Hi, author here.

Yeah, the active set implementation in Cython is relatively slow - see [1] for where I discussed how I benchmarked the existing algorithm and demonstrated the PAVA implementation was faster.

Then again, until two days ago the Cython active set algorithm was the production implementation of isotonic regression in scikit-learn, so it's not like it was a strawman example that I made up.

[1]: http://tullo.ch/articles/speeding-up-isotonic-regression/