[Biopython-dev] Post Biopython 1.62 release, clean-up after dropping Python 2.5

[Chris Mitchell]

I was going to take a stab at (3), but it seems that _namedtuple.py doesn't
exist.

Looking under _py3k as well as grep -Ri namedtuple ./*

fails to find it. I'm pulling from
https://github.com/biopython/biopython.git


On Thu, Aug 29, 2013 at 5:04 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Wed, Aug 28, 2013 at 7:53 PM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
> > Hello all - especially newcomers,
> >
> > There are going to be several boring but useful things to do to
> > the Biopython code base once we're finished with Python 2.5
> > (the imminent release of Biopython 1.62 has been clearly
> > described as the final Biopython release to support it).
> >
> > Some of these tasks are quite easy, and might tempt some
> > of our non-core contributors or new-comers to have a go,
> > however to avoid too much duplication of effort I'd suggest
> > **replying in this thread if you want to tackle anything** - and
> > then start working out how to send us your first pull request.
> >
> > Things which will need doing:
> >
> > (0) Disable the Python 2.5 and Jython 2.5 buildbot
> > (this will be done by me or Tiago)
>
> Done.
>
> > (1) Disable the Python 2.5 target in TravisCI, see
> > https://travis-ci.org/biopython/biopython/
> > (this is a simple one line edit to the .travis.yml file)
>
> Done by Wayne,
>
> https://github.com/biopython/biopython/commit/d134b3ae6d963b81510c40c621d640ee00b6f3de
>
> > (2) Remove all the with statement imports (and any
> > comment lines associated with them):
> >
> > from __future__ import with_statement
>
> Done by Wayne,
>
> https://github.com/biopython/biopython/commit/eeab501987de61ae5935153e1b1a0b225878cb84
>
> > (3) Remove Bio/_py3k/_namedtuple.py and adjust
> > import lines accordingly
>
> Any new volunteer want to try this?
>
> > (4) Scan over the code base looking for any comments
> > about Python 2.5 (e.g. using the grep command), and
> > reviewing them one by one to see if there is an old
> > workaround we can now remove.
>
> Lenna had a quick look, there should be some easy one here.
>
> > (5) More advanced code review, for example looking
> > for places we can better take advantage of context
> > managers (with statements) for file handles.
>
> Another new one, related to (5), and fairly easy:
>
> (6) Reviewing examples in the docstrings and Tutorial
> where it would make sense to use a 'with' for file handles.
>
> This should also solve many of the ResourceWarning:
> unclosed file ... warnings visible running the full test
> suite under Python 3, e.g. see:
>
> http://testing.open-bio.org/biopython/builders/Linux%2064%20-%20Python%203.3/builds/298/steps/shell/logs/stdio
>
> Peter
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