update

Author: TorkelE

src/networkapi.jl

@@ -585,21 +585,16 @@ function symmap_to_varmap(sys, symmap::Tuple)
     end
 end
 
-function symmap_to_varmap(sys, symmap::AbstractArray{Pair{T, V}}) where {T, V}
+function symmap_to_varmap(sys, symmap::AbstractArray{Pair{Symbol, T}}) where {T}
     [_symbol_to_var(sys, sym) => val for (sym, val) in symmap]
 end
 
-function symmap_to_varmap(sys, symmap::Dict{T, V}) where {T, V}
+function symmap_to_varmap(sys, symmap::Dict{Symbol, T}) where {T}
     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.
+# don't permute any other types and let varmap_to_vars handle erroring
 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.")
 
 ######################## reaction complexes and reaction rates ###############################

src/reaction_network.jl

@@ -370,7 +370,7 @@ function make_reaction_system(ex::Expr; name = :(gensym(:ReactionSystem)))
     variables = extract_syms(options, :variables)
 
     # Handles a (potential) noise scaling parameter.
-    #nosie_scaling_p_args = handle_noise_scaling_ps!(parameters_declared, options)
+    #noise_scaling_p_args = handle_noise_scaling_ps!(parameters_declared, options)
 
     # handle independent variables
     if haskey(options, :ivs)
@@ -417,6 +417,9 @@ function make_reaction_system(ex::Expr; name = :(gensym(:ReactionSystem)))
         push!(rxexprs.args, get_rxexprs(reaction))
     end
 
+    # Adds potentital noise scaling parameters.
+    #append!(ps.args, noise_scaling_p_args)
+    
     # Returns the rephrased expression.
     quote
         $ps
@@ -563,7 +566,7 @@ function get_pexpr(parameters_extracted, options)
     append!(pexprs.args, get_noise_scaling_pexpr(options))
     pexprs
 end
-# Extracts any decalred nosie scaling parameters.
+# Extracts any decalred noise scaling parameters.
 function get_noise_scaling_pexpr(options)
     haskey(options, :noise_scaling_parameters) || return []
     ns_expr = options[:noise_scaling_parameters]

src/reactionsystem.jl

@@ -1506,6 +1506,7 @@ function Base.convert(::Type{<:SDESystem}, rs::ReactionSystem;
                       default_u0 = Dict(), default_p = Dict(), defaults = _merge(Dict(default_u0), Dict(default_p)),
                       kwargs...)
     spatial_convert_err(rs::ReactionSystem, SDESystem)
+    isnothing(noise_scaling) && (noise_scaling = get_noise_scaling(rs)) # Required before final deprication of previous noise scaling functionality.
 
     flatrs = Catalyst.flatten(rs)
     error_if_constraints(SDESystem, flatrs)
@@ -1641,11 +1642,15 @@ end
 # SDEProblem from AbstractReactionNetwork
 function DiffEqBase.SDEProblem(rs::ReactionSystem, u0, tspan,
                                p = DiffEqBase.NullParameters(), args...;
-                               noise_scaling = get_noise_scaling(rs), name = nameof(rs),
+                               noise_scaling = nothing, name = nameof(rs),
                                combinatoric_ratelaws = get_combinatoric_ratelaws(rs),
                                include_zero_odes = true, checks = false,
                                check_length = false,
                                remove_conserved = false, kwargs...)
+    if !isnothing(noise_scaling) 
+        any(isnoisescalingparameter.(parameters(rs))) && error("You have declared some paraemters as noise scaling parameters, and also given a \"noise_scaling\" argument to SDEProblem. Please remove the \"noise_scaling\", as this way of scaling CLE noise is being depricated.")
+        @warn "Passing noise scaling input into SDEProblem will be depricated. New standard is to declare one (or several) paraemter as noise scaling parameters when the ReactionSystem is created. Please read https://docs.sciml.ai/Catalyst/stable/catalyst_applications/advanced_simulations/#Scaling-the-noise-magnitude-in-the-chemical-Langevin-equations." 
+    end
     u0map = symmap_to_varmap(rs, u0)
     pmap = symmap_to_varmap(rs, p)
     sde_sys = convert(SDESystem, rs; noise_scaling, name, combinatoric_ratelaws,

test/model_simulation/simulate_SDEs.jl

@@ -121,29 +121,6 @@ end
 
 ### Noise Scaling ###
 
-# Tests where a single noise scaling parameter is given directly to the SDEProblem.
-let
-    noise_scaling_network = @reaction_network begin (k1, k2), X1 ↔ X2 end
-    for repeat in 1:5
-        p = 1.0 .+ rand(rng, 2)
-        u0 = 10000 * (1.0 .+ rand(rng, 2))
-        sol001 = solve(SDEProblem(noise_scaling_network, u0, (0.0, 1000.0), vcat(p, 0.01),
-                                  noise_scaling = (@variables η1)[1]), ImplicitEM())
-        sol01 = solve(SDEProblem(noise_scaling_network, u0, (0.0, 1000.0), vcat(p, 0.1),
-                                 noise_scaling = (@variables η1)[1]), ImplicitEM())
-        sol1 = solve(SDEProblem(noise_scaling_network, u0, (0.0, 1000.0), vcat(p, 1.0),
-                                noise_scaling = (@variables η2)[1]), ImplicitEM())
-        sol10 = solve(SDEProblem(noise_scaling_network, u0, (0.0, 1000.0), vcat(p, 10.0),
-                                 noise_scaling = (@variables η3)[1]), ImplicitEM())
-        @test 2 * std(first.(sol001.u)[100:end]) < std(first.(sol01.u)[100:end])
-        @test 2 * std(last.(sol001.u)[100:end]) < std(last.(sol01.u)[100:end])
-        @test 2 * std(first.(sol01.u)[100:end]) < std(first.(sol1.u)[100:end])
-        @test 2 * std(last.(sol01.u)[100:end]) < std(last.(sol1.u)[100:end])
-        @test 2 * std(first.(sol1.u)[100:end]) < std(first.(sol10.u)[100:end])
-        @test 2 * std(last.(sol1.u)[100:end]) < std(last.(sol10.u)[100:end])
-    end
-end
-
 # Tests with multiple noise scaling parameters directly in the macro.
 let 
     noise_scaling_network_1 = @reaction_network begin 
@@ -160,10 +137,10 @@ let
         @noise_scaling_parameters η[1:2]
         (k1, k2), X1 ↔ X2 
     end
-    @unpack η = noise_scaling_network_2
-    sol_2_1 = solve(SDEProblem(noise_scaling_network_2, u0, (0.0, 1000.0), [:k1 => 2.0, :k2 => 0.66, η[1] => 2.0, η[2] => 2.0]), ImplicitEM(); saveat=1.0)
-    sol_2_2 = solve(SDEProblem(noise_scaling_network_2, u0, (0.0, 1000.0), [:k1 => 2.0, :k2 => 0.66, η[1] => 2.0, η[2] => 0.2]), ImplicitEM(); saveat=1.0)
-    sol_2_3 = solve(SDEProblem(noise_scaling_network_2, u0, (0.0, 1000.0), [:k1 => 2.0, :k2 => 0.66, η[1] => 0.2, η[2] => 0.2]), ImplicitEM(); saveat=1.0)
+    @unpack k1, k2, η = noise_scaling_network_2
+    sol_2_1 = solve(SDEProblem(noise_scaling_network_2, u0, (0.0, 1000.0), [k1 => 2.0, k2 => 0.66, η[1] => 2.0, η[2] => 2.0]), ImplicitEM(); saveat=1.0)
+    sol_2_2 = solve(SDEProblem(noise_scaling_network_2, u0, (0.0, 1000.0), [k1 => 2.0, k2 => 0.66, η[1] => 2.0, η[2] => 0.2]), ImplicitEM(); saveat=1.0)
+    sol_2_3 = solve(SDEProblem(noise_scaling_network_2, u0, (0.0, 1000.0), [k1 => 2.0, k2 => 0.66, η[1] => 0.2, η[2] => 0.2]), ImplicitEM(); saveat=1.0)
     @test var(sol_2_1[1,:]) > var(sol_2_2[1,:]) > var(sol_2_3[1,:]) 
 end
 
@@ -175,8 +152,7 @@ let
     end
     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, 4000.0]
+    @test SDEProblem(noise_scaling_network, u0, (0.0, 1000.0), p)[:η] == 0.0
 end
 
 # Complicated test with many combinations of options.
@@ -187,18 +163,16 @@ let
         (p, d), 0 ↔ X1 
         (k1, k2), X1 ↔ X2 
     end
-    @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]
+    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]
-    @test ss ≈ [200.0, 200.0]
+    sprob = SDEProblem(noise_scaling_network, u0, (0.0, 1000.0), p)
+    @test sprob[:η1] == sprob[:η2] == sprob[:η3] == sprob[:η4] == 0.0
 end
 
-# Tests that nosie scaling wor
 
 ### Checks Simulations Don't Error ###
 

test/model_simulation/u0_n_parameter_inputs.jl

@@ -71,24 +71,4 @@ let
             @test discrete_probs[1].u0 == discrete_probs[i].u0
         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