[Bioperl-l] Splitting out Bio::Microarray

Chris Fields cjfields at illinois.edu
Fri Jun 25 18:38:24 UTC 2010

An update to this:

I have attempted to run simple tests on bioperl-micrarray and found that they fail on the requirement of a non-existent core module (Bio::Expression::FeatureSet) that is also required of several of the Bio::Expression core modules.  Seeing as (1) there has been no active development on these in many years, (2) no tests are present for any of these modules outside of bioperl-microarray, and (3) the modules are largely central to bioperl-microarray, I suggest we move Bio::Expression modules out of core to bioperl-microarray and deprecate the whole lot completely.  

If there aren't any complaints I'll do this along with the other changes mentioned, and add Bio::Expression to DEPRECATED immediately.  Based on this I also suggest Marian's modules go into a separate distribution completely.


On Jun 25, 2010, at 11:44 AM, Chris Fields wrote:

> All, 
> We have had the Bio::Microarray code in bioperl-live for a while now, but it hasn't been released as part of bioperl core in the 1.6 series mainly b/c the code has been under active development.  Seeing as a paper has been recently published for the code, though (which indicates to me it's in a finished state), and seeing as we have been talking for a while about splitting out specific focused code into separate distributions, I vote we move the various Bio::Microarray modules either into their own separate distribution or into the bioperl-microarray distribution.  I also suggest Marian undertake primary or secondary maintainer status of that code for official CPAN releases.  Marian, let me know if you need help along those lines.
> I also suggest we eventually do the same for the PhyloNetwork modules down the line, and that we steer users who want to submit new publication-focused bioperl-reliant code into their own CPAN distributions. 
> If no one has complaints, I'll work on moving the code out over the next week, likely into bioperl-microarray.
> chris
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