-
Archives
- June 2010
- May 2010
- March 2010
- January 2010
- December 2009
- November 2009
- October 2009
- September 2009
- August 2009
- July 2009
- June 2009
- May 2009
- March 2009
- February 2009
- January 2009
- November 2008
- October 2008
- September 2008
- August 2008
- July 2008
- June 2008
- May 2008
- April 2008
- March 2008
- February 2008
- January 2008
- December 2007
- November 2007
- October 2007
- September 2007
- August 2007
- July 2007
- June 2007
- May 2007
- April 2007
- March 2007
- February 2007
- January 2007
- December 2006
- November 2006
- October 2006
- September 2006
- August 2006
- July 2006
- June 2006
- May 2006
- April 2006
- March 2006
- February 2006
- January 2006
- December 2005
-
Meta
Tag Archives: PyPedal
PyPedal Article Published in Python Magazine
The March 2009 issue of Python Magazine is on the news-stands. Guess whose article is mentioned on the cover?
PyPedal Release Candidate 7 Highlights Need for Unit Testing
Many thanks to Matthieu Authier for reporting several bugs, which in turn led to more bugs. The hunt started with broken code in examples/new_amatrix.py, which led to bugs in several subroutines in pyp_nrm, which exposed some small side issues. Notably, … Continue reading
PyPedal Release Candidate 6 Fixes Logging
I broke logging a while ago and didn’t notice it. Now it;s fixed. I’ve also modified pyp_metrics/renumber() so that it now cleans-up after itself by deleting ID map files when renumbering is complete; if you need to retain the file … Continue reading
PyPedal Release Candidate 4 is Easier to Install
I made some changes to __init__.py and setup.py that make PyPedal installable (is that a word?) using the very Pythonic “python setup.py install” method. I also updated the discussion of installation in the manual. However, in order to get this … Continue reading
This is a Quick Test of the Google Syntax Highlighter for WordPress Plugin
I read about the Google Syntax Highlighter for WordPress in a blog entry by Jacob Gube describing several purportedly-useful WordPress extensions. The plugin sounds like just the thing to pretty-up some entries I’m working on about PyPedal. Here’s a simple … Continue reading
An Article on PyPedal May Appear in Python Magazine
I received this morning an e-mail from the Technical Editor of Python Magazine asking if I’d be interested in writing an article about PyPedal. I hope to talk with with him soon to get more details and see if we … Continue reading
PyPedal Release Candidate 3 Features an Inbreeding Bugfix and Refactored Database Handling
The third release candidate of PyPedal 2.0 has been released. It includes a minor bugfix to pyp_nrm/inbreeding_vanraden() and a completely-refactored database backend. After a few days of writing, and a false start with SQLAlchemy, I’ve completely rewritten the database backend … Continue reading
PyPedal Release Candidates Feature Fewer Bugs!
One supposes that the titles of this entry is not particularly informative because that is, in fact, the point of release candidates: to iron out as many lingering bugs as possible. What do you from a guy with hair like … Continue reading
PyPedal now calculates ancestral inbreeding coefficients
PyPedal can now calculate ancestral inbreeding coefficients using either the recursion equation of Ballou (1997) or the gene dropping method of Suwanlee et al. (2007). Ancestral inbreeding is the probability of an individual inheriting an allele that has undergone inbreeding … Continue reading
Posted in Articles
Tagged ancestral inbreeding, conservation genetics, genetics, PyPedal
Leave a comment
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