Several files (equilibrium_odes.py, two_component_system_odes.py, two_component_system_odes_fitter.py, metabolism_constraints.py, others) written by one piece of upstream code (write_metabolic_constraints_file.py, write_ode_file.py) and executed by another (where?). This is confusing to both humans and code inspection tools, largely undocumented, and its relationship with version control is unclear.
Several files (equilibrium_odes.py, two_component_system_odes.py, two_component_system_odes_fitter.py, metabolism_constraints.py, others) written by one piece of upstream code (write_metabolic_constraints_file.py, write_ode_file.py) and executed by another (where?). This is confusing to both humans and code inspection tools, largely undocumented, and its relationship with version control is unclear.