[Biopython-dev] Developmental policies

Peter peter at maubp.freeserve.co.uk
Sat Jan 10 20:10:27 UTC 2009

On Sat, Jan 10, 2009 at 6:31 PM, Tiago Antão <tiagoantao at gmail.com> wrote:
> By the way, another issue that would be interesting to address is
> deprecation of older Python versions and Python 3. Like just having a
> clear stance on what is the current feeling about this. It seems to be
> a recurring question.

Regarding older versions of python, we have stated that Biopython 1.49
should work on Python 2.3 to 2.6, and we expect to do the same for
Biopython 1.50.  Thereafter, we will probably drop support for Python
2.3 (unless anyone has a strong need for it and makes their voice
heard).  See the mailing list archive and the corresponding new

Regarding Python 3, one hold up will be neither ReportLab nor NumPy
have a clear plan for Python 3 - or at least that is my impression.
However, even ignoring those parts of Biopython which use NumPy (e.g.
Bio.PDB and Bio.Cluster) and Bio.Graphics (the only use of ReportLab),
we have a lot of useful code.  In the short term we should be aiming
to have everything run under Python 2.6 in warnings mode, as a step
towards eventual Python 3 support.

Beyond that, I think that it is likely we'll want to use bytes rather
than (unicode) strings in Python 3 for the Seq object, but have not
given this much thought.

>>> 5. Legal issues
>> Try and avoid them?  What did you mean in particular?
> In my opinion something should be said about this. Actually I think
> (suggest) it is essencially a matter of mainly taking Bruce' s
> comments (e.g. one cannot have derived works of non-free software) and
> write them down on a wiki page. Just things potential contributor
> would have to be aware of on a legal front.

I see what you mean.  Perhaps I am naive in thinking this should be
common knowledge amongst potential contributors.

>> Testing:
>> I'd strongly resist adding any new module without an accompanying
>> test, and wish this had been a firm policy from day one.
> People should also be encouraged to test (in as much as possible) in
> at least Win/Linux/Mac. Of course, for some people it will be
> difficult as access to all platforms is not always possible for
> everybody. But at least encouragement should be made...

Also tests which require additional setup are a pain.  The BioSQL
tests are an example of this, where it is unavoidable - but any
situation like this reduces the number of people/machines where that
test will get checked.  Michiel has stressed this kind of thing as a
concern in the past (as I recall).


More information about the Biopython-dev mailing list