James,
You're doing it correctly.

We put the converted C files in the repository so that users are not 
required to have cython to build scikit-learn.  One way you can limit 
the number of changes from a small tweak in the .pyx file is  to use the 
same cython version between conversions.
    Jake

On 10/05/2012 03:39 PM, James Bergstra wrote:
> Every time I change a pyx file, I have to run cython, and then
> hundreds of lines change in the corresponding C file, which is under
> git.  This makes various git utilities hard to use, and fills the repo
> with cython output.  Am I doing things wrong?
>
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