[Biopython] Biopython 1.76 plans

[Peter Cock]

OK, release announcement is out on the blog and twitter:

https://www.open-bio.org/2019/12/20/biopython-1-76-released/
https://pypi.org/project/biopython/1.76/

Enjoy!

Peter

On Fri, Dec 20, 2019 at 2:35 PM Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
> 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