Handle noise parameter default values

Author: TorkelE

src/networkapi.jl

@@ -581,22 +581,24 @@ function symmap_to_varmap(sys, symmap::Tuple)
     if all(p -> p isa Pair{Symbol}, symmap)
         return ((_symbol_to_var(sys, sym) => val for (sym, val) in symmap)...,)
     else  # if not all entries map a symbol to value pass through
-        return symmapAny
+        return symmap
     end
 end
 
-function symmap_to_varmap(sys, symmap::AbstractArray{Pair{Any, T}}) where {T}
+function symmap_to_varmap(sys, symmap::AbstractArray{Pair{T, V}}) where {T, V}
     [_symbol_to_var(sys, sym) => val for (sym, val) in symmap]
 end
 
-function symmap_to_varmap(sys, symmap::Dict{Any, T}) where {T}
+function symmap_to_varmap(sys, symmap::Dict{T, V}) where {T, V}
     Dict(_symbol_to_var(sys, sym) => val for (sym, val) in symmap)
 end
 
 # don't permute any other types and let varmap_to_vars handle erroring.
 # If all keys are `Num`, conversion not needed.
 symmap_to_varmap(sys, symmap) = symmap
+symmap_to_varmap(sys, symmap::AbstractArray{Pair{SymbolicUtils.BasicSymbolic{Real}, T}}) where {T} = symmap
 symmap_to_varmap(sys, symmap::AbstractArray{Pair{Num, T}}) where {T} = symmap
+symmap_to_varmap(sys, symmap::Dict{SymbolicUtils.BasicSymbolic{Real}, T}) where {T} = symmap
 symmap_to_varmap(sys, symmap::Dict{Num, T}) where {T} = symmap
 #error("symmap_to_varmap requires a Dict, AbstractArray or Tuple to map Symbols to values.")
 

src/reaction_network.jl

@@ -568,10 +568,14 @@ function get_noise_scaling_pexpr(options)
     haskey(options, :noise_scaling_parameters) || return []
     ns_expr = options[:noise_scaling_parameters]
     for idx = length(ns_expr.args):-1:3
-        if ns_expr.args[idx] isa Symbol
-            insert!(ns_expr.args, idx+1, :([noisescalingparameter=true]))
-        elseif (ns_expr.args[idx] isa Expr) && (ns_expr.args[idx].head == :ref)
-            insert!(ns_expr.args, idx+1, :([noisescalingparameter=true]))
+        if (ns_expr.args[idx] isa Symbol) || # Parameter on form η.
+           (ns_expr.args[idx] isa Expr) && (ns_expr.args[idx].head == :ref) || # Parameter on form η[1:3].
+           (ns_expr.args[idx] isa Expr) && (ns_expr.args[idx].head == :(=)) # Parameter on form η=0.1.
+            if idx < length(ns_expr.args) && (ns_expr.args[idx+1] isa Expr)  && (ns_expr.args[idx+1].head == :vect)
+                push!(ns_expr.args[idx+1].args,:(noisescalingparameter=true))
+            else
+                insert!(ns_expr.args, idx+1, :([noisescalingparameter=true]))
+            end
         end
     end
     return ns_expr.args[3:end]

test/model_simulation/simulate_SDEs.jl

@@ -167,32 +167,35 @@ let
     @test var(sol_2_1[1,:]) > var(sol_2_2[1,:]) > var(sol_2_3[1,:]) 
 end
 
-# Tests using default values for nosie scaling.
+# Tests using default values for noise scaling.
 let
     noise_scaling_network = @reaction_network begin 
         @noise_scaling_parameters η=0.0
         (k1, k2), X1 ↔ X2 
     end
-    u0 = [:X1 => 1100.0, :X2 => 2900.0]
-    p = [:k1 => 2.0, :k2 => 0.66]
+    u0 = [:X1 => 1100.0, :X2 => 3900.0]
+    p = [:k1 => 2.0, :k2 => 0.5, :η=>0.0]
     ss = solve(SDEProblem(noise_scaling_network, u0, (0.0, 1000.0), p), ImplicitEM())[end]
-    @test ss ≈ [1000.0, 3000.0]
+    @test ss ≈ [1000.0, 4000.0]
 end
 
 # Complicated test with many combinations of options.
 let
     noise_scaling_network = @reaction_network begin 
         @parameters k1 par1 [description="Parameter par1"] par2 η1 [noisescalingparameter=true]
-        @noise_scaling_parameters η2=0.0 [description="Parameter η2"] η3=1.0 η4 [description="Parameter η4"] 
+        @noise_scaling_parameters η2=0.0 [description="Parameter η2"] η3=1.0 η4
         (p, d), 0 ↔ X1 
         (k1, k2), X1 ↔ X2 
     end
-    @unpack X1, η4 = noise_scaling_network
+    @unpack X1, η4, p = noise_scaling_network
     u0 = [X1 => 500.0, :X2 => 500.0]
     p = [p => 20.0, :d => 0.1, :η1 => 0.0, :η3 => 0.0, η4 => 0.0, :k1 => 2.0, :k2 => 2.0, :par1 => 1000.0, :par2 => 1000.0]
 
+    @test getdescription(parameters(noise_scaling_network)[2]) == "Parameter par1"
+    @test getdescription(parameters(noise_scaling_network)[8]) == "Parameter η2"
+
     ss = solve(SDEProblem(noise_scaling_network, u0, (0.0, 1000.0), p), ImplicitEM())[end]
-    ss ≈ [200.0, 200.0]
+    @test ss ≈ [200.0, 200.0]
 end
 
 # Tests that nosie scaling wor

test/model_simulation/u0_n_parameter_inputs.jl

@@ -72,3 +72,23 @@ let
         end
     end
 end
+
+# Tests uding mix of symbols and symbolics in input.
+let
+    test_network = @reaction_network begin 
+        (p1, d1), 0 ↔ X1 
+        (p2, d2), 0 ↔ X2 
+    end
+    @unpack p1, d1, p2, d2, X1, X2 = test_network
+    u0_1 = [X1 => 0.7, X2 => 3.6]
+    u0_2 = [:X1 => 0.7, X2 => 3.6]
+    u0_3 = [:X1 => 0.7, :X2 => 3.6]
+    p_1 = [p1 => 1.2, d1 => 4.0, p2 => 2.5, d2 =>0.1]
+    p_2 = [:p1 => 1.2, d1 => 4.0, :p2 => 2.5, d2 =>0.1]
+    p_3 = [:p1 => 1.2, :d1 => 4.0, :p2 => 2.5, :d2 =>0.1]
+
+    ss_base = solve(ODEProblem(test_network, u0_1, (0.0, 10.0), p_1), Tsit5())[end]
+    for u0 in [u0_1, u0_2, u0_3], p in [p_1, p_2, p_3]
+        @test ss_base == solve(ODEProblem(test_network, u0, (0.0, 10.0), p), Tsit5())[end]
+    end
+end