[Biopython-dev] [Wg-phyloinformatics] BioGeography update

Peter biopython at maubp.freeserve.co.uk
Tue Jul 7 14:56:01 UTC 2009

On Tue, Jul 7, 2009 at 3:25 PM, Eric Talevich<eric.talevich at gmail.com> wrote:
> On Tue, Jul 7, 2009 at 9:02 AM, Brad Chapman <chapmanb at 50mail.com> wrote:
>> Hi Stephen;
>> We can require lagrange to be installed and use imports to
>> grab the needed code. The other option is that y'all can explicitly
>> relicense a subset of the code under the Biopython license.
> Trivia: it looks like lagrange in turn depends on scipy, but quickly
> glancing through the code, I only see numpy functions being used.
> Since some other Biopython modules already depend on numpy,
> could the installation of lagrange for Bio.Geography be made
> simpler by just changing the import to numpy?

That sounds like a good idea to follow up with the lagrange team
(making lagrange depend on numpy but not scipy).

I think Brad is right to be asking questions about the lagrange
code and their license. How much code do you actually use from
lagrange, and can we either get those bits re-licensed (or
reimplemented) to include directly into Biopython? This may
not be realisitic, in which case a dependency on lagrange may
be the best bet...

Adding external python library dependencies in Biopython is
generally is discouraged, *especially* anything required at build
time as this makes installation much more complicated. As I recall,
we've been able to cut these down to just numpy (needed for
several modules, but we can install without it), plus optional
dependencies like database drivers (e.g. for BioSQL) and
ReportLab (only used in Bio.Graphics).


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