[Biopython-dev] Ideas for Biopython 2.0

[Peter Cock]

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