TypeError: in method 'Reaction_setReversible', argument 2 of type 'bool'

[bdelepine]

Problem description

Hello guys,

I was playing around when cobra refused to export a model to SBML with a TypeError: TypeError: in method 'Reaction_setReversible', argument 2 of type 'bool'.

I believe this is because I had one of my Reaction.lower_bound as a numpy.float64 instead of being a plain float, which in sbml.py would yield a numpy.bool_ at line reaction.setReversible((cobra_reaction.lower_bound < 0)), and ultimately would be refused by libsbml's Reaction_setReversible that is expecting a bool.

I would have expected that numpy.float to be valid bounds types.

I think the test in sbml.py should be cast to bool to prevent this error.

HTH, ++

Code Sample

import cobra.test

model = cobra.test.create_test_model("ecoli")
solution = model.optimize()

biomass = solution["BIOMASS_Ec_iJO1366_core_53p95M"]

model.reactions.BIOMASS_Ec_iJO1366_core_53p95M.bounds = (biomass * 0.5, 1000)         # this fails
#model.reactions.BIOMASS_Ec_iJO1366_core_53p95M.bounds = (float(biomass * 0.5), 1000)  # this works

failing_sbml_test = (model.reactions.BIOMASS_Ec_iJO1366_core_53p95M.lower_bound < 0)

print(type(failing_sbml_test))   # <class 'numpy.bool_'> or <class 'bool'>

cobra.io.write_sbml_model(model, "path.sbml")

Actual Output

Traceback:

TypeError                                 Traceback (most recent call last)
<ipython-input-29-4b9c356149ff> in <module>
     13 print(type(model.reactions.BIOMASS_Ec_iJO1366_core_53p95M.lower_bound), type(failing_sbml_test))
     14 
---> 15 cobra.io.write_sbml_model(model, "path.sbml")

XXX/cobra/io/sbml.py in write_sbml_model(cobra_model, filename, f_replace, **kwargs)
    829     f_replace: dict of replacement functions for id replacement
    830     """
--> 831     doc = _model_to_sbml(cobra_model, f_replace=f_replace, **kwargs)
    832 
    833     if isinstance(filename, string_types):

XXX/cobra/io/sbml.py in _model_to_sbml(cobra_model, f_replace, units)
   1014         reaction.setName(cobra_reaction.name)
   1015         reaction.setFast(False)
-> 1016         reaction.setReversible((cobra_reaction.lower_bound < 0))
   1017         _sbase_annotations(reaction, cobra_reaction.annotation)
   1018         _sbase_notes_dict(reaction, cobra_reaction.notes)

XXX/libsbml/__init__.py in setReversible(self, value)
  34480 
  34481         """
> 34482         return _libsbml.Reaction_setReversible(self, value)
  34483 
  34484 

TypeError: in method 'Reaction_setReversible', argument 2 of type 'bool'

Dependency Information

System Information ================== OS Linux OS-release 3.10.0-957.27.2.el7.x86_64 Python 3.7.4

Package Versions

cobra 0.16.0 depinfo 1.5.1 future 0.17.1 numpy 1.16.4 optlang 1.4.4 pandas 0.25.0 pip 19.2.2 python-libsbml-experimental 5.18.0 ruamel.yaml 0.16.5 setuptools 41.0.1 six 1.12.0 swiglpk 4.65.0 wheel 0.33.4

[gregmedlock]

I just came across the same incompatibility; it looks like libSBML will never accept numpy datatypes in bounds. @matthiaskoenig Would there be consequences to overriding this behavior within cobrapy by converting all numpy datatypes to native python floats when writing SBML (under the hood so that users aren't exposed to the issue)? I am guessing this is intentional within libsbml, but if not maybe the adjustment should be made in libsbml instead.

[matthiaskoenig]

No issue at all. I will just do a cast to float.

On Thu, Nov 14, 2019, 20:22 Greg Medlock [email protected] wrote:

I just came across the same incompatibility; it looks like libSBML will never accept numpy datatypes in bounds. @matthiaskoenig https://github.com/matthiaskoenig Would there be consequences to overriding this behavior within cobrapy by converting all numpy datatypes to native python floats when writing SBML (under the hood so that users aren't exposed to the issue)? I am guessing this is intentional within libsbml, but if not maybe the adjustment should be made in libsbml instead.

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