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

[Eric Talevich]

On Tue, Oct 6, 2015 at 3:55 AM, Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> Out of interest, for those of you on the biopython-dev list, what
> is your current default or main Python version/implementation?
> I'm wondering what the split is amongst our main contributors.
>

I'm still restricted to Python 2.7 for production code because my group's
pipeline runs on a cloud platform (DNAnexus) that uses Ubuntu 12.04 LTS
Server machine images and provides an API for Python 2.7 specifically. But
I believe they're quietly working on support for Python 3 and a newer base
machine image. If I could use Python 3.5, I would. As it is, I just "from
__future__ import print_function, division, absolute_import" at the top of
every Python script or module.

Python 2.6 deprecation sounds good to me. My sense is that virtually all of
the Python 2.6 usage we see is the system Python installation on clusters,
and usually CentOS. Users in this situation seem to be able to get a newer
Python up and running without a problem, especially if we point them to
Anaconda.

Jython was in a coma for a few years after Oracle bought Sun, but
alternative funding/time arrangements have been made and the project is
actively being developed now, though Python 3 support is just on the
horizon. PyPy is obviously active. It's nice to know that Biopython in its
pure form will run on both alternative platforms.

I suppose we "recommend" Python 3 for the same reason Python.org does: It's
a better language and the older versions will eventually be deprecated.

-Eric
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