SCHWED-4612: Get rid of some Numpy warnings, move from np.matrix to np.array, keeping the matrix variant as deprecated method.

The reason is that the check just scratches floating point accuracy and
occasionally failed on some machines

SCHWED-4612: Ignore warning about unused functions by GCC, while the functions are used by unit tests.

This reverts commit ef7bfdb6.

Didn't work with Sphinx 1.6.7 which needs an extra option at the start.
This needs to be fixed cleanly, or we need to upgrade the Sphinx version
requirements

This likely requires an up-to-date sphinx (tested with current version, 2.3.0)