[Bioperl-l] Problems with Bioperl-ext package on WinVista?

[Robert Buels]

Yee Man Chan wrote:
>     As to the release, my thinking is that I do understand that your desire to maintain a high level of quality in BioPerl code base. So if the HMM doesn't meet that standard, I am ok with it being spinned off. 

We're not pushing to spin it off because of code quality, we're pushing 
to spin it off because we're spinning everything off.  The plan is to 
break BioPerl up into many discrete distributions on CPAN with the 
dependencies between them well-known and codified.  This will make 
maintenance of BioPerl *much* easier in the long run.

So this means that the plan of action should be
   1.) get the code so that it's working on all platforms,
   2.) create a CPAN distribution for it and put it on CPAN,
   3.) remove it from bioperl-ext

Also, doing a search for bioperl-ext on CPAN brings to light a couple of 
issues that probably need to be dealt with.  To wit:


1.) there is an ancient version of bioperl-ext that probably needs to be 
removed, it's under ~birney's account.  Thoughts on this?

2.) Bio::Tools::( dpAlign | HMM | pSW ) all state that they depend on 
bioperl-ext, which suggests that these really need to be split off, each 
with the Bio::Ext::Modules they depend on.  Bio::Tools::HMM could be the 
first case of this:
    * make a dir in the repos called Bio-Tools-HMM alongside 
bioperl-live, having trunk/, and branches/ subdirs
    * move Bio::Tools::HMM out of bioperl-live into that
    * move Bio::Ext::HMM stuff out of bioperl-ext into that
    * repeat with Bio::Tools::dpAlign and pSW, which would probably
      go together into a Bio-Tools-Align distro, I think

Sounds like this is moving along nicely.

Rob