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

[Peter Cock]

On Mon, Jul 8, 2013 at 8:35 PM, Laurent Gautier <lgautier at gmail.com> wrote:
> On 07/08/2013 06:29 PM, Peter Cock wrote:
>>
>> On Mon, Jul 8, 2013, Laurent Gautier <lgautier at gmail.com> wrote:
>>>
>>> On 07/08/2013 05:00 PM, Peter Cock wrote:
>>>>
>>>> On Mon, Jul 8, 2013, Laurent Gautier <lgautier at gmail.com>
>>>> wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> I just tried installing biopython with pip (v-1.3.1) and Python 3.3
>>>>> (under a virtual environment created with pyvenv),
>>>>> but (after a a fairly long time) the process is failing with the last 3
>>>>> lines printed on the terminal:
>>>>>
>>>>> ```
>>>>>
>>>>> Python 2to3 processing done.
>>>>>
>>>>> running egg_info
>>>>>
>>>>> error: error in 'egg_base' option: 'pip-egg-info' does not exist or is
>>>>> not a directory
>>>>>
>>>>> ```
>>>>>
>>>>> Am I missing something ?
>>>>>
>>>>> Best,
>>>>>
>>>>>
>>>>> Laurent
>>>>
>>>> Hi Laurent,
>>>>
>>>> ...
>>>>
>>>> Which version of Biopython,
>>>
>>>
>>> Latest on Pypi.
>>
>> https://pypi.python.org/pypi/biopython
>>
>> That means Biopython 1.61 at the moment, so prior to Brad's
>> change landing on the trunk (which should be in 1.62 barring
>> any problems before then).
>>
>>> I am doing a vanilla:
>>>
>>> ```
>>> pip install biopython
>>> ```
>>>
>>>>    and if from git, which commit?
>>>
>>> Anyone on this list volunteering to run `git bisect` on my behalf ?
>>> (For now I more familiar with Mercurial, and plenty to do at the moment)
>>
>> Have you tried using the latest Biopython from source to see if Brad's
>> change fixed this for you? If that also fails the same way, there is no
>> point to a 'git bisect' ;)
>>
>
> ...
>
> For example, trying to install the master from github can be achieved the
> following single command:
>
> ```
> pip install https://github.com/biopython/biopython/archive/master.zip
> ```
>
> The outcome is the same error as before.

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?

Thanks,

Peter