[Biopython] When to drop Python 3.6 support?

[Peter Cock]

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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