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Ran into this via an esoteric route: When tinkering with user-defined dtypes, it seems that implementation of np.ones uses np.copyto(dst, 1, casting='unsafe'), where the 1 gets interpreted as np.array(1, dtype=np.int64) (at least, on my platform).
When I tried registered a caster using npy_descriptor_format<int64_t>::dtype() using the type_num field, I realized its value was for NPY_LONGLONG, whereas NPY_INT64 corresponds to NPY_LONG.
Will try to see if I can create a failing test, and then submit a tentative fix PR based on that.