[SciPy-User] Bottleneck

Keith Goodman kwgoodman@gmail....
Tue Nov 30 15:49:36 CST 2010


On Tue, Nov 30, 2010 at 1:34 PM, Christopher Barker
<Chris.Barker@noaa.gov> wrote:
> On 11/30/10 11:50 AM, Keith Goodman wrote:
>> Bottleneck is a collection of fast, NumPy array functions written in Cython.
>>
>> https://github.com/kwgoodman/bottleneck
>>
>> I'm almost ready for a first preview release. If anyone could install
>> the package (directions in readme) and run the unit tests on windows
>> or mac or 32-bit linux, I'd be very interested in the results.
>
> OK -- tested on Mac OS-X 10.6, Intel, 32 bit Python 2.6.6
>
> 1) How necessary is scipy as a dependency? It'd be nice to have these
> for numpy-only stuff. As  a rule, Scipy is way too inter-meshed as it is
> -- I'd love to have more packages that you could easily install and use
> without the whole scipy package.

I use SciPy for benchmarking (scipy.stats.nanmean, nanstd, etc). I
also unit test the moving window functions against a version that uses
scipy.ndimage. But I could make scipy optional in a later release.

> -- off to get scipy installed on this system --
>
> In [6]: scipy.__version__
> Out[6]: '0.8.0'
>
> In [2]: bottleneck.test()
> Running unit tests for bottleneck
> NumPy version 1.5.1
> NumPy is installed in
> /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy
> Python version 2.6.6 (r266:84374, Aug 31 2010, 11:00:51) [GCC 4.0.1
> (Apple Inc. build 5493)]
> nose version 0.11.4
>
> WOW! a LOT of these warnings:
>
> Warning: invalid value encountered in divide
> (and similar)

Yeah, I started getting those too when I upgraded to numpy 1.5.1. Any ideas?

> But:
>
> Ran 10 tests in 14.709s
>
> OK
> Out[7]: <nose.result.TextTestResult run=10 errors=0 failures=0>
>
> So -- looking good!

Thank you so much. Mac OS X: check!


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