[Biopython-dev] Updating Biopython requirements wording to recommend Python 3

[Peter Cock]

Hi Iddo,

We're supporting Python 2.6, 2.7 and 3.3+ with a single codebase
(with Bio._py3k holding a few hacks like the external module six
offers). This works fine for now, but we do often have to tweak new
code contributions to make them work on legacy Python 2.

The "major" dependencies like NumPy and ReportLab are also
available on Python 2 and 3. I'm actually not sure right now what
is missing in Python 3 (apart from mysqldb where there are forks
and alternatives here we might adopt).

I'm not suggesting we drop Python 2 support yet - just rephrase
the README to encourage Python 3 usage as the default.

Peter

On Thu, Oct 1, 2015 at 5:08 PM, Iddo Friedberg <idoerg at gmail.com> wrote:
> So, I admit I've been a bit out of touch. but:
>
> 1. Is biopython P2 no longer being developed?
> 2. Does biopython P3 have the needed optional dependencies now?
>
>
> I understand there is still a debate in the Python community as to the use
> of P3 fork, over maintenance and continuing use of P2. One argument is that
> 3rd party library support which is stronger on the P2 fork especially in a
> field like ours, which has a lot of "boutique" software.
>
> On Thu, Oct 1, 2015 at 8:42 AM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
>>
>> Hello all,
>>
>> Currently our README file says:
>>
>> We currently recommend using Python 2.7 from http://www.python.org which
>> is the final version of Python 2.  Early adopters are encouraged to try
>> Biopython under Python 3.3, 3.4, or 3.5 but not all the optional
>> dependencies are available yet.
>>
>> Would anyone object to a more forward looking phrasing, e.g.
>>
>> We currently recommend using Python 3.5 from http://www.python.org and
>> avoiding legacy Python 2.6 or 2.7 unless your choice is restricted due to
>> having to work with old code.
>>
>> Peter
>> _______________________________________________
>> Biopython-dev mailing list
>> Biopython-dev at mailman.open-bio.org
>> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
>
>
>
>
> --
> Iddo Friedberg
> http://iddo-friedberg.net/contact.html
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