These errors, in a way, exposed the tip of an iceberg: there is not nearly enough unit testing in PyPedal. Many of the example programs were written a long time ago (about three years) and not checked systematically since. This means that some programs, such as examples/new_amatrix.py, were still using methods that no longer exist (I’m thinking specifically about the info() method of NewAMatrix objects). Heck, that program still imported Numeric! So it’s a great idea to have examples, but it doesn’t help users when they run the program and everything fails. It makes the whole package look shoddy and undependable, and who wants to trust their work to that kind of code? If Matthieu hadn’t e-mailed me about those problems I’d still be shipping broken code. I hate writing unit tests as much as the next guy, but PyPedal’s grown to the point that it’s too big for me to keep track of, so I need a way to automate testing. So, it’s getting to be unit test time. With that and the work I want to do on the graphics module there’s plenty of work in the queue for version 2.0.1.

I’ve got no quarrel with SQLAlchemy — it looks very cool — but I could never quite get it to do what I wanted. After working with it for a day or so I concluded that it was just overkill for the few simple things I wanted to do, so I jumped ship to ADOdb for Python. It stood me in good stead many times in my PHP days,and it got the job done handily here, too.

I’m sure I’ll think about more that I want to say later. The dusting and polishing that goes along with preparing a release version is doing PyPedal a lot of good.

Now that I’ve established that my blood sugar’s off we can get down to brass tacks. Release candidates 1 and 2 have been released, and release candidate 3 is in the works. I won’t repeat everything that’s in the CHANGES.txt file, but I’ll hit the high points.

The big news is that I broke pyp_nrm/inbreeding_vanraden() at some point in the recent past. If I had regression tests I would have noticed this sooner. Maybe. Someone really should get on that. The bug affected only animals with both parents unknown or with unknown sires. The fix was very simple. I also fixed a bug that prevented the super-nifty Full-Sib Speedup from working. Wait, what, you’re not familiar with the Full-Sib Speedup? Let me explain.

The Full-Sib Speedup is a trick to avoid unnecessary calculations when you’ve got a pedigree with lots of full-sibs, such as dogs. The trick is that a list of observed sire-dam combinations is stored. The first time that combination is seen the resulting COI is stored in a dictionary. Any subsequent offspring of that combination receive the COI stored in the dictionary. Instead of calculating the COI for each offspring of the combination it is calculated only once. There are a number of steps avoided with this trick, such as pedigree extraction, reordering, and renumbering. And it now works correctly, which is a bonus.

The minor things include such stuff as lots of small fixes to the NewAMatrix class, fixes to inbreeding and relationship metadata, and added pedigree import/export from database and textstreams.

I also added a couple of chapters to the manual, one on input/output and one on performing calculations with pedigrees. The API documentation has been pulled out of the manual and is available on the website. I’m also now using Doxygen to generate those documents, which is working quite well.

Perhaps feature deletions are not as interesting as feature additions, but I’ve removed the GUI from PyPedal. The code that was hanging around was very old — it predated the current pedigree format system and used static format codes embedded in the pedigree file — and didn’t work very well. The fundamental idea behind PyPedal is that you get a set of tools that allow you to program (or metaprogram?) using pedigrees, and the GUI doesn’t fit in that paradigm. I’m also not comfortable with GUI programming and don’t have much interest in pursuing it. If someone wants to work on a GUI for PyPedal I’ll be happy to provide feedback, but do not intend to pursue it any further on my own.

Scientists have discovered a fossil of a missing link between fish and land animals which shows that creatures first walked out of the water and on to dry land more than 375 million years ago. Here’s the editor’s summary in this week’s issue of Nature, and their weekly podcast will focus on this story. If you’ve got institutional access, you can also read the papers “A Devonian tetrapod-like fish and the evolution of the tetrapod body plan” (Dasechler et al., 2006) and “The pectoral fin of Tiktaalik roseae and the origin of the tetrapod limb” (Shubin et al., 2006). This is yet another nail in the coffin of the so-called intelligent design movement. Suck it, creationists.

A Bob Ross video game is in the works. I kid you not. I don’t think it’s an April Fool’s joke, either.

Seriously, doesn’t do-it-yourself Lasik sound like a Really Bad Idea to anyone else? I’m pretty sure this is a joke, but the possibility that it is true fills me with horror.

• Stillbirth (co)variance components for a sire-maternal grandsire threshold model (JB Cole, GR Wiggans, and PM VanRaden) (Minneapolis)
• Genetic evaluation of stillbirth in United States Holsteins using a sire-maternal grandsire threshold model (JB Cole, GR Wiggans, and PM VanRaden) (Brasil)
• Separate genetic effects for first and later parities in a sire-maternal grandsire model for calving ease (GR Wiggans, CP Van Tassell and JB Cole) (Brasil)
• Genetic evaluations for mixed breed populations (PM VanRaden, ME Tooker, JB Cole, GR Wiggans, and JH Megonigal, Jr.) (Minneapolis)

Do you see a theme among the first three papers? I’ll be first author of a paper on the (forthcoming) national evaluation for stillbirth this year, and Paul’s mixed breed evaluation paper will also be going to the Journal of Dairy Science this year. So before our performance standards are even due I’ve got my two papers for the year taken care of. I also hope to have a paper out on some of our health data this year, too.