MAINT: Clean up code in calculations.py module (#112)

* Restructures all calculation functions so 
the symbolic output is first in the code path

* Changes all `output_strings`/`key` mismatch
errors to use the same error message

* Changes various variable names to make
code more readable

* Simplifies kinetic rate (name) capture
in `calc_state_probs` and `calc_sigma` for
the `ouput_strings=True` code path

* Simplifies returns for all functions so
it is clear what the difference is between
the `output_strings` code paths