Bounds checks and wraparound checks can be removed ONLY IF the code will otherwise never try to take advantage of those Python indexing features (i.e. boundscheck: x[i] for i > len(x) triggers IndexError; wraparound: x[i] for -len(x) <= i < 0 returns x[len(i) - i]). So you have to look through when indexing is performed in the code, assess what the indices are (where they get their values) and if for expression x[i], i can ever be <0 or >=len(x) for any data that may be passed to the function in question.

You can, for instance, perform more validation outside this function if necessary to avoid those possibilities.

Have you made this check?

I am perfectly aware of that hence added it to the Todo yesterday

I think I have commented that I have added the cython checks without elaborating on whether or not I did the "index checking" which I believe that is the source of confusion. Apologies.

Ok, I went through the code and I'm convinced that the things in the TODO can never happen, assuming that _centers_sparse is not used directly by anyone, giving labels as a non encoded array.

@ogrisel @TomDLT Quick look?

I agree this looks safe. +1

LGTM.