Cannot convert expression to float in build_me_model.ipynb

[bigsuicideparty]

I am running into an error with the build_me_model.ipynb:

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
/Users/bsp/unix/ecolime/ecolime/build_me_model.ipynb Cell 5' in <cell line: 4>()
      2 ijo_directory = join(flat_files.ecoli_files_dir, 'iJO1366.json')
      3 ijo = cobra.io.load_json_model(ijo_directory)
----> 4 me = cobrame.MEModel('iJL1678b-ME')
      6 # ME-models require special OptLang interface if cobrapy version >= 0.6.0
      7 # If cannot import SymbolicParameter, assume using cobrapy
      8 # versions <= 0.5.11
      9 try:

File /opt/homebrew/lib/python3.9/site-packages/cobrame/core/model.py:29, in MEModel.__init__(self, *args)
     27 self._biomass_dilution.add_metabolites({self._biomass: -1})
     28 self.add_reactions([self._biomass_dilution])
---> 29 self._biomass_dilution.upper_bound = mu
     30 self._biomass_dilution.lower_bound = mu
     31 # maintenance energy

File /opt/homebrew/lib/python3.9/site-packages/cobra/util/context.py:111, in wrapper(self, new_value)

File /opt/homebrew/lib/python3.9/site-packages/cobra/core/reaction.py:268, in upper_bound(self, value)
    266 # Rebuild the model with the new independent genes/metabolites
    267 self._metabolites = {}
--> 268 self.add_metabolites(new_metabolites)
    269 self._genes = set()
    270 for k in new_genes:

File /opt/homebrew/lib/python3.9/site-packages/cobra/core/reaction.py:220, in update_variable_bounds(self)
    217         return "system_boundary"
    218     return None
--> 220 @property
    221 def model(self):
    222     """returns the model the reaction is a part of"""
    223     return self._model

File /opt/homebrew/lib/python3.9/site-packages/sympy-1.10.1-py3.9.egg/sympy/core/expr.py:345, in Expr.__float__(self)
    343 if result.is_number and result.as_real_imag()[1]:
    344     raise TypeError("Cannot convert complex to float")
--> 345 raise TypeError("Cannot convert expression to float")

Any idea what might be the source of this error?

[coltonlloyd]

Hello,

What version of cobrapy are you using? Cobrame is only compatible with versions <0.6.0