05/04/2012: Ijust released version 2.0.2, which takes care of several bugs related to a NetworkX API change, as well as fixes pyp_newclasses/new_pedigree::fromgraph(). See the blog for details about what I'm planning.

02/26/2011: I have just created the development branch for the upcoming 2.1 work. See the blog for details about what I'm planning.

12/30/2010: I released bugfix version 2.0.1 is out. That fixed a bug in pyp_nrm/inbreeding(). See the blog for details.

09/29/2010: Production release 2.0.0 is out. This is the first production release of PyPedal. See the blog for details.

09/01/2010: Release candidate 9 is out. This release focused on clean-up for the upcoming final release of 2.0.0, as well as implementation of support for GENES 1.20 (dBase III) .DBF files.

09/01/2010: Release candidate 8 is out. This release focused on clean-up for the upcoming final release of 2.0.0, and has been sitting around my PC for far too long.

05/07/2008: Release candidate 7 is out. This includes a number of fixes to routines in pyp_nrm and pyp_graphics, and all of the example programs have been checked for correctness. See the blog for details.

05/01/2008: Release candidate 6 is out. This includes a fix for the logging module, which I broke a version or two ago and a few other small bugfixex. See the blog for details.

04/09/2008: Release candidate 4 is out. This includes improvements to the installation process. See the blog for details.

03/28/2008: Release candidate 3 is out. This includes a bugfix to the inbreeding_vanraden() routine and a major refactoring of the database support. See the blog for details.

03/11/2008: Release candidate 2 released. This includes a major bugfix to the inbreeding routines. See the blog for details.

03/03/2008: This afternoon I released beta23, which is the last beta release. From now on changes will be limited to bugfixes, and the next release will be tagged rc1 (release candidate 1). The API documentation was removed from the manual but can be found on the website courtesy of Doxygen. Note that I've removed all of the GUI components and have no plans to implement a graphical interface for Python. I also made a few small changes to support loading pedigreed from strings, which is a web services-type feature requested by Dan Cieslak, who is now outed as a PyPedal user. :-) Feedback and bug reports are welcome.

02/08/2008: Despite the absence of any new posts PyPedal is alive and well. I've added a link on the left to all of the entries on my blog tagged with PyPedal that may help people keep up with what's going on. The big news is that I finally got the partial inbreeding calculations working this morning. A side effect of that is that the reorder() routine now moves all founders to the beginning of the pedigree. In the past, founders were guaranteed to precede their offspring, but they were not guaranteed to be guaranteed to precede other animals with known parents. I'm also close to having the code done to support GEDCOM 5.5 files, which is widely-used by the human geneaology community, although support will be provided for only a small subset of the formal specification.

04/17/2007: Gregor Gorjanc has written a nice tutorial on installing PyPedal under Debian (I've linked to it under Installation, too). He's done a nice job with that, and I'd like to thank him for it. His tutorial will be included in the documentation as a HOWTO when I package the nect release.

04/09/2007: The bug in handling ASD pedigrees on 32-bit platforms has been fixed in Beta 21, which is available for download. The fix has been tested on 64-bit Linux (JBC) and 32-bit Windows XP and Mac OS/X (Matt Kelly). Many thanks to Matt for finding the bug in the first place and testing the fix on several machines to make sure it's working as advertised.

For the technically-minded: The old algorithm was using sys.maxint in the hash, which is platform specific. It's a much larger number on 64-bit hardware (obviously). I guess that led to a better distribution of keys or something on the 64-bit machine. I've implemented a new approach using the MD5 module in the Python core library.

04/05/2007: I've discovered a bug in the handling of ASD pedigrees (pedigrees in which the animal, sire, and dam names are strings rather than numerical IDs) that affects PyPedal running on the Microsoft Windows and Apple OS/X operating systems. The problem does not affect Linux. I hope to fix the problem in the next day or so.

For the technically-minded: I think that the problem is in the algorithm that PyPedal uses to hash (convert) strings to integers. I don't yet know why there is a platform-specific difference, and I also don't know if the algorithm is colliding or what.

03/23/2007: I've posted links to HTML and PDF versions of the forthcoming paper on PyPedal that's to appear in Computers and Electronics in Agriculture. The version I've posted is my own file, not the fancy typeset version from the publisher, but the content is identical to Elsevier's version.

PyPedal was recently mentioned on CANGEN-L, a canine genetics e-mail discussion list. If you've come here from there, welcome. Links to Installation instructions are provided over on the left. I've written PyPedal for use in my research program, and that perhaps shows in the lack-of-ease of the installation process and the console-based interface, but it's available free-of-charge under the terms of the GNU LGPL for anyone who wants to use it. I make no promises of support, but it's been my practice in the past to provide assistance within a reasonable amount of time. I will continue to do so as long as I'm able. Bug reports and feature requests can be made directly to me, but I'd prefer that you use the tools provided by Sourceforge for that purpose. I don't aways do a great job of keeping up with my e-mails, and I've got a very aggressive spam filter.

• In pyp_newclasses/NewPedigree.save() accepts an option, idformat, that specifies which animal, sire, and dam IDs are written. The 'o' (original) option writes a pedigree with the original IDs as read from the original input pedigree file. The 'r' (renumbered) option will write a pedigree file containing renumbered animal, sire, and dam IDs.
• In pyp_newclasses/NewPedigree.save() accepts an option, outformat, that specifies how the saved pedigree is written. The 'o' (original) option writes a pedigree with the same pedformat as the original input pedigree file; this is useful if you have computed CoI, inferred sex, and that kind of thing. The 'l' (long) option will write a pedigree file containing all known fields in the animal object for which there is are pedigree format codes (see the file PEDIGREE_FORMAT_CODES).
• In pyp_newclasses/NewPedigree.__init__() the default logfile name is now self.kw['filetag'].log.
• Some changes were made to layout options in pyp_graphics/draw_pedigree(). Pedigrees are now drawn landscaped on US letter-sized pages (8.5 in x 11 in) and will, in theory, be tiled across pages if they cannot fit on a single page. This does not work as well as hoped, but I am working on it.
• pyp_graphics/draw_pedigree() now takes an optional parameter, gdot, that tells draw_pedigree() whether or not write the raw (dot language) representation of the pedigree to a file. Code is written to a file named gfilename_pedigree.dot.
• pyp_graphics/draw_pedigree() now takes an optional parameter, gsize, that tells draw_pedigree() whether or not write the raw (dot language) representation of the pedigree to a file.
• pyp_graphics/draw_pedigree() now takes an optional parameter, gsize, that specifies the size of the resulting graphic: 'f' (default) produces as large a graph as necessary to accomodate the layout and 'l' produces a diagram scaled to fit on a letter-sized sheet of paper.
• Added a new method, save(), to pyp_newclasses/NewPedigree(). This long-overdue feature lets you easily save a pedigree after, for example, computing CoI. It eliminates the need to perform time-consuming computations on pedigrees every time they are accessed by making it easy to store a "large format" PyPedal pedigree.
• Fixed a bug in pyp_newclasses/NewPedigree.preprocess() in which records for sires and dams that appear in a pedigree, but which do not have individual entries in the pedigree file, were assigned birth years of 0 when dummy records were inserted into the pedigree. This was causing pyp_newclasses/NewAnimal.pad_id() to return a munged up paddedID that caused problems in pyp_utils/fast_reorder(). Tricky problem to find, that was.
• Made a small change to pyp_newclasses/NewPedigree.preprocess() so that blank lines are caught and handled correctly. Before this fix a blank line with, say, an embedded TAB character would cause a fatal error b/c it was treated as a "regular" record.

• I think that pyp_graphics/draw_pedigree() may be inserting a spurious node when drawing the pedigree, but I have not yet figured out where it is happening.
• Removed references to "species" from pyp_newclasses/NewAnimal.printme() and pyp_newclasses/NewAnimal.stringme().
• Tweaked pyp_newclasses/NewAnimal.pad_id() so that it casts values to INTs before concatenating them.
• pyp_newclasses/NewPedigree.preprocess has been fixed to handle parents that do not have their own entry in the pedigree file. They are added to the pedigree with an unknown sire and dam.
• Changed pyp_nrm/inbreeding() so that the output file written contains the original ID, the renumbered ID, and the CoI (in that order).
• Added a dictionary, "backmap", to pyp_newclasses/NewPedigree that maps renumbered IDs (keys) to original IDs (values). It is the reverse direction of that provided by idmap.
• Added pyp_graphics/plot_pct_founders_by_year() to plot the frequency of founders in each birth year. NOTE: This requires matplotlib. If matplotlib is not installed/cannot be imported, a value of 0 is returned.
• Fixed pyp_graphics/draw_pedigree() so that it labels animals with their original IDs instead of their renumbered IDs.
• Fixed pyp_graphics/draw_pedigree() so that it displays the gtitle.
• Fixed a typo in pyp_newclasses/NewAnimal.__init__() that broke proper birthyear assignment.
• Added pyp_graphics/plot_founders_by_year() to write a histogram of number-of-founders by year of birth. NOTE: This requires matplotlib. If matplotlib is not installed/cannot be imported, a value of 0 is returned.
• Changed pyp_demog/BASE_DEMOGRAPHIC_YEAR from 1950 to 1900. This brings it in line with the default birthyear of 1900 used in pyp_newclasses.
• Added pyp_demog/founders_by_year() which provides a dictionary, keyed by birthyear, of the number of founders with each birthyear.

• pyp_io/pyp_file_header() and pyp_io/pyp_file_footer() now work.
• Added pyp_metrics/effective_founders_lacy(), which is a re-write of pyp_metrics/a_effective_founders_lacy() that works with the new object model. Correctness was verified by comparing results against Table 3 in Lacy (1989) and Tables I and II in Boichard et al. (1997). You can use examples/new_lacy.py to verify the results.
• Fixed a nasty bug in pyp_metrics/a_effective_ancestors_definite() that was due to an indentation screwup when moving from one editor to another. Correctness was verified by comparing results against Tables I and II in Boichard et al. (1997). You can use examples/new_lacy.py to verify the results.
• Added pyp_utils/pyp_nice_time() which returns the current date and time as a nicely-formatted string.
• Added pyp_metrics/descendants() and pyp_metrics/founder_descendants() to support the rewritten pyp_metrics/effective_founders_lacy() routine.
• Added pyp_utils/assign_offspring(), which adds offspring of an animal to that animal's 'unks' list.
• Stubbed pyp_io/pyp_file_header() and pyp_io/pyp_file_footer() in preparation for standardizing the output files written by PyPedal.
• Added pyp_graphics module. It currently includes three functions from the ASPN Python Cookbook for visualizing the sparsity and the elements of matrices. I have also moved the draw_pedigree() function from pyp_utils to pyp_graphics. From now on, any functions related to visualization will go in pyp_graphics.
• It looks like the sons and daus lists get screwed up when the pedigree is renumbered, but I think that it is a consequence of the item below.
• When a pedigree that needs renumbering is read, pyp_utils/preprocess() throws an exception when trying to assign sex codes because it uses the sire's and dam's original IDs as keys. This represents fundamental breakage in the ordering of events in pedigree creation. I have sort-of hacked around this for the moment, but the bug is still there.
• Added a new pedigree format code, asdgb, to pyp_utils/preprocess().
• Added pyp_metrics/generation_lengths_all() which computes the average generation interval in years for each of the four selection paths (sire-son, sire-daughter, dam-son, and dam-daughter) for all births of a parent's offspring.
• Added pyp_utils/assign_sexes() which iterates over a renumbered PyPedal pedigree to update sexes of sires and dams based on knowledge of their sons and daughters. This seems to catch cases that are missed in pyp_utils/preprocess(), which needs to e cleaned up.
• Upon further examination, it seems like males and females are being correctly assigned. Hm...OK. Fixed a bug in pyp_utils/preprocess() that incorrectly assigned sires and dams with unknown parents to the sons and daus lists of the last animal in the pedigree. This was fixed by casting to an INT before a comparison with 0.
• See examples/generations.py -- sons and daughters are not being correctly assigned to foo.sons and foo.daus.
• Need to fix a bug in pyp_utils/new_preprocesss() in which unknown sires and dams (animals with IDs of 0) were being put into male, female, son, and daughter lists.
• Fixed a bug in pyp_utils/preprocesss() in which unknown sires and dams (animals with IDs of 0) were being put into male, female, son, and daughter lists.
• Added pyp_metrics/generation_lengths() which computes the average generation interval in years for each of the four selection paths (sire-son, sire-daughter, dam-son, and dam-daughter) for the oldest (first-born) of parents.
• Added pyp_metrics/num_traced_gens(), pyp_metrics/num_equiv_gens(), and pyp_metrics/pyp_partial_inbreeding().
• Lots of code cleanup in pyp_classes. Removed pad_id() and renamed pad_id_new() to pad_id().
• Removed the originalID and species attributes from the Animal() class.