This is certainly a bug. It has been mentioned before, but there was no comment. shuffle() doesn't handle arrays.

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from numpy import * from numpy.random import * a = arange(12) a.shape = (6,2) a array([[ 0, 1], [ 2, 3], [ 4, 5], [ 6, 7], [ 8, 9], [10, 11]]) shuffle(a) a array([[ 0, 1], [ 2, 3], [ 2, 3], [ 0, 1], [ 4, 5], [10, 11]])

This is with numpy 1.0. The [0, 1] element was duplicated. That's not right. Tom Holroyd, Ph.D. We experience the world not as it is, but as we expect it to be.