[Biopython-dev] Ideas for Biopython 2.0

Tiago Antão tiagoantao at gmail.com
Wed Jun 21 15:09:42 UTC 2017

If people are stuck on Python 2, they do have a simple solution: use
Biopython 1. That would probably be maintained at least until 2020.

If Biopython 2 goes ahead (a big if) then I doubt it would be launched very
soon: in the big scheme of things we are fast approaching 2020, and I doubt
a first release of Biopython 2 would occur before 2018.

With regards to the Python 3 version I would suggest supporting only the
most recent when we start Biopython 3. In any case nothing before 3.5.

In my mind the most important discussion is the module system. All the rest
seems easy (lots of work still) in comparison.

On Jun 21, 2017 5:21 AM, "Peter Cock" <p.j.a.cock at googlemail.com> wrote:

> On Tue, Jun 20, 2017 at 10:38 PM, João Rodrigues
> <j.p.g.l.m.rodrigues at gmail.com> wrote:
> > Iddo: +1
> >
> > However, we can make it explicit that a version 2.0 is not guaranteed to
> be
> > backwards compatible.
> Yes - this should be very clear up front to avoid user confusion and pain.
> At a minimum it will mean a lot of changes to imports, but beyond that
> I would expect to see other changes (eg the alphabet objects are a prime
> target for removing/replacing).
> > But again, we are all volunteers and a complete
> > rewrite is a really big effort. I'd prefer to have a wish list kind of
> thing
> > from our users/developers and then pick a few targets that are important
> to
> > the community as things we should work on.
> That might be wise, although in practice we had little enough discretionary
> time to spend on code we're not using directly in our day jobs / research
> projects.
> > Also, dropping Py2 support isn't a good idea in my opinion. This is
> science,
> > there is a lot of code still running FORTRAN77. Python 2 is going to
> stick
> > around for years to come, specially in HPC settings.
> Do you object to the plan to sign up to the 2020 pledge, dropping Python
> 2.7
> support no later than 2020? http://www.python3statement.org/
> http://mailman.open-bio.org/pipermail/biopython-dev/2017-June/021739.html
> I agree that Python 2 is likely to stick around for some time, but dropping
> Python 2 support as part of a big backward incompatible break seems
> very sensible to me. We might even go further an target a particular
> Python 3.x version onwards if there were a compelling new language
> feature?
> > As for the rest, modularity is nice.
> >
> Nice yes, but as we've seen with BioPerl interdependencies are quite
> painful to pick apart. On the bright side, BioRuby have done well with
> their modularity, and I don't see this as impossible for Biopython.
> > (sending again because of some mail error.. sorry if you get it twice..)
> Thanks,
> Peter
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