[Biopython-dev] Beta code in the official releases?

Peter Cock p.j.a.cock at googlemail.com
Wed Aug 22 11:07:11 UTC 2012

Hi all,

One of the ideas I discussed with Bow during this GSoC
project was introducing a new warning, something like
Bio.BiopythonBetaCode (the exact name isn't important),
to be used to label new experimental modules for which
we *expect* there to be changes in the next release.

The idea is to combine the simplicity of distribution and
installation of the 'monolithic' Biopython library with some
of the flexibility offered by a more modular approach.
This would be particularly helpful for those on Windows,
where installing a Biopython branch from git is quite a
daunting task.

The idea is that in one of the next releases you'd be able
to try Bio.SearchIO (or Bio.Struct or GFF or Variants or ...)
and see something like this:

>>> from Bio import SearchIO
Bio/SearchIO/__init__.py:16: BiopythonBetaCode: Bio.SearchIO is in
beta, and likely to change
  warnings.warn("Bio.SearchIO is in beta, and likely to change",

By using a specific warning class, any keen beta tester can
silence all the BiopythonBetaCode warnings if they wished to.

Is anyone familiar enough with Linux packaging polices to
have any thoughts on how they would treat this? Provided
we only use this for self contained modules, they could
potentially split the beta-modules into a sub-package (in the
same way that Biopython and its BioSQL support are split
in Debian).

I envision using this as a way to encourage wider 'beta testing'
of self contained modules which are close to a stable release.
Does anyone think this is a good idea? Are there any downsides
I'm overlooking?



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