[Biopython] Biopython 1.76 plans

[Peter Cock]

The release is in progress, Tutorial and API documentation live:

http://biopython.org/DIST/docs/tutorial/Tutorial.html
http://biopython.org/DIST/docs/tutorial/Tutorial.pdf
https://biopython.org/docs/1.76/api/

I recall no objections to the idea, so I am not intending to
update the epydoc API docs,

https://biopython.org/DIST/docs/api/

A small post-release project will be to replace those pages
with redirection stubs to the Sphinx generated output.

Peter

On Wed, Dec 18, 2019 at 8:06 PM Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
> A brief discussion with Chris about next steps in 2020 once this release is done.
>
> Peter
>
> ---------- Forwarded message ---------
> From: Chris Rands <c_rands100 at hotmail.com>
> Date: Wed, 18 Dec 2019 at 18:03
> Subject: Re: [Biopython] Biopython 1.76 plans
> To: Peter Cock <p.j.a.cock at googlemail.com>
>
>
> Thanks Peter, I like your plan, and please do fwd to the mailing list if you think it's of broad interest
>
> Chris
>
> ________________________________
> From: Peter Cock <p.j.a.cock at googlemail.com>
> Sent: 18 December 2019 6:09 PM
> To: Chris Rands <c_rands100 at hotmail.com>
> Subject: Re: [Biopython] Biopython 1.76 plans
>
> Shall we stay on the list? My plan:
>
> (1) Release Biopython 1.76 with Python 2.7 and 3.5 support
> (2) Turn off testing under Python 2.7 and 3.5
>
> Then tackle the low handing fruit (in no particular order):
>
> (3) Remove Bio._py3k compatibility shim
> (4) Look for and remove other Python 2 specific workarounds
> (5) Remove no longer needed __future__ imports etc
> (6) Remove all the Python 2/3 overhead in the C code
>
> Also, where sensible and after appropriate discussion, take
> advantage of new language or standard library features in
> Python 3.6+ as appropriate (e.g. sorted dictionaries by default
> without needing to import OrderedDict from collections).
>
> I hadn't thought much about f-strings (beyond that I'm not
> used to them and that makes me dislike them), but that could
> be a good example.
>
> Peter
>
> On Wed, Dec 18, 2019 at 4:52 PM Chris Rands <c_rands100 at hotmail.com> wrote:
> >
> > Dear Peter,
> >
> > Apologies if this has already been discussed, but is the plan to merely passively drop support for Python 2/Python 3.5 or to also actively update existing code?
> >
> > For example, in 2020, would you merge a PR converting all string formatting to f-strings (supported since Python 3.6) or removing all `from __future__ import print_function` lines?
> >
> > Best, Chris
> >
> >
> > ________________________________
> > From: Biopython <biopython-bounces+c_rands100=hotmail.com at mailman.open-bio.org> on behalf of Peter Cock <p.j.a.cock at googlemail.com>
> > Sent: 18 December 2019 5:16 PM
> > To: Biopython Mailing List <biopython at mailman.open-bio.org>
> > Subject: [Biopython] Biopython 1.76 plans
> >
> > Dear Biopythoneers,
> >
> > As has been discussed earlier, we hope to release Biopython 1.76 this
> > month (December 2019). This will be a significant milestone as our
> > final release to support Python 2 which is now officially at end of
> > life:
> >
> > https://mailman.open-bio.org/pipermail/biopython/2019-November/016735.html
> >
> > https://python3statement.org/
> >
> > Additionally, I am proposing this also be the final release to support
> > Python 3.5:
> >
> > https://mailman.open-bio.org/pipermail/biopython/2019-December/016737.html
> >
> > We had a couple of issues reported with Biopython 1.75 post release,
> > mainly from the Debian packaging team covering C code doctests and C
> > code on alternative CPUs - which are now being tested via TravisCI.
> >
> > Otherwise I am not aware of any reported issues which would be a
> > release blocker.
> >
> > If no one has any objections, I propose to do the release this Friday,
> > 20 December 2019.
> >
> > Any thoughts?
> >
> > Thank you,
> >
> > Peter
> > _______________________________________________
> > Biopython mailing list  -  Biopython at mailman.open-bio.org
> > https://mailman.open-bio.org/mailman/listinfo/biopython