This has been fixed upstream. The fix is here:
https://github.com/numpy/numpy/pull/8713
https://github.com/numpy/numpy/commit/2fe5a4757e840362b7158e8548e26ffc9ef8b562
Only the one-line addition to loops.c.src is required; the rest is a test.
Could we have this fixed in Stretch?
Package: python-numpy
Version: 1:1.12.1-2
On amd64:
$ python
Python 2.7.13 (default, Jan 19 2017, 14:48:08)
[GCC 6.3.0 20170118] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>> abs(numpy.nan)
nan
>>> numpy.abs(numpy.nan)
nan
>>>
On arm64:
$
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