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Do I understand this correctly, then

(1)  doctests are still run, and contribute to coverage

(2)  The code that creates a test should not be measured for 
coverage. ???

(3)  Because doctests are in the same file as the code, 
rather than the other tests, they get mistaken for code 
whose own coverage should be measured.

If so, it seems like the right solution is to add a 
subdirectory for test-portions-that-didn't-run, and put 
doctests there instead of in the main directory.  

Or are you saying that is OK if some of the tests (and some 
of the doctests) don't actually run in full?

-jJ