I’m glad you asked that. If you’ve seen the website recently then you know that there’s been no development activity for quite a long time. What can I say? I’ve been pretty busy on other things. The important point is that PyPedal is not abandonware.
On September 1, 2010, I uploaded Release Candidate 9 and let it go into the wild. In addition to adding GENES 1.20 input and output, the changes include some minor documentation updates and a few small code fixes.
In Release Candidate 10, which will be released this week, all I’ve done is add an option to pyp_nrm.fast_a_matrix() to add coefficients of inbreeding read from the pedigree file to the diagonal elements for founders when forming the relationship matrix. I need to update the documentation and check the files once more because I think that there are still some stray hard-coded debugging messages which need to be removed.
The only other thing I’m thinking of adding is support for unknown parent groups, and possibly adding methods to the NewPedigree class that support adding (merging) and subtracting (splitting) pedigrees, but I think that’s going to get punted to the 2.1 development branch because it’s a much harder problem than it may sound on the surface.
I still need bug reports and feature requests. I’ll do my best to fix bugs promptly. I can’t make any promises about feature requests. My thinking right now is that I need to focus on polishing things. The demographics (pyp_demog), graphics (pyp_graphics) and reporting (pyp_reports) modules all could use a lot of fine-tuning to make them more useful. The documentation always needs work. I’m still concerned about the implementation of the algorithms in pyp_metrics for calculating effective ancestor numbers. They’re much less fun that implementing new features, but probably necessary. And then there’s the whole issue of dense SNP data…
