How should I unit test a code-generator?

I started writing up a summary of my experience with my own code generator, then went back and re-read your question and found you had already touched upon the same issues yourself, focus on the execution results instead of the code layout/look.

Problem is, this is hard to test, the generated code might not be suited to actually run in the environment of the unit test system, and how do you encode the expected results?

I've found that you need to break down the code generator into smaller pieces and unit test those. Unit testing a full code generator is more like integration testing than unit testing if you ask me.

Recall that "unit testing" is only one kind of testing. You should be able to unit test the internal pieces of your code generator. What you're really looking at here is system level testing (a.k.a. regression testing). It's not just semantics... there are different mindsets, approaches, expectations, etc. It's certainly more work, but you probably need to bite the bullet and set up an end-to-end regression test suite: fixed C++ files -> SWIG interfaces -> python modules -> known output. You really want to check the known input (fixed C++ code) against expected output (what comes out of the final Python program). Checking the code generator results directly would be like diffing object files...

Yes, results are the ONLY thing that matters. The real chore is writing a framework that allows your generated code to run independently... spend your time there.