[Bioperl-l] RFC: Refactoring the Hyphy module

Fields, Christopher J cjfields at illinois.edu
Mon Aug 27 16:34:18 EDT 2012

Yes, fixing things on a github fork and submitting a pull request is generally the best approach to this.  If you have more substantial improvements over time we can add you as a developer on Github.


On Aug 27, 2012, at 3:05 PM, Daisie Huang <daisieh at zoology.ubc.ca> wrote:

> I've been playing around in the guts of the Hyphy module in bioperl-run, and it strikes me that a lot of the code in the modules is redundant and could be refactored to streamline things and fix some crashes I've been seeing in the test code. Generally, my coding philosophy is to mess with things as little as possible because of the possibility of unintentional side effects, but sometimes a refactor will be beneficial going forward, especially if it doesn't affect the API. What is the group policy on such things? Should I go ahead and attempt it on a branch, make the pull request, and see if anyone has a problem with the code? 
> Thanks,
> Daisie
> -----------------------------------------
> Daisie Huang, PhD
> Rm 318, Beaty Biodiversity Centre
> Department of Botany
> University of British Columbia
> http://cronklab.wikidot.com/daisie-huang
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