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Devops: Address various deprecation warnings from `aiida-core` #2363

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Run time

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Job	Run time
integration (3.10)	2m 28s
pre-commit	2m 11s
tests (3.8)	3m 8s
tests (3.9)	3m 28s
tests (3.10)	3m 18s
tests (3.11)	2m 52s
	17m 25s