[Bioperl-l] Bio::Tree::Compatible, Bio::Tree::Draw::Cladogram

[Heikki Lehvaslaiho]

Gabriel,

While testing bioperl module SYNOPSIS sections for runnability I found out  
that there are two modules in bioperl-live that have external dependencies 
that are not in Makefile.PL:

Bio::Tree::Compatible 
  Testing compatibility of phylogenetic trees with nested taxa.
  depends on Set::Scalar

Bio::Tree::Draw::Cladogram
  Drawing phylogenetic trees in Encapsulated PostScript (EPS) format.
  depends on PostScript::TextBlock.pm

They both are yours. 

I have not been that active on the mailing list lately, so I searched the list 
for a discussion on these new modules. I started getting a bit alarmed that 
there were none, no emails ever to the bioperl mailing list from you. 
Finally, I checked the t (test) directory and there were no tests for these 
modules.

Could we have that discussion now and hopefully at the end of the discussion 
add the dependencies to the Makefile.PL? In a project this big, we have to 
keep each others informed so that we can keep all parts of bioperl functional 
and to avoid confusing and alienating users.


Where do these modules come from?
What functionality do they add?
Is the name space used correct?
Could we see test code that demonstrates the functionality?
Is there something else that you are planning to do?


Yours,

 -Heikki, who feels that he is probably overreacting ;-)
                 ... so do not take it personally


-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_ebi _ac _uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambridge, CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________