Merge pull request #797 from SciML/handle_different_paraemter_types

Handle different parameters types

Author: TorkelE

src/reactionsystem.jl

@@ -500,7 +500,7 @@ struct ReactionSystem{V <: NetworkProperties} <:
     """Dependent unknown variables representing species"""
     species::Vector{BasicSymbolic{Real}}
     """Parameter variables. Must not contain the independent variable."""
-    ps::Vector{BasicSymbolic{Real}}
+    ps::Vector{Any}
     """Maps Symbol to corresponding variable."""
     var_to_name::Dict{Symbol, Any}
     """Equations for observed variables."""
@@ -546,6 +546,11 @@ struct ReactionSystem{V <: NetworkProperties} <:
                             name, systems, defaults, connection_type, nps, cls, cevs, devs,
                             metadata = nothing, complete = false; checks::Bool = true)
 
+        # Checks that all parameters have the appropriate Symbolics type.
+        for p in ps
+            (p isa Symbolics.BasicSymbolic) || error("Parameter $p is not a `BasicSymbolic`. This is required.")
+        end
+
         # unit checks are for ODEs and Reactions only currently
         nonrx_eqs = Equation[eq for eq in eqs if eq isa Equation]
         if checks && isempty(sivs)

src/spatial_reaction_systems/spatial_reactions.jl

@@ -92,26 +92,28 @@ function check_spatial_reaction_validity(rs::ReactionSystem, tr::TransportReacti
     end
 
     # Checks that the species does not exist in the system with different metadata.
-    if any([isequal(tr.species, s) && !isequivalent(tr.species, s) for s in species(rs)]) 
+    if any(isequal(tr.species, s) && !isequivalent(tr.species, s) for s in species(rs)) 
         error("A transport reaction used a species, $(tr.species), with metadata not matching its lattice reaction system. Please fetch this species from the reaction system and used in transport reaction creation.")
     end
-    if any([isequal(rs_p, tr_p) && !equivalent_metadata(rs_p, tr_p) 
-            for rs_p in parameters(rs), tr_p in Symbolics.get_variables(tr.rate)]) 
+    if any(isequal(rs_p, tr_p) && !isequivalent(rs_p, tr_p) 
+            for rs_p in parameters(rs), tr_p in Symbolics.get_variables(tr.rate)) 
         error("A transport reaction used a parameter with metadata not matching its lattice reaction system. Please fetch this parameter from the reaction system and used in transport reaction creation.")
     end
 
     # Checks that no edge parameter occur among rates of non-spatial reactions.
-    if any([!isempty(intersect(Symbolics.get_variables(r.rate), edge_parameters)) for r in reactions(rs)])
+    if any(!isempty(intersect(Symbolics.get_variables(r.rate), edge_parameters)) for r in reactions(rs))
         error("Edge paramter(s) were found as a rate of a non-spatial reaction.")
     end
 end
-equivalent_metadata(p1, p2) = isempty(setdiff(p1.metadata, p2.metadata, [Catalyst.EdgeParameter => true]))
 
 # Since MTK's "isequal" ignores metadata, we have to use a special function that accounts for this.
 # This is important because whether something is an edge parameter is defined in metadata.
+const ep_metadata = Catalyst.EdgeParameter => true
 function isequivalent(sym1, sym2)
-    !isequal(sym1, sym2) && (return false)
-    (sym1.metadata != sym2.metadata) && (return false)
+    isequal(sym1, sym2) || (return false)
+    any((md1 != ep_metadata) && !(md1 in sym2.metadata) for md1 in sym1.metadata) && (return false)
+    any((md2 != ep_metadata) && !(md2 in sym1.metadata) for md2 in sym2.metadata) && (return false)
+    (typeof(sym1) != typeof(sym2)) && (return false)
     return true
 end
 

test/dsl/dsl_options.jl

@@ -4,6 +4,7 @@
 
 # Fetch packages.
 using Catalyst, ModelingToolkit, OrdinaryDiffEq, Plots, Test
+using Symbolics: unwrap
 
 # Sets the default `t` to use.
 t = default_t()
@@ -344,6 +345,50 @@ let
     @test merge(ModelingToolkit.defaults(rn28), defs28) == ModelingToolkit.defaults(rn27)
 end
 
+# Tests that parameter type designation works.
+let
+    # Creates a model.
+    rn = @reaction_network begin
+        @parameters begin
+            k1
+            l1
+            k2::Float64 = 2.0
+            l2::Float64
+            k3::Int64 = 2, [description="A parameter"]
+            l3::Int64
+            k4::Float32, [description="Another parameter"]
+            l4::Float32
+            k5::Rational{Int64}
+            l5::Rational{Int64}
+        end
+        (k1,l1), X1 <--> Y1
+        (k2,l2), X2 <--> Y2
+        (k3,l3), X3 <--> Y3
+        (k4,l4), X4 <--> Y4
+        (k5,l5), X5 <--> Y5
+    end
+
+    # Checks parameter types.
+    @test unwrap(rn.k1) isa SymbolicUtils.BasicSymbolic{Real}
+    @test unwrap(rn.l1) isa SymbolicUtils.BasicSymbolic{Real}
+    @test unwrap(rn.k2) isa SymbolicUtils.BasicSymbolic{Float64}
+    @test unwrap(rn.l2) isa SymbolicUtils.BasicSymbolic{Float64}
+    @test unwrap(rn.k3) isa SymbolicUtils.BasicSymbolic{Int64}
+    @test unwrap(rn.l3) isa SymbolicUtils.BasicSymbolic{Int64}
+    @test unwrap(rn.k4) isa SymbolicUtils.BasicSymbolic{Float32}
+    @test unwrap(rn.l4) isa SymbolicUtils.BasicSymbolic{Float32}
+    @test unwrap(rn.k5) isa SymbolicUtils.BasicSymbolic{Rational{Int64}}
+    @test unwrap(rn.l5) isa SymbolicUtils.BasicSymbolic{Rational{Int64}}
+
+    # Checks that other parameter properties are assigned properly.
+    @test !ModelingToolkit.hasdefault(unwrap(rn.k1))
+    @test ModelingToolkit.getdefault(unwrap(rn.k2)) == 2.0
+    @test ModelingToolkit.getdefault(unwrap(rn.k3)) == 2
+    @test ModelingToolkit.getdescription(unwrap(rn.k3)) == "A parameter"
+    @test ModelingToolkit.getdescription(unwrap(rn.k4)) == "Another parameter"
+    @test !ModelingToolkit.hasdescription(unwrap(rn.k5))
+end
+
 ### Observables ###
 
 # Test basic functionality.