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Fix sphinx and doxygen, add test debug statement, change tolerance
This commit fixes all sphinx or doxygen warnings, adds a statement to debug the python reactor test, test_tolerances, and changes the problem tolerance from 1e-6 to 1e-5. This test should still test what intended. The change fixes the test for the MoleReactor class on Windows. Thought about how tolerances are set for mole reactors is needed.
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