[Biopython] Versions of Python 3 to support in Biopython?

[Nick Lindberg]

Hello,

The current production versions are Python 2.7.5 and Python 3.3.2.  Per
Ivan's comments, I do not think you should drop support for 2.x when
adding for 3.x.  However, I think it's completely fair that you should
require the latest current production version of each (or at least put the
caveat in that it's only been tested on 2.7.* and 3.3.*.

If you need any help with the testing or compatibility, I'd be glad to
help.

Also, for any Mac users out there, I am working on a Homebrew formula for
a package-install of Biopython.  More details incoming.

Thanks,

Nick Lindberg
Sr. Consulting Engineer, HPC
Milwaukee Institute
414.727.6413 (W)
http://www.mkei.org











On 5/30/13 8:23 AM, "Ivan Gregoretti" <ivangreg at gmail.com> wrote:

>Hi Bow,
>
>I think that we should drop support for Python 2.x once it is left out
>in favour of Python 3.
>
>I am not aware of any major linux distrubution that uses Python 3 as
>default. By major linux distribution I mean Debian, Ubuntu, CentOS,
>Fedora and Red Hat Enterprise Linux.
>
>Out of all the five distributions listed above, most administrators
>use CentOS. Perhaps we should schedule Python v2.x support to be
>dropped when CentOS switches to Python 3. That is likely to happen a
>long time from now.
>
>Thank you,
>
>Ivan
>
>
>
>
>Ivan Gregoretti, PhD
>Bioinformatics
>
>
>On Thu, May 30, 2013 at 8:51 AM, Wibowo Arindrarto
><w.arindrarto at gmail.com> wrote:
>> Hi everyone,
>>
>>> For the forthcoming Biopython 1.62 release, we are planning to
>>> officially support Python 3 (as well as Python 2, including PyPy,
>>> and Jython). However, which versions of Python 3 would people
>>> want to use?
>>>
>>> One possibility is we'd require at least Python 3.2.5 (which would
>>> simplify dealing with things broken in older releases of Python 3).
>>>
>>> Alternatively, would it be acceptable to insist on at least Python 3.3
>>> for example?
>>>
>>> If you are interested in running Biopython under Python 3
>>> (which you can already try out), please could you reply with
>>> what version of Python 3 you have installed, and if being
>>> required to update would be a problem or not.
>>
>> I'm leaning towards insisting on Python >=3.3 support (I'm running
>> 3.3.2). I suppose that even if Python3.3 is not available on a machine
>> or through the default package manager, it's always installable on its
>> own. If that's not the case, I imagine Python2.x is most likely
>> present in these machines (so Biopython can still be used).
>>
>> On a related note, do we have a defined timeline on when we would drop
>> support for Python2.x? Are there any plans to have our codebase
>> written in Python3.x instead of Python2.x?
>>
>> Best,
>> Bow
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