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Update ruff to 0.16.1 and adopt its new default ruleset #3745

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Run time

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Job	Run time
test-notebooks (Firefox, edge)	4m 17s
test-notebooks (Chrome, edge)	3m 10s
test-package (3.12, lowest-direct)	3m 29s
test-package (3.9, highest)	2m 36s
test-package (3.12, highest)	2m 47s
	16m 19s