Thermotools

- Changing bias_energy_sequence axes in util's sample restriction function
- Minor changes in util's transition count function
- Replacing lse module by additional functions in util module
- Fix missing break statement in dTRAM estimation
- Making dTRAM prior available on Python level
- Adding loglikelihood/increment tracking to WHAM/dTRAM
- WHAM/dTRAM code cleanup

- Fixing float argument for range()
- Refactoring API
- Adding function to restrict samples and state sequence to a set of conf states

- Fixing docstrings
- Adding util module for counting state visits and transitions
- Adding msmtools (>=1.1) and scipy (>=0.11) dependencies

- Fixing MANIFEST.in

- Changing f_K_i to be b_K_i + f_i in dTRAM/WHAM
- Adding MBAR
- Refactoring WHAM/dTRAM
- Adding self-consistent iteration functions to pyx files in WHAM/MBAR/dTRAM

- Adding and refactoring unit tests
- Refactoring dTRAM
- Placing normalisation into iterate_fi
- Adding placeholders for TRAM/xTRAM