[Biopython-dev] Planning to drop Python 2 support by 2020?

[Peter Cock]

Thanks Andrew,

I think we are agreed about dropping Python 2.7 support by 2020, although
please do comment on the Biopython 2 thread as well.

I will prepare a pull request adding the 2020 language to the README.rst
and NEWS.rst files, and once that's merged we can ask to be added to
http://www.python3statement.org/

Peter

On Mon, Jun 26, 2017 at 5:46 AM, Andrew Guy <andrew.guy at burnet.edu.au>
wrote:

> Hi all,
>
> Just wanted to add my thoughts as someone who is a relatively new user of
> Biopython (last ~3 years) and Python in general.
>
> I thankfully started with Python 3.x when I was first learning, and have
> never needed to use Python 2.7 (that I can recall) other than to check
> backwards compatibility for code I've written - the bulk of the big Python
> scientific modules (e.g. Numpy, Scipy, scikit-learn) are all Python 3
> compatible. To add to this, using a virtual environment (e.g. pip
> virtualenv) to manage dependencies is something that everyone should be
> doing, and I don't think it's asking too much to require this if anyone
> wants to use an older compute cluster and a new version of Biopython.
>
> To add to sentiments that have been expressed a few times already, I also
> think it would be wonderful to be able to use some of the newer Python
> features in the code base going forward, especially if there is talk of
> moving to a new Biopython 2.x version.
>
> I'll add my vote to* a)* moving to Python 3.x for Biopython 2.x and* b)*
> keep a Biopython 1.x version that supports *critical* bug fixes but is
> otherwise considered to be unsupported. I think the move to Biopython 2.x
> would mark an excellent point from which to drop Python 2.x. Old
> scripts/programs will still use the final 1.x release, whereas code that
> uses the new API will be written with Python 3.x in mind.
>
> Regards,
>
> Andrew
>
> On 26 June 2017 at 11:51, João Rodrigues <j.p.g.l.m.rodrigues at gmail.com>
> wrote:
>
>> As we say in Portuguese, 'this discussion grew a beard'. Tiago, you are
>> absolutely right.
>> ​
>> I'll say it again. My opinion is that we should move to Python 3.x for
>> Biopython 2.x *but* keep a version of Biopython 1.x that we support for
>> critical bug fixes for those users stuck with Python 2.x (for whatever
>> reason).
>>
>> I think we should focus on other topics such as modularity. What do the
>> proponents of the said modularity say about it? What are its advantages? I
>> personally think a big disadvantage is that with one package install you
>> get a wide array of tools for a variety of subjects. With a constellation
>> of modules you might end up with an up-to-date core and an out-of-date lone
>> module somewhere, which makes things much much harder not only to maintain
>> but also to debug in case of issues.
>>
>> (I have the impression I'm of the youngest here and already this guy
>> <https://en.wikipedia.org/wiki/The_Old_Man_of_Restelo>)
>>
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>>
>
>
>
> --
> *Andrew Guy*
> PhD Student
> *Burnet Institute*
> T +613 9282 2346 <+613+9282+2346>
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> E andrew.guy at burnet.edu.au
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