BUG: Fix errors from deprecated API use with NumPy 2.0 API #328

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Run time

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Job	Run time
linux-x86-no-mpi (3.10)	44m 33s
linux-x86-no-mpi (3.11)	44m 43s
linux-x86-with-mpi (3.8)	16m 57s
linux-x86-no-mpi (3.9)	13m 31s
	1h 59m 44s