In some cases when using numpy arrays, using random.shuffle created duplicate data in the array.
An alternative is to use numpy.random.shuffle. If you're working with numpy already, this is the preferred method over the generic random.shuffle.
numpy.random.shuffle
Example
>>> import numpy as np
>>> import random
Using random.shuffle:
>>> foo = np.array([[1,2,3],[4,5,6],[7,8,9]])
>>> foo
array([[1, 2, 3],
[4, 5, 6],
[7, 8, 9]])
>>> random.shuffle(foo)
>>> foo
array([[1, 2, 3],
[1, 2, 3],
[4, 5, 6]])
Using numpy.random.shuffle:
>>> foo = np.array([[1,2,3],[4,5,6],[7,8,9]])
>>> foo
array([[1, 2, 3],
[4, 5, 6],
[7, 8, 9]])
>>> np.random.shuffle(foo)
>>> foo
array([[1, 2, 3],
[7, 8, 9],
[4, 5, 6]])