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[python] Include `tiledbsoma_upgrade_shape` for `DenseNDArray` #5391

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Job	Run time
build (macos-latest, 3.12) / build	11m 36s
build (macos-latest, 3.12) / lint	46s
build (macos-latest, 3.9) / build	11m 18s
build (macos-latest, 3.9) / lint	0s
build (ubuntu-latest, 3.12) / build	16m 12s
build (ubuntu-latest, 3.12) / lint	29s
build (ubuntu-latest, 3.9) / build	14m 48s
build (ubuntu-latest, 3.9) / lint	0s
	55m 9s