[Biopython] can't compile version from github

[Peter]

On Thu, Dec 3, 2009 at 12:17 PM, Michael Thon <mike.thon at gmail.com> wrote:
>
> Yup, I'm using the Apple-provided python.  Below is the full output of the build phase.

I'll take a look at it, but until I have a machine with Snow Leopard,
solving this will be tricky. Any other Snow Leopard users please
speak up.

> ...so, as usual, I am off on a tangent instead of working on the stuff that
> actually needs to get done.  I don't really need to get this installed.  I just
> wanted to try the SeqFeature.extract method that you mentioned in a
> previous thread.  I realized that I probably don't need to compile all the
> C extensions to get that to work so I opened up SeqFeature.py to see
> what this method looks like.  I couldn't find it so I suppose this method
> has not made its way into the main git repo on github.  In the end, I
> wrote one myself but it would still be good to compare its output to
> what you have in biopython.

I'm not sure why you couldn't find this in the latest code from git.
The method is in Bio/SeqFeature.py, search for "def extract":
http://github.com/biopython/biopython/blob/master/Bio/SeqFeature.py

You can probably take a working Biopython 1.52 install, and manually
update just the Bio/SeqFeature.py file if you really need to.

You could also try installing just the "pure Python" part of Biopython
by hacking setup.py to set EXTENSIONS = [], as done for Jython.

> ...but I still have this biopython from github that won't compile and it
> probably should.  So, if you have any ideas what might be wrong and
> how to fix it I can try it and report back.

I'll try to get back to you on this shortly.

Peter