Remove setuptools code (see mailing list)

The idea of using setuptools was to handle dependencies
automatically, particularly numpy. However, pip didn't
finish installing NumPy before Biopython. Using setuptools
had downsides too so we (Peter, Michiel and Brad) agreed
to remove it - see:

http://lists.open-bio.org/pipermail/biopython-dev/2013-July/010726.html
http://lists.open-bio.org/pipermail/biopython-dev/2013-July/010729.html
http://lists.open-bio.org/pipermail/biopython-dev/2013-July/010731.html
http://lists.open-bio.org/pipermail/biopython-dev/2013-July/010734.html
http://lists.open-bio.org/pipermail/biopython-dev/2013-July/010733.html