Cannot convert expression to float in build_me_model.ipynb
bigsuicideparty opened this issue · 1 comments
bigsuicideparty commented
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 commented
Hello,
What version of cobrapy are you using? Cobrame is only compatible with versions <0.6.0