CLN: Cleaned up some directories
PY: Generated Figures 2-4 in python
JL: Updated figures.jl
PY: No longer using numpy matrix
INFO: mcmc_vars.txt describes kind and type of all vars in mcmc loop'
PY: Updated main python to not use negative indexes. Should make Cython/Numba faster.

Still need to update functions to do the same
PY: Now all functions avoid negative indexing
PY: Began modularizing main mcmc loop
PY: cleaned up imports and added some run-time user params
PY: MCMC loop fully modularized
INFO: Groups mcmc_vars.txt into types of arguments
PY: First numba implementation. 18% speedup. not bad, but we can do better
INFO: Note in todo.todo to find better func names