deprecation error in sklearn about empty array without any empty array in my code

Question

I am just playing around encoding and decoding but I get this error from sklearn:

Warning (from warnings module): File \"C:\\Python36\\lib\\site-packa

Answer 1

TLDR: You can ignore the warning. It is caused by sklearn doing something internally that is not quite ideal.

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The warning is actually caused by numpy, which deprecated truth testing on empty arrays:

The long and short is that truth-testing on empty arrays is dangerous, misleading, and not in any way useful, and should be deprecated.

This means one is not supposed to do something like if array: to check if array is empty. However, sklearn does this in the 0.19.1 release:

    diff = np.setdiff1d(y, np.arange(len(self.classes_)))
    if diff:
        raise ValueError("y contains new labels: %s" % str(diff))

Because your version of numpy is recent enough it complains and issues a warning.

The problem has been fixed in sklearn's current master branch, so I'd expect the fix to be included in the next release.

Answer 2

After updated numpy, the warning was cleared away:

conda update numpy

You can also update it by pip or something else.