Problem with CONSERVED_MOIETIES calculation

[matthiaskoenig]

When setting the the conserved moites load option the following model cannot be loaded any more. This worked without any problem for the model before.

import roadrunner
print(roadrunner.__version__)
!wget https://raw.githubusercontent.com/matthiaskoenig/multiscale-galactose/develop/python/multiscalepy/multiscale/examples/models/demo/Koenig_demo_10_annotated.xml -O test.xml

roadrunner.Config.setValue(roadrunner.Config.LOADSBMLOPTIONS_CONSERVED_MOIETIES, True)
r = roadrunner.RoadRunner("test.xml")

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-14-f3b417378487> in <module>()
      5 
      6 roadrunner.Config.setValue(roadrunner.Config.LOADSBMLOPTIONS_CONSERVED_MOIETIES, True)
----> 7 r = roadrunner.RoadRunner("test.xml")
      8 
      9 # r = roadrunner.RoadRunner("https://raw.githubusercontent.com/matthiaskoenig/multiscale-galactose/develop/python/multiscalepy/multiscale/examples/models/demo/Koenig_demo_10_annotated.xml")

/usr/local/lib/python2.7/dist-packages/roadrunner/roadrunner.pyc in _new_init(self, *args)
   2632 
   2633     def _new_init(self, *args):
-> 2634         RoadRunner._swig_init(self, *args)
   2635         RoadRunner._makeProperties(self)
   2636 

/usr/local/lib/python2.7/dist-packages/roadrunner/roadrunner.pyc in __init__(self, *args)
   1898     __getattr__ = lambda self, name: _swig_getattr(self, RoadRunner, name)
   1899     def __init__(self, *args):
-> 1900         this = _roadrunner.new_RoadRunner(*args)
   1901         try: self.this.append(this)
   1902         except: self.this = this

RuntimeError: error converting document to conserved moieties, at rrllvm::ModelGeneratorContext::ModelGeneratorContext(const string&, unsigned int)

[0u812]

Our bundled version of libSBML doesn't support fbc version 2 and it doesn't have the logic to convert the document even though you have fbc:required="false" in your SBML. Apart from that, roadrunner was throwing away the fbc namespace, which I fixed (so now you can use fbc version 1 in the SBML). 1/2 way there. I'll add a separate issue for upgrading the bundled libSBML.

[luciansmith]

For what it's worth, libsbml provides an fbc l2 to l1 converter (and the reverse).

[0u812]

Updated sys-bio/libroadrunner-deps to libSBML 5.12.0 (sys-bio/libroadrunner-deps#1). fbc version 2 support is available.