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Devops: Address various deprecation warnings from `aiida-core` #2291

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Run time

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Job	Run time
tests (3.8)	3m 33s
pre-commit	2m 26s
tests (3.9)	3m 35s
integration (3.10)	2m 12s
tests (3.10)	3m 13s
tests (3.11)	3m 9s
	18m 8s