up

Author: TorkelE

HISTORY.md

@@ -24,7 +24,7 @@ rn = @reaction_network begin
     @parameters η
     k, 2X --> X2, [noise_scaling=η]
 end
-get_noise_scaling(rn)
+getnoisescaling(rn)
 ```
 - `SDEProblem` no longer takes the `noise_scaling` argument (see 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.

docs/pages.jl

@@ -8,20 +8,20 @@ pages = Any[
     "Model Creation and Properties" => Any[
         "model_creation/dsl_basics.md",
         "model_creation/dsl_advanced.md",
-        "model_creation/programmatic_CRN_construction.md",
-        "model_creation/compositional_modeling.md",
-        "model_creation/constraint_equations.md",
+        #"model_creation/programmatic_CRN_construction.md",
+        #"model_creation/compositional_modeling.md",
+        #"model_creation/constraint_equations.md",
         # Events.
-        "model_creation/parametric_stoichiometry.md",# Distributed parameters, rates, and initial conditions.
+        #"model_creation/parametric_stoichiometry.md",# Distributed parameters, rates, and initial conditions.
         # Loading and writing models to files.
         # Model visualisation.
         "model_creation/network_analysis.md",
         "model_creation/chemistry_related_functionality.md",
         "Model creation examples" => Any[
             "model_creation/examples/basic_CRN_library.md",
             "model_creation/examples/programmatic_generative_linear_pathway.md",
-            "model_creation/examples/hodgkin_huxley_equation.md",
-            "model_creation/examples/smoluchowski_coagulation_equation.md"
+            #"model_creation/examples/hodgkin_huxley_equation.md",
+            #"model_creation/examples/smoluchowski_coagulation_equation.md"
         ]
     ],
     "Model simulation" => Any[
@@ -67,6 +67,6 @@ pages = Any[
     #     # Contributor's guide.
     #     # Repository structure.
     # ],
-    "FAQs" => "faqs.md",
-    "API" => "api.md"
+    #"FAQs" => "faqs.md",
+    #"API" => "api.md"
 ]

docs/src/assets/Project.toml

@@ -1,18 +1,25 @@
 [deps]
+BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
 BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665"
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 DiffEqParamEstim = "1130ab10-4a5a-5621-a13d-e4788d82bd4c"
-DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DynamicalSystems = "61744808-ddfa-5f27-97ff-6e42cc95d634"
+GlobalSensitivity = "af5da776-676b-467e-8baf-acd8249e4f0f"
 HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327"
+IncompleteLU = "40713840-3770-5561-ab4c-a76e7d0d7895"
+JumpProcesses = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5"
 Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
+LinearSolve = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
 Optim = "429524aa-4258-5aef-a3af-852621145aeb"
 Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba"
+OptimizationBBO = "3e6eede4-6085-4f62-9a71-46d9bc1eb92b"
 OptimizationNLopt = "4e6fcdb7-1186-4e1f-a706-475e75c168bb"
 OptimizationOptimJL = "36348300-93cb-4f02-beb5-3c3902f8871e"
 OptimizationOptimisers = "42dfb2eb-d2b4-4451-abcd-913932933ac1"
@@ -21,37 +28,39 @@ Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 QuasiMonteCarlo = "8a4e6c94-4038-4cdc-81c3-7e6ffdb2a71b"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 SciMLSensitivity = "1ed8b502-d754-442c-8d5d-10ac956f44a1"
-Setfield = "efcf1570-3423-57d1-acb7-fd33fddbac46"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 SteadyStateDiffEq = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f"
 StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
 StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544"
 Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 
 [compat]
+BenchmarkTools = "1.5"
 BifurcationKit = "0.3"
+CairoMakie = "0.12"
 Catalyst = "13"
-DataFrames = "1"
-DiffEqParamEstim = "2.1"
-DifferentialEquations = "7.7"
+DataFrames = "1.6"
+DiffEqParamEstim = "2.2"
 Distributions = "0.25"
 Documenter = "1.4.1"
-HomotopyContinuation = "2.6"
-Latexify = "0.15, 0.16"
-ModelingToolkit = "9.5"
-NonlinearSolve = "3.4.0"
-Optim = "1"
-Optimization = "3.19"
-OptimizationNLopt = "0.1.8"
-OptimizationOptimJL = "0.1.14"
-OptimizationOptimisers = "0.1.1"
-OrdinaryDiffEq = "6"
-Plots = "1.36"
-SciMLBase = "2.13"
-SciMLSensitivity = "7.19"
-Setfield = "1.1"
-SpecialFunctions = "2.1"
-SteadyStateDiffEq = "2.0.1"
-StochasticDiffEq = "6"
-StructuralIdentifiability = "0.5.1"
-Symbolics = "5.14"
+DynamicalSystems = "3.3"
+GlobalSensitivity = "2.6"
+HomotopyContinuation = "2.9"
+IncompleteLU = "0.2"
+JumpProcesses = "9.11"
+Latexify = "0.16"
+LinearSolve = "2.30"
+ModelingToolkit = "9.15"
+NonlinearSolve = "3.12"
+Optim = "1.9"
+Optimization = "3.25"
+OrdinaryDiffEq = "6.80.1"
+Plots = "1.40"
+QuasiMonteCarlo = "0.3"
+SciMLBase = "2.39"
+SciMLSensitivity = "7.60"
+SpecialFunctions = "2.4"
+SteadyStateDiffEq = "2.2"
+StochasticDiffEq = "6.65"
+StructuralIdentifiability = "0.5.7"
+Symbolics = "5.28"

src/Catalyst.jl

@@ -93,7 +93,6 @@ end
 include("reaction.jl")
 export isspecies
 export Reaction
-export get_noise_scaling, has_noise_scaling
 
 # The `ReactionSystem` structure and its functions.
 include("reactionsystem.jl")

src/reaction.jl

@@ -377,8 +377,8 @@ function ModelingToolkit.get_variables!(set, rx::Reaction)
     for stoichs in (rx.substoich, rx.prodstoich), stoich in stoichs
         (stoich isa BasicSymbolic) && get_variables!(set, stoich)
     end
-    if has_noise_scaling(rx)
-        get_variables!(set, get_noise_scaling(rx))
+    if hasnoisescaling(rx)
+        get_variables!(set, getnoisescaling(rx))
     end
     return (set isa AbstractVector) ? unique!(set) : set
 end
@@ -440,7 +440,7 @@ end
 
 
 ### Reaction Metadata Implementation ###
-# These are currently considered internal, but can be used by public accessor functions like get_noise_scaling.
+# These are currently considered internal, but can be used by public accessor functions like getnoisescaling.
 
 """
 getmetadata_dict(reaction::Reaction)
@@ -507,7 +507,7 @@ end
 
 # Noise scaling.
 """
-has_noise_scaling(reaction::Reaction)
+hasnoisescaling(reaction::Reaction)
 
 Returns `true` if the input reaction has the `noise_scaing` metadata field assigned, else `false`.
 
@@ -517,15 +517,15 @@ Arguments:
 Example:
 ```julia
 reaction = @reaction k, 0 --> X, [noise_scaling=0.0]
-has_noise_scaling(reaction)
+hasnoisescaling(reaction)
 ```
 """
-function has_noise_scaling(reaction::Reaction)
+function hasnoisescaling(reaction::Reaction)
     return hasmetadata(reaction, :noise_scaling)
 end
 
 """
-get_noise_scaling(reaction::Reaction)
+getnoisescaling(reaction::Reaction)
 
 Returns `noise_scaing` metadata field for the input reaction.
 
@@ -535,11 +535,11 @@ Arguments:
 Example:
 ```julia
 reaction = @reaction k, 0 --> X, [noise_scaling=0.0]
-get_noise_scaling(reaction)
+getnoisescaling(reaction)
 ```
 """
-function get_noise_scaling(reaction::Reaction)
-    if has_noise_scaling(reaction)
+function getnoisescaling(reaction::Reaction)
+    if hasnoisescaling(reaction)
         return getmetadata(reaction, :noise_scaling)
     else
         error("Attempts to access noise_scaling metadata field for a reaction which does not have a value assigned for this metadata.")
@@ -548,7 +548,7 @@ end
 
 # Description.
 """
-has_description(reaction::Reaction)
+hasdescription(reaction::Reaction)
 
 Returns `true` if the input reaction has the `description` metadata field assigned, else `false`.
 
@@ -558,15 +558,15 @@ Arguments:
 Example:
 ```julia
 reaction = @reaction k, 0 --> X, [description="A reaction"]
-has_description(reaction)
+hasdescription(reaction)
 ```
 """
-function has_description(reaction::Reaction)
+function hasdescription(reaction::Reaction)
     return hasmetadata(reaction, :description)
 end
 
 """
-get_description(reaction::Reaction)
+getdescription(reaction::Reaction)
 
 Returns `description` metadata field for the input reaction.
 
@@ -576,11 +576,11 @@ Arguments:
 Example:
 ```julia
 reaction = @reaction k, 0 --> X, [description="A reaction"]
-get_description(reaction)
+getdescription(reaction)
 ```
 """
-function get_description(reaction::Reaction)
-    if has_description(reaction)
+function getdescription(reaction::Reaction)
+    if hasdescription(reaction)
         return getmetadata(reaction, :description)
     else
         error("Attempts to access `description` metadata field for a reaction which does not have a value assigned for this metadata.")
@@ -589,7 +589,7 @@ end
 
 # Misc.
 """
-has_misc(reaction::Reaction)
+hasmisc(reaction::Reaction)
 
 Returns `true` if the input reaction has the `misc` metadata field assigned, else `false`.
 
@@ -599,15 +599,15 @@ Arguments:
 Example:
 ```julia
 reaction = @reaction k, 0 --> X, [misc="A reaction"]
-misc(reaction)
+hasmisc(reaction)
 ```
 """
-function has_misc(reaction::Reaction)
+function hasmisc(reaction::Reaction)
     return hasmetadata(reaction, :misc)
 end
 
 """
-get_misc(reaction::Reaction)
+getmisc(reaction::Reaction)
 
 Returns `misc` metadata field for the input reaction.
 
@@ -617,7 +617,7 @@ Arguments:
 Example:
 ```julia
 reaction = @reaction k, 0 --> X, [misc="A reaction"]
-get_misc(reaction)
+getmisc(reaction)
 ```
 
 Notes:
@@ -629,7 +629,7 @@ creating a `ReactionSystem` programmatically (in which case any symbolic variabl
 
 """
 function get_misc(reaction::Reaction)
-    if has_misc(reaction)
+    if hasmisc(reaction)
         return getmetadata(reaction, :misc)
     else
         error("Attempts to access `misc` metadata field for a reaction which does not have a value assigned for this metadata.")

src/reactionsystem.jl

@@ -497,7 +497,7 @@ function make_ReactionSystem_internal(rxs_and_eqs::Vector, iv, us_in, ps_in; spa
         end
 
         # Extract all quantities encountered in relevant `Reaction` metadata.
-        has_noise_scaling(rx) && findvars!(ps, us, get_noise_scaling(rx), ivs, vars)
+        hasnoisescaling(rx) && findvars!(ps, us, getnoisescaling(rx), ivs, vars)
     end
 
     # Extracts any species, variables, and parameters that occur in (non-reaction) equations.

src/reactionsystem_conversions.jl

@@ -121,7 +121,7 @@ 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)))
-        has_noise_scaling(rx) && (rlsqrt *= get_noise_scaling(rx))
+        hasnoisescaling(rx) && (rlsqrt *= getnoisescaling(rx))
         remove_conserved && (rlsqrt = substitute(rlsqrt, depspec_submap))
 
         for (spec, stoich) in rx.netstoich

test/reactionsystem_core/reaction.jl

@@ -116,10 +116,10 @@ let
     r1 = Reaction(k, [X], [X2], [2], [1])
     r2 = Reaction(k, [X], [X2], [2], [1]; metadata=[:noise_scaling => η])
 
-    @test !Catalyst.has_noise_scaling(r1)
-    @test Catalyst.has_noise_scaling(r2)
-    @test_throws Exception Catalyst.get_noise_scaling(r1)
-    @test isequal(Catalyst.get_noise_scaling(r2), η)
+    @test !Catalyst.hasnoisescaling(r1)
+    @test Catalyst.hasnoisescaling(r2)
+    @test_throws Exception Catalyst.getnoisescaling(r1)
+    @test isequal(Catalyst.getnoisescaling(r2), η)
 end
 
 # Tests the description metadata.
@@ -131,10 +131,10 @@ let
     r1 = Reaction(k, [X], [X2], [2], [1])
     r2 = Reaction(k, [X], [X2], [2], [1]; metadata=[:description => "A reaction"])
 
-    @test !Catalyst.has_description(r1)
-    @test Catalyst.has_description(r2)
-    @test_throws Exception Catalyst.get_description(r1)
-    @test isequal(Catalyst.get_description(r2), "A reaction")
+    @test !Catalyst.hasdescription(r1)
+    @test Catalyst.hasdescription(r2)
+    @test_throws Exception Catalyst.getdescription(r1)
+    @test isequal(Catalyst.getdescription(r2), "A reaction")
 end
 
 # Tests the misc metadata.
@@ -146,8 +146,8 @@ let
     r1 = Reaction(k, [X], [X2], [2], [1])
     r2 = Reaction(k, [X], [X2], [2], [1]; metadata=[:misc => ('M', :M)])
 
-    @test !Catalyst.has_misc(r1)
-    @test Catalyst.has_misc(r2)
-    @test_throws Exception Catalyst.get_misc(r1)
-    @test isequal(Catalyst.get_misc(r2), ('M', :M))
+    @test !Catalyst.hasmisc(r1)
+    @test Catalyst.hasmisc(r2)
+    @test_throws Exception Catalyst.getmisc(r1)
+    @test isequal(Catalyst.getmisc(r2), ('M', :M))
 end

test/simulation_and_solving/simulate_SDEs.jl

@@ -2,6 +2,7 @@
 
 # Fetch packages.
 using Catalyst, Statistics, StochasticDiffEq, Test
+using Catalyst: getnoisescaling
 
 # Sets stable rng number.
 using StableRNGs
@@ -325,8 +326,8 @@ let
     @test issetequal([X, H], species(rs))
     @test issetequal([X, H, h], unknowns(rs))
     @test issetequal([p, d, η], parameters(rs))
-    @test isequal(get_noise_scaling(reactions(rs)[1]), η*H + 1)
-    @test isequal(get_noise_scaling(reactions(rs)[2]), h)
+    @test isequal(getnoisescaling(reactions(rs)[1]), η*H + 1)
+    @test isequal(getnoisescaling(reactions(rs)[2]), h)
 end
 
 # Tests the `remake_noise_scaling` function.
@@ -369,9 +370,9 @@ let
 
     # Checks that systems have the correct noise scaling terms.
     rn = set_default_noise_scaling(rn, 0.5)
-    rn1_noise_scaling = [get_noise_scaling(rx) for rx in Catalyst.get_rxs(rn)]
-    rn2_noise_scaling = [get_noise_scaling(rx) for rx in Catalyst.get_rxs(Catalyst.get_systems(rn)[1])]
-    rn_noise_scaling = [get_noise_scaling(rx) for rx in reactions(rn)]
+    rn1_noise_scaling = [getnoisescaling(rx) for rx in Catalyst.get_rxs(rn)]
+    rn2_noise_scaling = [getnoisescaling(rx) for rx in Catalyst.get_rxs(Catalyst.get_systems(rn)[1])]
+    rn_noise_scaling = [getnoisescaling(rx) for rx in reactions(rn)]
     @test issetequal(rn1_noise_scaling, [2.0, 0.5])
     @test issetequal(rn2_noise_scaling, [5.0, 0.5])
     @test issetequal(rn_noise_scaling, [2.0, 0.5, 5.0, 0.5])