[Biopython-dev] [Bug 2657] Improved Bio/Statistics/lowess.py

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2657





------- Comment #11 from eric.pruitt at gmail.com  2008-11-15 11:29 EST -------
(In reply to comment #10)
> A few comments:
> 
> 1) Is there a reason to use numpy.abs instead of Python's built-int abs? Timing
> these two functions suggests that they are equally fast.
> 2) I have no objection against James' suggestion to speed up the code. The
> original call to numpy.linalg.solve was probably overkill.
> 3) Can you submit a unit test that does not use scipy and rpy? We should avoid
> adding additional dependencies to Biopython.
> 4) In the long run, I am not sure whether Biopython is the right place for the
> lowess function. Probably NumPy or Matplotlib would be better. (that shouldn't
> stop us from improving the code here, though).
> 

Yes, I only had the scipy and rpy dependencies in my unit test because I wanted
to have something to compare your function to when I was going to first use it
in my code and to make sure it worked after I made changes to it.


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