Antoine Pitrou added the comment:

Here is a much faster patch, around 30x faster than the original code.

With exhuma's data set and tester.py, the original code gives:

$ time python3.4 tester.py 
Execution time: 5.949284339199949 seconds

real    0m30.152s
user    0m30.104s
sys     0m0.016s

The patched code gives:

$ time ./python tester.py 
Execution time: 0.25444041779992405 seconds

real    0m1.695s
user    0m1.681s
sys     0m0.012s


exhuma, perhaps you want to test with other data sets?

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Added file: http://bugs.python.org/file35228/faster_collapse.patch

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