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

Peter Cock p.j.a.cock at googlemail.com
Fri Jul 21 13:23:10 UTC 2017

I'm in Prague for the pre-BOSC 2017 CodeFest, where quite a few
Biopython contributors are present, and finally wrote this pull request:



On Mon, Jun 26, 2017 at 9:47 AM, Peter Cock <p.j.a.cock at googlemail.com>

> 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>)
>>> _______________________________________________
>>> Biopython-dev mailing list
>>> Biopython-dev at mailman.open-bio.org
>>> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
>> --
>> *Andrew Guy*
>> PhD Student
>> *Burnet Institute*
>> T +613 9282 2346 <+613+9282+2346>
>> M +614 1987 2670 <+614+1987+2670>
>> E andrew.guy at burnet.edu.au
>> W burnet.edu.au <http://www.burnet.edu.au/>
>> The Macfarlane Burnet Institute for Medical Research and Public Health
>> Ltd,
>> 85 Commercial Road, Melbourne, VIC 3004, Australia
>> ABN 49 007 349 984
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