'make test' intersperses stdout and logging with test results

Makes diagnosis messages easier to spot, to help debugging.
DEBUG: atomType prints warning whenever its incrementRadical is changed.

Something in one of the unit tests is changing this when it shouldn't be.
Give error message when failing some groupTests unit tests.

The self.assertTrue() method can report a message when it fails,
which helps diagnose the problem.
Fix unit test for AtomType which was changing things that shouldn't change.

To test whether the AtomType.setActions() method works, the unit test for
it would change all the properties of the "R" atom type to be those of "Cd".
This then messes up later unit tests that depend on "R" being "R"!!
Specifically, the functional group atom type tests.

We now test the setActions() method on a dummy test atomType.
Revert "DEBUG: atomType prints warning whenever its incrementRadical is changed."

This reverts commit f86a9036ddbde2d34f2ff1b1b1d2134135ef8edb.
It was only needed for debugging purposes.
Added comment to TransportData about redundancy of calculateCollisionFrequency

calculateCollisionFrequency is duplicated in rmgpy.pdep.configuration.
Maybe it should be in one place only.