[Biopython-dev] Statistics code

Michiel de Hoon mjldehoon at yahoo.com
Thu Apr 3 00:13:15 UTC 2008

> >  Its not out of the question, but what exactly do you need from SciPy?
> I know that this will sound ridiculous, but, in the long run I will
> need almost everything.
I don't think we should include a dependency now because we may need it in the long run.

> Bio.Statistics has not much content now...
I agree, and probably it is not a good idea to have too much statistics code in Biopython. Such code would fit in better in a numerical or statistics library.

> SciPy is a stable project, not an obscure library.
While this is true, in my experience SciPy is also difficult to install. It may mean fewer people using your code because they don't want to go through the hassle of installing SciPy. Particularly users coming from a biology rather than a computer science background.

Previously we also discussed switching from the old Numerical Python to the new NumPy. I've heard rumors that the NumPy documentation will be declared open at the SciPy conference this year. Not having this documentation was my biggest argument against NumPy. In my understanding, NumPy has more functionality than Numeric. Maybe it has better statistics support also?


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