add Jet

remove Dates compat

interchange .. with interval in CTLibrary

Project.toml

@@ -5,6 +5,7 @@ repo = "https://github.com/juliadynamics/CriticalTransitions.jl.git"
 version = "0.3.0"
 
 [deps]
+Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 Dierckx = "39dd38d3-220a-591b-8e3c-4c3a8c710a94"
 DiffEqNoiseProcess = "77a26b50-5914-5dd7-bc55-306e6241c503"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"

src/CoupledSDEs.jl

@@ -167,7 +167,7 @@ function CoupledSDEs(
 )
     return CoupledSDEs(
         dynamic_rule(ds),
-        prob.g,
+        g,
         current_state(ds),
         p,
         noise_strength;

src/CriticalTransitions.jl

@@ -34,6 +34,7 @@ using Symbolics: Symbolics
 
 # io and documentation
 using Format: Format
+using Dates: Dates
 using Printf: Printf
 using Markdown: Markdown
 using DocStringExtensions: TYPEDSIGNATURES

src/largedeviations/action.jl

@@ -75,11 +75,11 @@ Computes the action functional specified by `functional` for a given CoupledSDEs
 * `functional = "FW"`: Returns the Freidlin-Wentzell action ([`fw_action`](@ref))
 * `functional = "OM"`: Returns the Onsager-Machlup action ([`om_action`](@ref))
 """
-function action(sys::CoupledSDEs, path::Matrix, time, functional; kwargs...)
+function action(sys::CoupledSDEs, path::Matrix, time, functional)
     if functional == "FW"
-        action = fw_action(sys, path, time; kwargs...)
+        action = fw_action(sys, path, time)
     elseif functional == "OM"
-        action = om_action(sys, path, time; kwargs...)
+        action = om_action(sys, path, time)
     end
     return action
 end;

src/largedeviations/geometric_min_action_method.jl

@@ -141,6 +141,8 @@ function heymann_vandeneijnden_step(sys::CoupledSDEs, path, N, L; tau=0.1, diff_
     lambdas, lambdas_prime = zeros(N), zeros(N)
     x_prime = path_velocity(path, 0:dx:L; order=diff_order)
 
+    A = inv(covariance_matrix(sys))
+
     for i in 2:(N - 1)
         lambdas[i] = anorm(drift(sys, path[:, i]), A) / anorm(path[:, i], A)
     end

systems/CTLibrary.jl

@@ -1,6 +1,8 @@
 module CTLibrary
 
-using CriticalTransitions
+using CriticalTransitions: CriticalTransitions, smoothabs
+using IntervalArithmetic: interval
+using StaticArrays: SA, SVector
 
 include("fitzhughnagumo.jl")
 include("truscottbrindley_mod.jl")

systems/fitzhughnagumo.jl

@@ -34,10 +34,6 @@ function fitzhugh_nagumo(u, p, t)
     return SA[dx, dy]
 end
 
-# For backwards compatibility
-FitzHughNagumo(u, p, t) = fitzhugh_nagumo(u, p, t)
-FitzHughNagumo!(u, p, t) = fitzhugh_nagumo!(u, p, t)
-
 # """
 #     fhn_ϵσ(ϵ,σ)
 # A shortcut command for returning a CoupledSDEs of the FitzHugh Nagumo system in a default setup with additive isotropic noise.

systems/truscottbrindley_mod.jl

@@ -82,7 +82,7 @@ function rampedmodifiedtruscottbrindley!(du, u, p, t)
         P₁ *
         (α * (P / P₁) * (1 - β * (P / P₁)) - γ * (Z / Z₁) * (P / P₁)^2 / (1 + (P / P₁)^2))
     du[2] = ξ * Z₁ * ((Z / Z₁) * (P / P₁)^2 / (1 + (P / P₁)^2) - (Z / Z₁)^2)
-    return du[3] = t ∈ Ttrans .. (Ttrans + Tramp) ? v : 0
+    return du[3] = t ∈ interval(Ttrans, (Ttrans + Tramp)) ? v : 0
 end
 
 """
@@ -99,7 +99,7 @@ function rampedmodifiedtruscottbrindley(u, p, t)
         P₁ *
         (α * (P / P₁) * (1 - β * (P / P₁)) - γ * (Z / Z₁) * (P / P₁)^2 / (1 + (P / P₁)^2))
     dZ = ξ * Z₁ * ((Z / Z₁) * (P / P₁)^2 / (1 + (P / P₁)^2) - (Z / Z₁)^2)
-    dα = t ∈ Ttrans .. (Ttrans + Tramp) ? v : 0
+    dα = t ∈ interval(Ttrans, (Ttrans + Tramp)) ? v : 0
 
     return SA[dP, dZ, dα]
 end

systems/truscottbrindley_orig.jl

@@ -46,7 +46,7 @@ function rampedoriginaltruscottbrindley!(du, u, p, t)
 
     du[1] = r * P * (1 - P / K) - Rₘ * Z * P^2 / (α^2 + P^2)
     du[2] = γ * Rₘ * Z * P^2 / (α^2 + P^2) - μ * Z
-    return du[3] = t ∈ Ttrans .. (Ttrans + Tramp) ? v : 0
+    return du[3] = t ∈ interval(Ttrans, (Ttrans + Tramp)) ? v : 0
 end
 
 """
@@ -61,7 +61,7 @@ function rampedoriginaltruscottbrindley(u, p, t)
 
     dP = r * P * (1 - P / K) - Rₘ * Z * P^2 / (α^2 + P^2)
     dZ = γ * Rₘ * Z * P^2 / (α^2 + P^2) - μ * Z
-    dr = t ∈ Ttrans .. (Ttrans + Tramp) ? v : 0
+    dr = t ∈ interval(Ttrans, (Ttrans + Tramp)) ? v : 0
 
     return SA[dP, dZ, dr]
 end

systems/truscottbrindley_orig1.jl

@@ -46,7 +46,7 @@ function rampedoriginaltruscottbrindley1!(du, u, p, t)
 
     du[1] = (1 / γ) * (r * P * (1 - P / K) - Rₘ * Z * P^2 / (α^2 + P^2))
     du[2] = Rₘ * Z * P^2 / (α^2 + P^2) - μ * Z
-    return du[3] = t ∈ Ttrans .. (Ttrans + Tramp) ? v : 0
+    return du[3] = t ∈ interval(Ttrans, (Ttrans + Tramp)) ? v : 0
 end
 
 """
@@ -61,7 +61,7 @@ function rampedoriginaltruscottbrindley1(u, p, t)
 
     dP = (1 / γ) * (r * P * (1 - P / K) - Rₘ * Z * P^2 / (α^2 + P^2))
     dZ = Rₘ * Z * P^2 / (α^2 + P^2) - μ * Z
-    dr = t ∈ Ttrans .. (Ttrans + Tramp) ? v : 0
+    dr = t ∈ interval(Ttrans, (Ttrans + Tramp)) ? v : 0
 
     return SA[dP, dZ, dr]
 end

test/runtests.jl

@@ -41,7 +41,7 @@ end
 
 @testset "Code linting" begin
     using JET
-    # JET.test_package(HarmonicBalance; target_defined_modules=true)
+    JET.test_package(CriticalTransitions; target_defined_modules=true)
 end
 
 @testset "CoupledSDEs" begin