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The problem in this case is different, actually. It's the comparison:
 if o_time <= i_time:
 # generated file is older, touch
 need_touch = True
In check_rule. The script is pretty quick so when it touches both Python-ast.h and .c they get the same stat time exactly. In the next run, then, this comparison succeeds and .c is touched again.
I'm not sure what's the right way to go about this? Changing the comparison to < may theoretically miss cases in which the input was updated an epsilon after it auto-generated its output, and the change will go unnoticed. A different solution would be to introduce a micro-wait between each 'touch' to make sure that transitive dependencies don't need to be revisited in the future.