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Author: TorkelE

docs/src/assets/Project.toml

@@ -29,6 +29,7 @@ QuasiMonteCarlo = "8a4e6c94-4038-4cdc-81c3-7e6ffdb2a71b"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 SciMLSensitivity = "1ed8b502-d754-442c-8d5d-10ac956f44a1"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
+StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 SteadyStateDiffEq = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f"
 StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
 StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544"
@@ -54,12 +55,17 @@ ModelingToolkit = "9.15"
 NonlinearSolve = "3.12"
 Optim = "1.9"
 Optimization = "3.25"
+OptimizationBBO = "0.2.1"
+OptimizationNLopt = "0.2.1"
+OptimizationOptimJL = "0.3.1"
+OptimizationOptimisers = "0.2.1"
 OrdinaryDiffEq = "6.80.1"
 Plots = "1.40"
 QuasiMonteCarlo = "0.3"
 SciMLBase = "2.39"
 SciMLSensitivity = "7.60"
 SpecialFunctions = "2.4"
+StaticArrays = "1.9"
 SteadyStateDiffEq = "2.2"
 StochasticDiffEq = "6.65"
 StructuralIdentifiability = "0.5.7"

test/reactionsystem_core/events.jl

@@ -97,9 +97,9 @@ let
     @test Symbolics.unwrap(rs_ce_de.α) isa Symbolics.BasicSymbolic{Int64}
     @test Symbolics.unwrap(rs_de.α) isa Symbolics.BasicSymbolic{Int64}
     @test Symbolics.unwrap(rs_ce_de.α) isa Symbolics.BasicSymbolic{Int64}
-    @test getdescription(rs_ce_de.A) == "A species"
-    @test getdescription(rs_de.A) == "A species"
-    @test getdescription(rs_ce_de.A) == "A species"
+    @test ModelingToolkit.getdescription(rs_ce_de.A) == "A species"
+    @test ModelingToolkit.getdescription(rs_de.A) == "A species"
+    @test ModelingToolkit.getdescription(rs_ce_de.A) == "A species"
 
     # Tests that species/variables/parameters can be accessed correctly one a MTK problem have been created.
     u0 = [X => 1]

test/simulation_and_solving/simulate_SDEs.jl

@@ -244,8 +244,8 @@ let
     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)[5]) == "Parameter η2"
+    @test ModelingToolkit.getdescription(parameters(noise_scaling_network)[2]) == "Parameter par1"
+    @test ModelingToolkit.getdescription(parameters(noise_scaling_network)[5]) == "Parameter η2"
 
     sprob = SDEProblem(noise_scaling_network, u0, (0.0, 1000.0), p)
     @test sprob.ps[:η1] == sprob.ps[:η2] == sprob.ps[:η3] == sprob.ps[:η4] == 0.0