PyPedal / News: Recent posts

Beta 2 released

The second Beta has been released. There are some major bugfixes, so all users are encouraged to upgrade.

Posted by John B. Cole 2005-11-22

HTML Manual online

An HTML version of the PyPedal manual is now available on the website (

Posted by John B. Cole 2005-11-22

Beta 1 ('Vetinari') CVS checkin looks good

I checked a few files this morning and it looks like the merging that went on last night when I checked Beta 1 into CVS worked correctly, that is, the way I expected it to. Sync away.

Posted by John B. Cole 2005-11-22

Beta 1 ('Vetinari') checked into CVS

I checked the current tree into CVS tonight. I always seem to break things using CVS, so I can't guarantee that I have everything correctly merged. Unless you're a hardy soul, I recommend that you stick with the source tarball in the latest release.

Posted by John B. Cole 2005-11-22

Beta 1 ('Vetinari')

The first Beta release of PyPedal is out! The API is frozen for version 2.0.0 and no new features are planned. I'm currently in fix-bugs-and-improve-documentation mode.

Posted by John B. Cole 2005-11-15

Alpha 19

Alpha 19 is out. Changes:

Added new functions to pyp_network for identifying ancestors, identifying descendants, identifying immediate family members (defined as parents and offspring, and does not include siblings), and identifying influential progeny based on the number of progeny they produce.

Fixed to pyp_network/ped_to_graph() so that graphs are now ordered in the correct direction. Before this fix, the graph was ordered backwards, so that offspring preceded parents in the graph.... read more

Posted by John B. Cole 2005-10-25

Alpha 18 Problems

I am trying to get Alpha 18 uploaded to SourceForge but all of my FTP sessions timeout. I know that the files that are in the release folder are all junk. I will fix this as soon as I can.

Posted by John B. Cole 2005-07-21

Alpha 16

Alpha 16 is out. New class (NewAMatrix) and a few cleanups. Documentation revisions started.

Posted by John B. Cole 2005-05-03

Alpha 13

Alpha 13 is out. It includes a couple of serious bugfixes, a snazzy new save() method for NewPedigree objects, and some tinkering in the graphics module.

Posted by John B. Cole 2005-04-26

Alpha 9

Changes committed to CVS. I really do not get CVS, I am ashamed to say, and I hope that I have not munged anything too badly with the latest commits. There are BIG changes to, and examples/ demonstrates (a little) how things are going to work under that system. I also added a new module, pyp_graphics, with a couple of tools for visualizing matrices. Um...I am also going to start on a new manual.tutorial this weekend to replace what is on the website.

Posted by John B. Cole 2005-03-04

Double the fun!

It looks like a second programmer is going to be joining the project. He will be working on Postgres integration, a new, usable GUI, and Italian-language localization.

Posted by John B. Cole 2004-08-31

Alpha 7 released!

Have fun.

Posted by John B. Cole 2004-08-12

Alpha 7 on the way!

John is currently working very hard on Alpha 7, which will include a revamped pedigree completeness measure. There are a number of tweaks to the Animal() class, and a new procedure for recursing through a pedigree to a set depth.

Posted by John B. Cole 2004-05-27

Drop everything!

As of Alpha 6 PyPedal has a new routine, pyp_metrics/effective_founder_genomes(), that uses a gene-dropping algorithm to compute the effective number of founder genomes as described in Lacy (1989) and Boichard et al. (1997). There is also a new pedigree code, '% asdt', for pedigrees that include animal, sire, dam, and genotype information.

Posted by John B. Cole 2004-05-27

Alpha 5

Mostly bugfixes. Added procedure to compute actual coefficients of relationship (numerator relationships adjusted for the inbreeding of the parents). Uploaded new versions of all of the documentation.

Posted by John B. Cole 2004-05-06

Alpha 4

There are lots of bugfixes, feature additions, and feature enhancements in alpha4. My favorite is the interface to Graphviz (via pydot) for drawing pedigrees. I am also glad to have the relationship() and mating_coi() routines in place, even if they are not very exciting. Finally, I have some ideas for a caching mechanism to improve the performace of relationship() and mating(coi() that may show up in alpha5.

Posted by John B. Cole 2004-04-23

Effective Ancestors

The a_effective_ancestors_definite() has finally been debugged and determiend to be working correctly. Bugs were fixed in other routines, as well, and a couple of convenience-type functions were added. Please see the CHANGELOG. With the effective ancestors bugfix all known bugs are fixed. Which is not the same as saying that there are no rough edges that need smoothing...

Posted by John B. Cole 2004-04-19

Eat, read, and be merry!

The initial release of PyPedal 2.0.0 has been made! In addition to RPMs, a source tarball, and a Windows installer, some project documentation has been released.

Posted by John B. Cole 2004-04-15

Sourceforge site launched!

PyPedal is moving to Sourceforge. This marks teh first truly public release of PyPedal. I am in the process migrating the codebase into a CVS tree. Documentation and more information will be made available on the website as it is available.

Posted by John B. Cole 2004-04-14