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

Laurent Gautier lgautier at gmail.com
Mon Jul 8 16:18:30 UTC 2013

On 07/08/2013 05:00 PM, Peter Cock wrote:
> On Mon, Jul 8, 2013 at 3:38 PM, 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,
> The 2to3 conversion does take a while (sigh), but I have a plan for that:
> http://lists.open-bio.org/pipermail/biopython-dev/2013-May/010633.html

For it is worth, I have started doing the following 2 rules for all 
Python projects (and it is working fairly well):

1- Develop for Python 3.3 (not worrying about anything earlier in the 
3.x series)
2- When considering support for Python 2, consider 2.7. Forget about 
anything earlier
The rationale is: if you want the latest version of a package, get a 
recent Python as well. A variant of "you can't have your cake and eat 
it", I suppose. It might seem a bit radical, but that's not that bad; it 
has worked for bioconductor  (where each BioC release depends on the 
latest R version).

If no C-extension is involved, rule #2 is only introducing few 
conditional definitions that are hand-coded. There are only few things 
to consider.

> Which version of Biopython,

Latest on Pypi.

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)

> In particular was it before or after this change from Brad which
> I recently committed?
> https://github.com/biopython/biopython/commit/bc828342716218b84908c1a4435163e564f31445

The distutils/distutils2/distribute/setuptools/whatever can be an 
endless source of headaches. Do you check with one of them in particular ?
If so, may be worthwhile to enforce the use of that one in setup.py.



> Thanks,
> Peter

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