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[python] Fix some warnings at `anndata==0.11` #5431

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Job	Run time
build (macos-latest, 3.9) / build	7m 57s
build (macos-latest, 3.9) / lint	0s
build (macos-latest, 3.12) / lint	43s
build (macos-latest, 3.12) / build	8m 8s
build (ubuntu-latest, 3.12) / build	11m 39s
build (ubuntu-latest, 3.12) / lint	40s
build (ubuntu-latest, 3.9) / build	10m 45s
build (ubuntu-latest, 3.9) / lint	0s
	39m 52s