Merge pull request #340 from LCSB-BioCore/mk-sbml050-compat

SBML-0.5.0 compat

Project.toml

@@ -30,7 +30,7 @@ MAT = "0.10"
 MacroTools = "0.5.6"
 OSQP = "0.6"
 OrderedCollections = "1.4"
-SBML = "0.4"
+SBML = "0.4, 0.5"
 Tulip = "0.7"
 julia = "1"
 

src/base/types/SBMLModel.jl

@@ -182,6 +182,7 @@ function Base.convert(::Type{SBMLModel}, mm::MetabolicModel)
                     metabolite_formula(mm, mid),
                     metabolite_charge(mm, mid),
                     nothing, # initial amount
+                    nothing, # initial concentration
                     nothing, # only substance unit flags
                     _sbml_export_notes(metabolite_notes(mm, mid)),
                     _sbml_export_annotation(metabolite_annotations(mm, mid)),
@@ -200,7 +201,8 @@ function Base.convert(::Type{SBMLModel}, mm::MetabolicModel)
                         x -> _unparse_grr(SBML.GeneProductAssociation, x),
                         reaction_gene_association(mm, rid),
                     ),
-                    nothing,
+                    nothing, # no kinetic math
+                    true, # reversible by default
                     _sbml_export_notes(reaction_notes(mm, rid)),
                     _sbml_export_annotation(reaction_annotations(mm, rid)),
                 ) for (ri, rid) in enumerate(rxns)