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It turns out I misunderstood what pybind11's py::array::ensure does.
Looking at the code superficially (https://github.com/pybind/pybind11/blob/master/include/pybind11/numpy.h#L785)
I assumed this function steals a reference, hence the call to
release(). But the reference is being stolen from the return value
of raw_array(), which returns a new reference. Hence ensure() itself
does not steal anything but in fact increases the refcount (and will
decref it in ~array).
Thanks to @yobibyte for both finding this issue and insisting that
it happens on the Python side (I thought this might be related to
malloc calls in NetHack itself).