ups

Author: TorkelE

src/reactionsystem.jl

@@ -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

@@ -92,29 +92,38 @@ 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) && !isequivalent(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
 
 # 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)
-    (ignore_ep_metadata(sym1.metadata) != ignore_ep_metadata(sym2.metadata)) && (return false)
+    in_skip_ep_metadata(md1, md2) || (return false)
+    in_skip_ep_metadata(md2, md1) || (return false)
     (typeof(sym1) != typeof(sym2)) && (return false)
     return true
 end
-ignore_ep_metadata(metadata) = setdiff(metadata, [Catalyst.EdgeParameter => true])
+# Checks if metadata 1 is in metadata 2 (but always return true if md1 is the edge parameter metadata.
+function in_skip_ep_metadata(md1, md2)
+    (md1 == ep_metadata) && (return true)
+    for md1 in sym1.metadata
+        (md1 in md2) || return false
+    end
+    return true
+end
 
 # Implements custom `==`.
 """

test/dsl/dsl_options.jl

@@ -347,6 +347,7 @@ end
 
 # Tests that parameter type designation works.
 let
+    # Creates a model.
     rn = @reaction_network begin
         @parameters begin
             k1
@@ -366,7 +367,8 @@ let
         (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}
@@ -377,6 +379,14 @@ let
     @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/miscellaneous_tests/symbolic_stoichiometry.jl

@@ -19,7 +19,7 @@ include("../test_functions.jl")
 
 # Checks that systems with symbolic stoichiometries, created using different approaches, are identical.
 let 
-    @parameters p k d n1 n2 n3
+    @parameters p k d::Float64 n1::Int64 n2 n3
     @species X(t) Y(t)
     rxs1 = [
         Reaction(p, nothing, [X], nothing, [n1])
@@ -29,13 +29,14 @@ let
     rs1 = ReactionSystem(rxs1, t; name = :rs)
 
     rxs2 = [
-        @reaction p, 0 --> n1*X
+        @reaction p, 0 --> $n1*X
         @reaction k, n2*X --> n3*Y
-        @reaction d, Y --> 0
+        @reaction $d, Y --> 0
     ]
     rs2 = ReactionSystem(rxs2, t; name = :rs)
 
     rs3 = @reaction_network rs begin
+        @parameters d::Float64 n1::Int64
         p, 0 --> n1*X
         k, n2*X --> n3*Y
         d, Y --> 0
@@ -44,15 +45,17 @@ let
     @test rs1 == rs2 == rs3
     @test issetequal(unknowns(rs1), [X, Y])
     @test issetequal(parameters(rs1), [p, k, d, n1, n2, n3])
+    @test unwrap(d) isa SymbolicUtils.BasicSymbolic{Float64}
+    @test unwrap(n1) isa SymbolicUtils.BasicSymbolic{Int64}
 end
 
 # Declares a network, parameter values, and initial conditions, to be used for the next couple of tests.
 begin
     # Prepares parameters and species and their values.
     @parameters k α::Int64
     @species A(t), B(t), C(t), D(t)
-    u0_1 = [A => 3.0, B => 2.0, C => 3.0, D => 5.0]
-    ps_1 = [k => 5.0, α => 2.0]
+    u0_1 = (A => 3.0, B => 2.0, C => 3.0, D => 5.0)
+    ps_1 = (k => 5.0, α => 2)
     u0_2 = [Int64(u[2]) for u in u0_1]
     ps_2 = [Int64(p[2]) for p in ps_1]
     τ = 1.5