test_Phylo: use io.BytesIO unconditionally (Python2.6 has it)

We used BytesIO here because Py3 needs a byte stream handle to parse XML.
Use sys.stderr.write instead of print >> sys.stderr
Convert commented out print statements into print functions

This isn't really important, but it cuts down on the
false-positives when searching with grep.
Use print function style in MaxEntropy
Python 2.6+ supports sys.maxsize, Python 3 lacks sys.maxint