[Biopython-dev] Ideas for Biopython 2.0

João Rodrigues j.p.g.l.m.rodrigues at gmail.com
Wed Jun 21 17:44:41 UTC 2017

Hi Peter,

Regarding the pledge, the more I think about it the more conflicted I feel.
On one hand, this will push adoption of Py3.x for the end-user and allow us
to take advantage of new language features. On the other hand, I still work
on clusters with system Py2.6 and with code that chokes with anything over

For Biopython 2, I think it might be reasonable to say look, we support
only 3.x, and maintain versions 1.x supporting Py2.x but dropping support
altogether might be a bad move.

Also, in general, for any new version, I think it would be interesting to
see what is out there in the python ecosystem that 'competes' or depends on
biopython. When this first started there wasn't much around, now there are
a few packages. We should define our own philosophy and identity and not
just rewrite to end up overlapping with other packages. I looking
specifically at Bio.PDB, for which we have mdtraj, biskit, prody, etc. We
have a distinct feature (the hierarchical model) that in my opinion makes
biopython unique and powerful. We should keep features like these and just
add, e.g format converters, to have better interoperability with other
packages. This is also easier than a full rewrite.

+5 for a wiki page, thanks Tiago.

A qua, 21/06/2017, 09:52, Peter Cock <p.j.a.cock at googlemail.com> escreveu:

> On Wed, Jun 21, 2017 at 5:41 PM, Tiago Antão <tiagoantao at gmail.com> wrote:
> >
> > If no one opposes, I would like to open a page on the wiki about this.
> Just
> > as a place to put ideas, so that they will not be forgotten.
> >
> That's a really good idea, please go ahead and link to it
> from http://biopython.org//wiki/Active_projects
> Peter
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