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

Peter Cock p.j.a.cock at googlemail.com
Wed Aug 28 18:53:21 UTC 2013

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)

(1) Disable the Python 2.5 target in TravisCI, see
(this is a simple one line edit to the .travis.yml file)

(2) Remove all the with statement imports (and any
comment lines associated with them):

from __future__ import with_statement

(3) Remove Bio/_py3k/_namedtuple.py and adjust
import lines accordingly

(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.

(5) More advanced code review, for example looking
for places we can better take advantage of context
managers (with statements) for file handles.

Of this list, (1), (2) and (3) are certainly things suitable
for relative newcomers - and assuming I'm not away I
will happily do the pull request reviews.

For the more advances issues (4) and (5) we may need
more eyes on the code...

Thank you,


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