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When ipdb.set_trace() is called, it calls this function:
def update_stdout():
# setup stdout to ensure output is available with nose
io.stdout = sys.stdout = sys.__stdout__
This results in output being written back to the terminal where the notebook was launched, instead of appearing in the notebook itself. It will do the wrong thing in any context where you want the output to be redirected. Commenting out the call to this function makes it behave as expected.
I'm not sure what's the right heuristic to guess whether output should be redirected or not.