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