Replicate and enhance all necessary functionality from Matlab in Python.
Matlab is no longer needed, primary use of Gemini is now from Python.

Simulations are completely defined in config.nml.
If additional functions are added to Python, add fields / group to config.nml and Python will read it so your function can access the new parameters. Likewise for Fortran.

Main Python programs:

• job.py: setup and run a simulation, or generate HPC batch script if HPC detected
• vis/plotall.py: plot all quantities output from simulation
• script_utils/compare_all.py: compare simulation outputs with reference output from same files (validate code changes)
• setup/model_setup.py: setup a simulation without running it