Branch commit.
Passes all* unit tests on badger.
Note I have only changed those parts of the system necessary to get the
unit tests to pass. There are still references to numarray in some
files.
* I have disabled the testBoolLists test in run_xml.py.
The issue there is that numarray converts a list of bools into ints.
The test tries to convert items into floats.
numpy leaves a list of bools as bools (which float()) doesn't like.
Somebody needs to decide what the correct behviour is so the code can
be corrected.
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