[Biopython] When to drop Python 3.6 support?

[Peter Cock]

I have submitted a pull request to drop support for Python 3.6 in our
next release:

https://github.com/biopython/biopython/pull/3714

We should probably declare support for Python 3.7 deprecated soon too,
with Python 3.10 due out next month.

Peter

On Wed, Jun 9, 2021 at 8:43 PM Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
> NumPy are already talking about dropping Python 3.7 support, noting
> Python 3.10 is due soon (October 2021):
>
> https://mail.python.org/pipermail/numpy-discussion/2021-June/081858.html
>
> Peter
>
> On Sat, Jun 5, 2021 at 10:32 AM Peter Cock <p.j.a.cock at googlemail.com> wrote:
> >
> > Dear Biopythoneers,
> >
> > We had various delays due in part to key people's availability, but
> > six months after the last email in this thread, we have now released
> > Biopython 1.79.
> >
> > Biopython 1.79 is planned to be our final release to support Python
> > 3.6, so if there are any last minute pleas to keep supporting it,
> > please reply within the next week.
> >
> > Otherwise we will drop testing Python 3.6 on the main repository and
> > continuous integration, and raise an error trying to install under
> > Python 3.6.
> >
> > Thank you,
> >
> > Peter
> >
> > On Tue, Dec 8, 2020 at 10:27 AM Peter Cock <p.j.a.cock at googlemail.com> wrote:
> > >
> > > Thank you for your comments Stéphane,
> > >
> > > Ubuntu LTS releases (and similar) are the only use case I could think
> > > of where people might still want to use Python 3.6, and I
> > > believe/assume they are a minority now. I may be wrong. Relatively few
> > > people have replied to this discussion, and you are the first doing
> > > so. Are you actually using the system provided Python 3.6 here?
> > >
> > > NumPy is our only required dependency, and they have now dropped
> > > support for Python 3.6. We don't currently require an especially new
> > > version of NumPy, so this in itself would not stop us supporting
> > > Python 3.6, but it would stop us using new functionality in numpy as
> > > desired.
> > >
> > > You asked about conda, the institute where I work, and many local
> > > universities are using conda on their clusters nowadays, and likely
> > > servers too. The big advantage here is giving users easy access to
> > > install tools on their own (using bioconda and conda-forge as well as
> > > the default channel for packages of relevance), while the underlying
> > > cluster OS remains with whatever older tools and libraries it comes
> > > with (including an old version of Python which would not be used).
> > > This separation and duplication also avoids version conflicts (e.g.
> > > between two different users of the cluster, or indeed using conda
> > > environments different tools anyone might wish to have installed at
> > > the same time). In contrast, while DebianMed for Debian/Ubuntu (and
> > > similar groups for other Linux distributions) do an excellent job of
> > > keeping bioinformatics packages up to date, this is only available to
> > > local systems administrators. i.e. Fine for a self managed Linux
> > > desktop or server (which is how I used Debian/Ubuntu for years), but
> > > not a multi-user system.
> > >
> > > Docker too has a role, especially in deployment. Unless you are trying
> > > to combine other tools requiring an older base image / older Python,
> > > then I don't see Biopython dropping Python 3.6 support being a
> > > barrier. But not being a Docker user, I may be missing something?
> > >
> > > Would anyone else like to speak in favour of keeping Python 3.6 support longer?
> > >
> > > Peter
> > >
> > > On Tue, Dec 8, 2020 at 9:54 AM Téletchéa Stéphane
> > > <stephane.teletchea at univ-nantes.fr> wrote:
> > > >
> > > > Le 10/11/2020 à 10:50, Peter Cock a écrit :
> > > > > I note that Python 3.6 has now been dropped from NumPy 1.20. It would be
> > > > > good to start preparing to drop Python 3.6 support in Biopython. According
> > > > > tohttps://www.python.org/downloads/  and also PEP494, Python will end
> > > > > support for Python 3.6 in December 2021, about a year away.
> > > > >
> > > > > Are there any major platforms (e.g. popular Linux distributions) where the
> > > > > default is Python 3.6 where our users might be inconvenienced? Personally
> > > > > I switched to using conda (with conda-forge and bioconda) a while back, and
> > > > > their default Python is quite up to date - so I don't usually worry about the
> > > > > system provided Python anymore.
> > > > Hi all,
> > > >
> > > > Ubuntu for one, in its 18.04 LTS (10 years, up to April 2028) is still
> > > > using python 3.6(.9)
> > > > as its official python version, and will probably default to this one
> > > > for "a moment":
> > > > https://wiki.ubuntu.com/Python/Python36Transition
> > > >
> > > > Out of numpy, is there any requirements in biopython "forcing" this
> > > > migration?
> > > >
> > > > As I see it for now, Python3 is still evolving rapidly, so getting "the
> > > > latest one"
> > > > may not seem a good idea if you want to break the community's work :-/
> > > >
> > > > And for conda, except if you are a Windows user, I don't get the point
> > > > of using
> > > > a whole new system in a directory (taking more space than the original
> > > > one...)
> > > > since when you want to combine multiple large collection software
> > > > (django + apache + rdkit + biopython in my case) conda is certainly not
> > > > the easiest
> > > > to use (better use docker in this situation).
> > > >
> > > > My 0.02 cents/pennies :-)
> > > >
> > > > Stéphane
> > > >
> > > >
> > > > --
> > > > Team Protein Design In Silico
> > > > UFIP, UMR 6286 CNRS, UFR Sciences et Techniques,
> > > > 2, rue de la Houssinière, Bât. 25, Nantes cedex 03, France
> > > > Tél : +33 251 125 636 - Fax : +33 251 125 632
> > > > http://www.ufip.univ-nantes.fr/ - http://www.steletch.org
> > > >
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