Python CI

Bump `pre-commit` versions (#1344) #3293

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Run time

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Job	Run time
lint-and-test (3.9)	10m 56s
lint-and-test (3.10)	11m 2s
lint-and-test (3.11)	12m 0s
lint-and-test (3.12)	21m 39s
	55m 37s