You grossly overvalue using the "in" operator on lists.  It's far more
common to use a dict or set for containment tests, due to O(1)
performance rather than O(n).  I doubt the numpy array supports
hashing, so an error for misuse is all you should expect.

In the rare case that you want to test for identity in a list, you can
easily write your own function to do it upfront:

def idcontains(seq, obj):
    for i in seq:
        if i is obj:
            return True
    return False
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