[Biopython-dev] Releasing biopython - lessons

Tiago Antão tiagoantao at gmail.com
Fri Dec 6 12:26:09 UTC 2013

Dear all,

With much help from Peter, 1.63 was released. I have a few comments/ideas I
would like to share:

1. I think that there is a need to maintain an exhaustive list of
dependencies that a full biopython distribution will need (python packages
and external applications). I am offering to do that here:
http://biopython.org/wiki/List_of_applications_executed_via_Biopython (over
the next few days).

2. I was planning on creating a Linux virtual box image (and make it
available) with everything that is needed to fully test and run a Biopython
distribution. This would allow to have an extremely stable environment for
testing (testing PCs normally have other uses and things can be broken by
other stuff).

3. I think that it would be nice to change run_tests to have an option to
run in an "extremely picky mode": Basically fail if there is a warning that
is not a Deprecation warning. Some silent warnings can actually be somewhat
irritating if not understood/acted upon (e.g the RDFlib case). This would
be run before release and maybe once a week on buildbot?

1 and 2 are trivial (and go very well together) and I am offering to do it
in the very next few days if that is OK. Any views on 3? This would require
changing run_tests and that might not be easy/desirable...

My 2p,
"The truth may be out there, but the lies are already in your head" - Terry

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