[Biopython] Problem building from PyPi: Affy package directory is missing

[Brad Chapman]

Walter;

> I generally install biopython either using easy_install or pip (if
> I need to enforce a particular version). Today was rebuilding the
> dependencies for a project I'm working on and when I went to build
> biopython I got the following error:
>
> error: package directory 'Bio/Affy' does not exist

Thanks for the heads up. There were a couple of compounding issues
that led to the easy_install problem. Normally, pypi pulls the
source files directly from the Biopython server. However, it looks
like a spammer added an index.html in biopython.org/DIST, which
forced pypi to use the uploaded .tar.gz as a last resort. This file
was missing the Bio/Affy directories and other information because
the main biopython distribution didn't have the MANIFEST.in.

Whew, so in summary:

- Things are fixed now on all ends. The pypi upload is new correct,
  you can access the biopython files again, and the MANIFEST.in was
  updated so we shouldn't see this again in the future.

- You are apparently the first lucky person to see the problem 
  since the biopython.org/DIST problem appears to be brand new.

Thanks again. Let us know if you have any other problems,
Brad