[Biopython-dev] BioGeography update/BioPython tree module discussion

Brad Chapman chapmanb at 50mail.com
Tue Jul 14 12:35:34 UTC 2009

Hi Nick;
Thanks for the comprehensive update. It sounds like your discussion
with Eric resolved most of the questions about the tree
representation. It's great to see y'all converging on this.

> It sounds like for my immediate purposes, Bio.Nexus.Trees is the 
> solution for now, I will reorganize my code accordingly based on this. 
> If/when Bio.Nexus.Trees accepts node labels I will remove a function 
> stripping out node labels.  Also I have not forgotten previous comments 
> from Brad et al. about bringing the other code up to specs. So I will 
> update the BioGeography schedule and overall organization I hope to have 
> at the end (with classes/methods etc., instead of just a 
> list-o-functions, which is how my original schedule was explicitly laid 
> out), and post an update when done.

Agreed, and seconding Hilmar that the best thing about open source
code is having others looking at your code. Conversely, feel free to
dig in and fix current code where it is holding you up. To remove
this blocking issue on Nexus and get us rolling again, I
put together an initial fix. You can grab the patch from:


Let us know if this works for your files of interest.

If this clears up the Nexus issue, it would be great to see the
revised schedule incorporating the refactoring. Sounds like we 
are moving in the right direction. Good stuff.


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