gemini3d/GEMINI: all Python PyGemini: initial release

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