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

[Laurent Gautier]

On 07/09/2013 11:43 AM, Peter Cock wrote:
> 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.

The install process is now working with the master on Github.

Thanks,


Laurent

>
> Thanks,
>
> Peter