[Biopython] When to drop Python 3.6 support?

[Peter Cock]

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
>
>
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