CoupledSDEs test's

Author: oameye

Project.toml

@@ -45,7 +45,7 @@ Dierckx = "0.5.3"
 DiffEqNoiseProcess = "5.22"
 DocStringExtensions = "0.9.3"
 Documenter = "^1.4.1"
-DynamicalSystemsBase = "3.11"
+DynamicalSystemsBase = "3.11.1"
 ExplicitImports = "1.9"
 Format = "1"
 ForwardDiff = "0.10.36"

src/CoupledSDEs.jl

@@ -2,7 +2,7 @@ module CriticalTransitions
 
 # Base
 using Statistics: Statistics, mean
-using LinearAlgebra: LinearAlgebra, I, norm, dot, tr #, Diagonal, tr
+using LinearAlgebra: LinearAlgebra, I, norm, dot, tr
 using StaticArrays: StaticArrays, SVector
 
 # Core
@@ -22,7 +22,7 @@ using StochasticDiffEq:
 using DynamicalSystemsBase:
     DynamicalSystemsBase,
     #ContinuousTimeDynamicalSystem,
-    CoupledODEs,
+    # CoupledODEs,
     CoupledSDEs,
     #StateSpaceSets,
     #dimension,
@@ -56,15 +56,9 @@ using Reexport: @reexport
 @reexport using StochasticDiffEq
 @reexport using DiffEqNoiseProcess
 
-StochasticSystemsBase = Base.get_extension(DynamicalSystemsBase, :StochasticSystemsBase)
-covariance_matrix = StochasticSystemsBase.covariance_matrix
-diffusion_matrix = StochasticSystemsBase.diffusion_matrix
-
 include("extention_functions.jl")
 include("utils.jl")
 include("system_utils.jl")
-#include("CoupledSDEs.jl")
-#include("CoupledSDEs_utils.jl")
 include("io.jl")
 include("trajectories/simulation.jl")
 include("trajectories/transition.jl")
@@ -79,13 +73,9 @@ using .CTLibrary
 
 # Core types
 export CoupledSDEs,
-    idfunc!,
-    idfunc,
-    add_noise_strength,
-    #noise_process,
-    #covariance_matrix,
-    #noise_strength,
-    CoupledODEs
+    noise_process,
+    covariance_matrix,
+    diffusion_matrix
 
 # Methods
 export equilib, basins, basinboundary, basboundary

src/CoupledSDEs_utils.jl

@@ -1,8 +1,28 @@
+StochasticSystemsBase = Base.get_extension(DynamicalSystemsBase, :StochasticSystemsBase)
+covariance_matrix = StochasticSystemsBase.covariance_matrix
+diffusion_matrix = StochasticSystemsBase.diffusion_matrix
+
+"""
+    StochSystem
+
+An alias to [`CoupledSDEs`](@ref).
+This was the name these systems had in CriticalTransitions.jl before v0.3
+"""
+const StochSystem = CoupledSDEs
+
 """
 $(TYPEDSIGNATURES)
 
-Returns the deterministic drift ``f(x)`` of the CoupledSDEs `sys` at state `x`. For time-
-dependent systems, the time can be specified as a keyword argument `t` (by default `t=0`).
+Fetches the stochastic process ``\\mathcal{N}`` specified in the intergrator of `sys`. Returns the type `DiffEqNoiseProcess.NoiseProcess`.
+"""
+function noise_process(sys::CoupledSDEs)
+    return sys.integ.W
+end
+
+"""
+$(TYPEDSIGNATURES)
+
+Returns the deterministic drift ``f(x)`` of the CoupledSDEs `sys` at state `x`. For time-dependent systems, the time can be specified as a keyword argument `t` (by default `t=0`).
 """
 function drift(sys::CoupledSDEs{IIP}, x; t=0) where {IIP}
     f = dynamic_rule(sys)
@@ -24,4 +44,4 @@ dependent systems, the time can be specified as a keyword argument `t` (by defau
 function div_drift(sys::CoupledSDEs, x; t=0)
     b(x) = drift(sys, x; t)
     return tr(ForwardDiff.jacobian(b, x))
-end;
+end;