[Biopython] Biopython 1.76 plans

[Peter Cock]

The tar-ball, Linux, Mac and Windows binaries are on PyPY.

Note that since PyPI now blocks having both tar-ball and zip file,
would there be any objection to dropping the zip file in future?
Currently we build it and put both the tar-ball and zip are on
biopython.org

Next I will turn off TravisCI and AppVeyor testing under Python 2.7
and Python 3.5 (an immediate benefit here is that should about
halve the time AppVeyor takes as it runs sequentially).

Peter

On Fri, Dec 20, 2019 at 1:11 PM Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
> 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