fix bidirectional math and completion of ODESystems

Author: paulflang

src/reactions.jl

@@ -30,7 +30,7 @@ Infer forward and reverse components of bidirectional kineticLaw
 """
 function get_unidirectional_components(bidirectional_math)
     bm = ModelingToolkit.value(bidirectional_math)  #  Symbolics.tosymbol(bidirectional_math)
-    bm = simplify(bm; expand = true)
+    bm = expand(simplify(bm))
     if !SymbolicUtils.isadd(bm)
         @warn "Cannot separate bidirectional kineticLaw `$bidirectional_math` to forward and reverse part. Setting forward to `$bidirectional_math` and reverse to `0`. Stochastic simulations will be inexact."
         return (bidirectional_math, Num(0))

src/systems.jl

@@ -39,8 +39,9 @@ See also [`Model`](@ref) and [`ODESystemImporter`](@ref).
 """
 function SBML.readSBML(sbmlfile::String, ::ODESystemImporter;
         include_zero_odes::Bool = true, kwargs...)  # Returns an MTK.ODESystem
-    convert(ODESystem, readSBML(sbmlfile, ReactionSystemImporter(), kwargs...),
+    odesys = convert(ODESystem, readSBML(sbmlfile, ReactionSystemImporter(), kwargs...),
         include_zero_odes = include_zero_odes)
+    complete(odesys)
 end
 
 """
@@ -108,7 +109,8 @@ See also [`ReactionSystem`](@ref).
 function ModelingToolkit.ODESystem(model::SBML.Model; include_zero_odes::Bool = true,
         kwargs...)
     rs = ReactionSystem(model; kwargs...)
-    convert(ODESystem, rs; include_zero_odes = include_zero_odes)
+    odesys = convert(ODESystem, rs; include_zero_odes = include_zero_odes)
+    complete(odesys)
 end
 
 function get_mappings(model::SBML.Model)

test/systems.jl

@@ -93,9 +93,9 @@ isequal(nameof(odesys), :odesys)
 
 odesys = ODESystem(readSBML(sbmlfile))
 m = readSBML(sbmlfile)
-trueeqs = Equation[Differential(IV)(s1) ~ -(k1 * s1 * s2) / c1,
+trueeqs = Equation[Differential(IV)(s1) ~ -((k1 * s1 * s2) / c1),
     Differential(IV)(s1s2) ~ (k1 * s1 * s2) / c1,
-    Differential(IV)(s2) ~ -(k1 * s1 * s2) / c1]
+    Differential(IV)(s2) ~ -((k1 * s1 * s2) / c1)]
 @test isequal(Catalyst.get_eqs(odesys), trueeqs)
 @test isequal(Catalyst.get_iv(odesys), IV)
 @test isequal(Catalyst.get_unknowns(odesys), [s1, s1s2, s2])