fix numpy.i for python 3

PyFile_Check and PyInstance_Check have been removed from the C API
for python 3.  This removes calls to those two functions from
numpy.i for PY_MAJOR_VERSION >= 3 so that it builds with a
python 3 Python.h.
Merge pull request #2923 from baeuml/swig-fix-python3

fix numpy.i for python 3