This discussion inspired me to refine Scalene's output further. Scalene now separates out CPU time spent in Python from time spent in C (that is, not executing in the interpreter). I think this is the best of both worlds: all CPU time is accounted for, and it's easy for users to see what code is running where. Thanks!

  sample-sample.py: % of CPU time =  99.58% out of   3.34s.
           | CPU %    | CPU %    | 
    Line   | (Python) | (C)      | [sample-sample.py]
  --------------------------------------------------------------------------------
       1   |          |          | #!/usr/bin/env python
       2   |          |          |  
       3   |          |          | import time
       4   |          |          |      
       5   |          |          | def timed(f):
       6   |          |          |     def f_timed(*args, **kwargs):
       7   |          |          |         t = time.time()
       8   |          |          |         r = f(*args, **kwargs)
       9   |          |          |         t = time.time() - t
      10   |          |          |         print('%s %.4f %s' % (f.__name__, t, r))
      11   |          |          |     return f_timed
      12   |          |          | 
      13   |          |          | @timed
      14   |          |          | def f1(n):
      15   |          |          |     s = 0
      16   |   6.61%  |   0.41%  |     for i in range(n):
      17   |  35.17%  |   3.97%  |         s += i
      18   |          |          |     return s
      19   |          |          | 
      20   |          |          | @timed
      21   |          |          | def f2(n):
      22   |   0.30%  |  53.53%  |     return sum(range(n))
      23   |          |          | 
      24   |          |          | @timed
      25   |          |          | def f3(t):
      26   |          |          |     time.sleep(t)
      27   |          |          |     return t
      28   |          |          | 
      29   |          |          | if __name__ == '__main__':
      30   |          |          |     f1(25000000)
      31   |          |          |     f2(75000000)
      32   |          |          |     f3(1.5)