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Draft: No Setup files dependency in tests

Nikos Karastathis requested to merge no-Setupfiles-dependency into master

closes #462 (closed) and #401

The purpose of this MR is to completely decouple the SetupEnvironment and SetupStack dependecies in the unit tests.

The unit tests should use a specific environment so the original Setup files stay as general as possible. I have specified the environment needed for the tests to be successful and I have added a refractive index interface on the original SetupEnvironment file.

That should be related to #461 if I am not mistaken.

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