[Bioperl-l] Splitting out Bio::Microarray
cjfields at illinois.edu
Fri Jun 25 15:39:36 EDT 2010
Marian's code has been moved into the github Bio-Microarray repo (we can rename that if needed). Bio::Expression modules have been moved into bioperl-microarray for the time being, though I would like to allow use of that namespace for others if needed.
Bio::Expression and Bio::Microarray have been removed on a branch of bioperl-live, all tests pass, so it just needs merging.
On Jun 25, 2010, at 1:38 PM, Chris Fields wrote:
> 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:
>> 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.
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