[erdewit]

It's that the array access of numpy is surprisingly slow compared to a Python list:

  lst = [0]
  %timeit lst[0] = 1
  33.9 ns ± 0.0415 ns per loop (mean ± std. dev. of 7 runs, 10000000 loops each)
  
  arr = np.empty(1, dtype=int)  
  %timeit arr[0] = 1
  73.4 ns ± 0.306 ns per loop (mean ± std. dev. of 7 runs, 10000000 loops each)