[Biopython-dev] biopython, pip, and Python 3.3 + virtualenv

[Peter Cock]

On Tue, Jul 9, 2013 at 10:41 AM, Brad Chapman <chapmanb at 50mail.com> wrote:
>
> Laurent and Peter;
>
>> OK, so you get the same error from a 'pip install' from both the
>> Biopython 1.61 release, and the latest code from github as of
>> 8 July 2013, which would have included Brad's pip-related
>> commit which evidently made no difference to this issue:
>>
>> https://github.com/biopython/biopython/commit/bc828342716218b84908c1a4435163e564f31445
>>
>> Thanks for checking that. Having confirmed the latest code is
>> still affected, I'm out of ideas - how about you Brad, any thoughts?
>
> Laurent, can you try this branch and see if it installs cleanly for you
> using pip on Python 3.3:
>
> https://github.com/chapmanb/biopython
>
> I pulled the fix from numpy's older setup.py (before they moved to a
> combined 2.7 and 3.3 code base) and it worked on my tests, but would
> like to confirm before merging:
>
> https://github.com/biopython/biopython/pull/172/files
>
> Thanks for reporting the issue,
> Brad

Ah - those changes are now live on the master guys:

https://github.com/biopython/biopython/commit/1d3d2fe43ae776d30777ffdab7b6528cd3164cfd
https://github.com/biopython/biopython/commit/0f821c5b69ab5f6b888d36fb29b1ba3b51ce8590

It was perhaps a little premature but since Brad pushed it up to
the pull request I thought it was good to go. We can revert it
need be.

Laurent, you can just re-test the master rather than Brad's branch.

Thanks,

Peter