Allow parameters to be passed as a vector of :symbol => value pairs

src/build_rhs.jl

@@ -139,6 +139,6 @@ Return an `ODEProblem` for use in `DifferentialEquations`. This function implici
 calls `convert(ODEFunction, sys)`. It is usually more efficient to create an `ODEFunction` 
 first and then use that to create `ODEProblem`s.
 """
-function Base.convert(::Type{ODEProblem}, sys::FSPSystem, u0, tint, p=NullParameters())
-    ODEProblem(convert(ODEFunction, sys), u0, tint, p)
+function Base.convert(::Type{ODEProblem}, sys::FSPSystem, u0, tint, pmap=NullParameters())
+    ODEProblem(convert(ODEFunction, sys), u0, tint, pmap_to_p(sys, pmap))
 end

src/build_rhs_ss.jl

@@ -72,6 +72,6 @@ Base.convert(::Type{ODEFunction}, sys::FSPSystem, ::SteadyState) = ODEFunction{t
 
 Return a `SteadyStateProblem` for use in `DifferentialEquations.
 """
-function Base.convert(::Type{SteadyStateProblem}, sys::FSPSystem, u0, p=NullParameters())
-    SteadyStateProblem(convert(ODEFunction, sys, SteadyState()), u0, p)
+function Base.convert(::Type{SteadyStateProblem}, sys::FSPSystem, u0, pmap=NullParameters())
+    SteadyStateProblem(convert(ODEFunction, sys, SteadyState()), u0, pmap_to_p(sys, pmap))
 end

src/fspsystem.jl

@@ -49,3 +49,8 @@ function compile_ratefunc(ex_rf, params)
     ex = :((idx_in, t, $(params...)) -> $(ex_rf)) |> MacroTools.flatten
     @RuntimeGeneratedFunction(ex)
 end
+
+function pmap_to_p(sys::FSPSystem, pmap)
+    pmap_conv = eltype(pmap) <: Pair{Symbol} ? Catalyst.symmap_to_varmap(sys.rs, pmap) : pmap
+    ModelingToolkit.varmap_to_vars(pmap_conv, Catalyst.parameters(sys.rs)) 
+end

src/matrix.jl

@@ -84,8 +84,8 @@ Chemical Master Equation. `dims` is a tuple denoting the dimensions of the FSP a
 `ps` is the tuple of parameters. The sparse matrix works on the flattened version
 of the state obtained using `vec`.
 """
-function Base.convert(::Type{SparseMatrixCSC}, sys::FSPSystem, dims::NTuple, ps, t::Real)
-    create_sparsematrix(sys, dims, ps, t)
+function Base.convert(::Type{SparseMatrixCSC}, sys::FSPSystem, dims::NTuple, pmap, t::Real)
+    create_sparsematrix(sys, dims, pmap_to_p(sys, pmap), t)
 end
 
 """
@@ -94,6 +94,6 @@ end
 Convert the reaction system into a sparse matrix defining the right-hand side of the
 Chemical Master Equation, steady-state version.
 """
-function Base.convert(::Type{SparseMatrixCSC}, sys::FSPSystem, dims::NTuple, ps, ::SteadyState)
-    create_sparsematrix_ss(sys, dims, ps)
+function Base.convert(::Type{SparseMatrixCSC}, sys::FSPSystem, dims::NTuple, pmap, ::SteadyState)
+    create_sparsematrix_ss(sys, dims, pmap_to_p(sys, pmap))
 end