Tag Archives: PyPedal

PyPedal Article Published in Python Magazine

Posted on March 30, 2009 by jcole

The March 2009 issue of Python Magazine is on the news-stands. Guess whose article is mentioned on the cover?

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PyPedal Release Candidate 7 Highlights Need for Unit Testing

Posted on May 8, 2008 by jcole

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 →

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PyPedal Release Candidate 6 Fixes Logging

Posted on May 1, 2008 by jcole

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 →

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PyPedal Release Candidate 4 is Easier to Install

Posted on April 9, 2008 by jcole

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 →

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This is a Quick Test of the Google Syntax Highlighter for WordPress Plugin

Posted on April 4, 2008 by jcole

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 →

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An Article on PyPedal May Appear in Python Magazine

Posted on March 31, 2008 by jcole

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 →

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PyPedal Release Candidate 3 Features an Inbreeding Bugfix and Refactored Database Handling

Posted on March 28, 2008 by jcole

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 →

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PyPedal Release Candidates Feature Fewer Bugs!

Posted on March 12, 2008 by jcole

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 →

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PyPedal now calculates ancestral inbreeding coefficients

Posted on February 13, 2008 by jcole

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 →

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PyPedal now calculates partial inbreeding coefficients

Posted on February 8, 2008 by jcole

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 →

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