[Biopython] problem building with pip

[Brad Chapman]

David and Peter;

> On Fri, Dec 17, 2010 at 9:06 PM, David Koppstein
> <david.koppstein at gmail.com> wrote:
> > Hio,
> >
> > First time biopythoner here. I just wanted to mention that installing with
> > pip fails with the following error. ...
> > error: option --single-version-externally-managed not recognized

David, thanks for the report. That flag is added in the
'setuptools' and 'distribute' code bases, but not in 'distutils,'
which Biopython uses. The world of python packaging and best practices
is a bit murky to me, but distutils is included with Python itself, 
so it seems no harm in continuing to use this in Biopython.

Looking at the distribute source code, this flag forces installation 
the distutils way which is what we do by default:

https://bitbucket.org/tarek/distribute/src/4ab9b96dc540/setuptools/command/install.py

So I added in the fix to Biopython's setup.py which handles the flag 
without failing and doesn't need to do any additional work:

https://github.com/biopython/biopython/commit/4e4c3aa1df3d6848afed4783c4e54186a751accd

Peter, I didn't re-roll 1.56 tarballs with the fix but we could do
if lots of people are running into a wall with pip.

Thanks again for reporting the issue,
Brad