Devops: Address various deprecation warnings from `aiida-core` #2264

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Run time

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Job	Run time
tests (3.8)	4m 45s
tests (3.9)	4m 12s
pre-commit	2m 31s
integration (3.10)	2m 57s
tests (3.10)	5m 48s
tests (3.11)	3m 32s
	23m 45s