty of the additional tools as compared with the upstream which can lead to some weird interactions. Would be good to revise it.