old_contents: from pytfa.redgem.redgem import RedGEM
  
  from pytfa.io import import_matlab_model
  from pytfa.io.base import load_thermoDB
  from pytfa.thermo.tmodel import ThermoModel
  from pytfa.io import  read_compartment_data, apply_compartment_data, read_lexicon, annotate_from_lexicon
  
  
  
  path_to_model = 'models/small_ecoli.mat'
  thermoDB = "data/thermo_data.thermodb"
  carbon_uptake = 60000
  growth = 0.5
  
  model = import_matlab_model(path_to_model)
  thermo_data = load_thermoDB(thermoDB)
  lexicon = read_lexicon('models/iJO1366/lexicon.csv')
  compartment_data = read_compartment_data('models/iJO1366/compartment_data.json')
  
  tfa_model = ThermoModel(thermo_data, model)
  annotate_from_lexicon(tfa_model, lexicon)
  apply_compartment_data(tfa_model, compartment_data)
  
  tfa_model.name = 'Lumped Model'
  
  path_to_params = 'tests/redgem_params.yml'
  
  redgem = RedGEM(tfa_model, path_to_params, False)
  redgem.run()
  
new_contents: from pytfa.redgem.redgem import RedGEM
  
  from pytfa.io import import_matlab_model
  from pytfa.io.base import load_thermoDB
  from pytfa.thermo.tmodel import ThermoModel
  from pytfa.io import  read_compartment_data, apply_compartment_data, read_lexicon, annotate_from_lexicon
  
  
  path_to_model = 'models/small_ecoli.mat'
  thermoDB = "data/thermo_data.thermodb"
  path_to_lexicon = 'models/iJO1366/lexicon.csv'
  path_to_compartment_data = 'models/iJO1366/compartment_data.json'
  
  model = import_matlab_model(path_to_model)
  thermo_data = load_thermoDB(thermoDB)
  lexicon = read_lexicon(path_to_lexicon)
  compartment_data = read_compartment_data(path_to_compartment_data)
  
  tfa_model = ThermoModel(thermo_data, model)
  annotate_from_lexicon(tfa_model, lexicon)
  apply_compartment_data(tfa_model, compartment_data)
  
  tfa_model.name = 'Lumped Model'
  
  path_to_params = 'tests/redgem_params.yml'
  
  redgem = RedGEM(tfa_model, path_to_params, False)
  redgem.run()
  
subject: Remove unused parameters in test script