up

Author: TorkelE

HISTORY.md

@@ -24,6 +24,7 @@ rn = @reaction_network begin
 end
 getnoisescaling(rn)
 ```
+- `SDEProblem` no longer takes the `noise_scaling` argument (she above for new approach to handle noise scaling).
 - Changed fields of internal `Reaction` structure. `ReactionSystems`s saved using `serialize` on previous Catalyst versions cannot be loaded using this (or later) versions.
 - Simulation of spatial ODEs now supported. For full details, please see https://github.com/SciML/Catalyst.jl/pull/644 and upcoming documentation. Note that these methods are currently considered alpha, with the interface and approach changing even in non-breaking Catalyst releases.
 - LatticeReactionSystem structure represents a spatial reaction network:

src/reactionsystem.jl

@@ -945,16 +945,6 @@ function get_metadata(reaction::Reaction, md_key::Symbol)
     return metadata[findfirst(isequal(md_key, entry[1]) for entry in get_metadata_dict(reaction))][2]
 end
 
-"""
-    get_noise_scaling(reaction::Reaction)
-
-Retrives the nosie scaling factor for the reaction's noise term (as generated by the reaction in an SDE). 
-If a specific noise scaling expression have been provided in the reactions "noise_scaling" metadata,
-returns that. If not, returns `1.0`.
-"""
-function get_noise_scaling(reaction::Reaction)
-    has_metadata(reaction, :noise_scaling) ?  get_metadata(reaction, :noise_scaling) : 1.0
-end
 
 ######################## Conversion to ODEs/SDEs/jump, etc ##############################
 
@@ -1075,7 +1065,7 @@ function assemble_diffusion(rs, sts, ispcs; combinatoric_ratelaws = true,
 
     for (j, rx) in enumerate(get_rxs(rs))
         rlsqrt = sqrt(abs(oderatelaw(rx; combinatoric_ratelaw = combinatoric_ratelaws)))
-        rlsqrt *= get_noise_scaling(rx)
+        rlsqrt *= getnoisescaling(rx)
         remove_conserved && (rlsqrt = substitute(rlsqrt, depspec_submap))
 
         for (spec, stoich) in rx.netstoich
@@ -1497,7 +1487,6 @@ function Base.convert(::Type{<:SDESystem}, rs::ReactionSystem;
                       default_u0 = Dict(), default_p = Dict(), defaults = _merge(Dict(default_u0), Dict(default_p)),
                       noise_scaling = nothing, # To be removed (used for deprication message only).
                       kwargs...)
-    isnothing(noise_scaling) || error("Supplying a noise_scaling agument to SDESystems have been depricated. Please see the \"Scaling the noise magnitude in the chemical Langevin equations\" section of the \"Advanced Simulation Options\" page of the documentation for the new approach.")
     spatial_convert_err(rs::ReactionSystem, SDESystem)
 
     flatrs = Catalyst.flatten(rs)
@@ -1548,7 +1537,6 @@ function Base.convert(::Type{<:JumpSystem}, rs::ReactionSystem; name = nameof(rs
                       default_u0 = Dict(), default_p = Dict(), defaults = _merge(Dict(default_u0), Dict(default_p)),
                       noise_scaling = nothing, # To be removed (used for deprication message only).
                       kwargs...)
-    isnothing(noise_scaling) || error("Supplying a noise_scaling agument to SDESystems have been depricated. Please see the \"Scaling the noise magnitude in the chemical Langevin equations\" section of the \"Advanced Simulation Options\" page of the documentation for the new approach.")
     spatial_convert_err(rs::ReactionSystem, JumpSystem)
 
     (remove_conserved !== nothing) &&