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

[Peter Cock]

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