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Tag Archives: PyPedal
PyPedal now calculates partial inbreeding coefficients
After sitting on the “coming soon” list for a couple of years PyPedal can finally calculate coefficients of partial inbreeding! As side effect, the pyp_nrm/reorder() routine now moves all founders to the beginning of the pedigree. In the past, founders … Continue reading
I’m a code monkey
Today has been another three-language day: Fortran [Wikipedia] for the best prediction code, Python for PyPedal, and PHP for my latest side project, Middleton. Oh, wait, I also did some LaTeX in the PyPedal manual and write a one-liner in … Continue reading
Working for the Man
I know, it’s been a long time since I last blogged. I’ve been busy, what with successfully completing my probationary period and getting my new employee up to speed. I’ve been much busier than I expected this week, but that … Continue reading
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Tagged cake, Discworld, Google, PyPedal, quilt, Science, visualization
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Perl without tears, the perils of revenge
A couple of days ago I needed to install html2latex on the server because it’s part of the documentation toolchain for PyPedal. Which meant a long, strange trip into Perl-land which required that I install packages from CPAN without root … Continue reading
What I’ve learned from my Open Source project
Here are a few things that I’ve learned while working on my pedigree analysis software, PyPedal. If you’re a programmer, or spend much time reading about programming and the Open Source movement, you’ll find most of this to be quite … Continue reading
[PyPedal] Beta 11 fixes some reordering and ID hashing problems
This release of PyPedal fixes some small problems in pyp_utils/reorder(), cleans up some ID-handling issues in pyp_newclasses/NewAnimal::__init__(), and replaces the hashing algorithm used in pyp_newclasses/NewAnimal::string_to_int(). The previous hashing algorithm was colliding on similar keys and the side effects were showing … Continue reading
[PyPedal] Beta 9 released, Beta 10 imminent
Last night I released Beta 9 to address a showstopper bug reported by a colleague at the University of Guelph. I won;t bore you with all of the details, but it has to do with the handling of user-specified missing … Continue reading
[PyPedal] Beta 7 released!
Woohoo! I’ve made a new release of PyPedal. Get it hot from the oven over at Sourceforge, if their site ever starts answering back. I really want to brag about my three-generation pedigree report because it took a lot of … Continue reading
[PyPedal] Stepwise refinement
Well, I had good intentions. I was going to finish writing pyp_reports/pdf3GenPed() this morning and then start writing the new PyPedal manuscript. I only finished one of those things. Guess which one? The three-times-longer rule strikes again! On the plus … Continue reading
[PyPedal] NumPy, new methods, pyp_metrics
This moring I thought that I woud spend an hour or so tidying up a few corners in PyPedal and making a small extension to pyp_metrics/mating_coi() to add a feature of interest to a potential user. By the time the … Continue reading