Merge branch 'main' into compathelper/new_version/2024-09-09-00-58-02…

…-628-00883591779

.github/workflows/Format.yml

@@ -1,9 +1,41 @@
-name: Format suggestions
+name: format-check
 
-on: [pull_request]
+on:
+  push:
+    branches:
+      - 'main'
+    tags: '*'
+  pull_request:
 
 jobs:
-  code-style:
-    runs-on: ubuntu-latest
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version: [1]
+        julia-arch: [x86]
+        os: [ubuntu-latest]
     steps:
-      - uses: julia-actions/julia-format@v3
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia-version }}
+
+      - uses: actions/checkout@v4
+      - name: Install JuliaFormatter and format
+        # This will use the latest version by default but you can set the version like so:
+        #
+        # julia  -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter", version="0.13.0"))'
+        run: |
+          julia  -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter"))'
+          julia  -e 'using JuliaFormatter; format(".", verbose=true)'
+      - name: Format check
+        run: |
+          julia -e '
+          out = Cmd(`git diff`) |> read |> String
+          if out == ""
+              exit(0)
+          else
+              @error "Some files have not been formatted !!!"
+              write(stdout, out)
+              exit(1)
+          end'

CHANGELOG.md

@@ -1,5 +1,27 @@
 # Changelog for `CriticalTransitions.jl`
 
+## v0.4.0
+New `CoupledSDEs` design
+
+This release upgrades CriticalTransitions.jl to be compatible with the re-design of `CoupledSDEs`, which has now been integrated in [`DynamicalSystemsBase.jl v3.11`](https://juliadynamics.github.io/DynamicalSystemsBase.jl/stable/CoupledSDEs/).
+
+Since we have updated the syntax of defining a `CoupledSDEs` system, this is a breaking change.
+
+#### Changed functions
+- `CoupledSDEs` is now constructed with different args and kwargs
+- `fw_action`, `geometric_action` and `om_action` now normalize the covariance matrix when computing the action functional
+- `noise_strength` is not a function anymore but a kwarg for `CoupledSDEs` and other functions
+- `om_action` now requires `noise_strength` as input argument
+- `relax` was renamed to `deterministic_orbit`
+- `trajectory` has been added to replace `simulate`
+
+#### Deprecations
+- `add_noise_strength`, `idfunc` and `idfunc!` are no longer needed and have been removed
+- the function `noise_strength(::CoupledSDEs)` has been removed
+- `simulate` has been removed
+
+Full changelog [here](https://github.com/JuliaDynamics/CriticalTransitions.jl/compare/v0.3.0...v0.4.0).
+
 ## v0.3.0
 Major overhaul introducing `CoupledSDEs`
 

Project.toml

@@ -2,7 +2,7 @@ name = "CriticalTransitions"
 uuid = "251e6cd3-3112-48a5-99dd-66efcfd18334"
 authors = ["Reyk Börner, Ryan Deeley, Raphael Römer, Orjan Ameye"]
 repo = "https://github.com/juliadynamics/CriticalTransitions.jl.git"
-version = "0.3.0"
+version = "0.4.0"
 
 [deps]
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
@@ -29,6 +29,7 @@ StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
 Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 
 [weakdeps]
+StateSpaceSets = "40b095a5-5852-4c12-98c7-d43bf788e795"
 Attractors = "f3fd9213-ca85-4dba-9dfd-7fc91308fec7"
 ChaosTools = "608a59af-f2a3-5ad4-90b4-758bdf3122a7"
 
@@ -38,31 +39,32 @@ CoupledSDEsBaisin = ["ChaosTools", "Attractors"]
 
 [compat]
 Aqua = "0.8.7"
-Attractors = "1.18"
-ChaosTools = "3.1"
+Attractors = "1.19.12"
+ChaosTools = "3.2.1"
 Dates = ">=1.9.0"
 Dierckx = "0.5.3"
 DiffEqNoiseProcess = "5.22"
 DocStringExtensions = "0.9.3"
 Documenter = "^1.4.1"
-DynamicalSystemsBase = "3.7.1"
+DynamicalSystemsBase = "3.11.1"
 ExplicitImports = "1.9"
 Format = "1"
 ForwardDiff = "0.10.36"
 HDF5 = "0.17.1"
 IntervalArithmetic = "0.20"
-JET = "0.9"
+JET = "0.9.9"
 JLD2 = "0.4.46, 0.5"
 Markdown = ">=1.9.0"
 ModelingToolkit = "9.25"
 Optim = "1.9.3"
-OrdinaryDiffEq = "6.82"
+OrdinaryDiffEq = "6.89"
 ProgressBars = "1.5.1"
 ProgressMeter = "1.10.0"
 Reexport = "1.2.2"
+StateSpaceSets = "2.1.2"
 StaticArrays = "1.9.3"
 Statistics = ">=1.9"
-StochasticDiffEq = "6.65.1"
+StochasticDiffEq = "6.69"
 Symbolics = "5.32"
 julia = "1.9"
 

README.md

@@ -26,22 +26,22 @@ function fitzhugh_nagumo(u, p, t)
     dx = (-α * x^3 + γ * x - κ * y + I) / ϵ
     dy = -β * y + x
 
-    return SA[dx, dy]
+    return SVector{2}([dx, dy])
 end
 
 # System parameters
-p = [1., 3., 1., 1., 1., 0.]
+params = [1., 3., 1., 1., 1., 0.]
 noise_strength = 0.02
+initial_state = zeros(2)
 
 # Define stochastic system
-sys = CoupledSDEs(fitzhugh_nagumo, id_func, zeros(2), p, noise_strength)
+sys = CoupledSDEs(fitzhugh_nagumo, initial_state, params; noise_strength)
 
-# Get stable fixed points
-fps, eigs, stab = fixedpoints(sys, [-2,-2], [2,2])
-fp1, fp2 = fps[stab]
+# Run a sample trajectory
+traj = trajectory(sys, 10.0)
 
-# Generate noise-induced transition from one fixed point to the other
-path, times, success = transition(sys, fp1, fp2)
+# Compute minimum action path using gMAM algorithm
+instanton = geometric_min_action_method(sys, initial_state, current_state(sys))
 
 # ... and more, check out the documentation!
 ```

docs/Project.toml

@@ -1,14 +1,16 @@
 [deps]
 Attractors = "f3fd9213-ca85-4dba-9dfd-7fc91308fec7"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
-Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 ChaosTools = "608a59af-f2a3-5ad4-90b4-758bdf3122a7"
 CriticalTransitions = "251e6cd3-3112-48a5-99dd-66efcfd18334"
+DiffEqNoiseProcess = "77a26b50-5914-5dd7-bc55-306e6241c503"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244"
 DocumenterInterLinks = "d12716ef-a0f6-4df4-a9f1-a5a34e75c656"
+DynamicalSystemsBase = "6e36e845-645a-534a-86f2-f5d4aa5a06b4"
+Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
-
+StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
 
 [compat]
 Documenter = "1"

docs/make.jl

@@ -4,6 +4,7 @@ using DocumenterInterLinks
 using Pkg
 
 using CriticalTransitions, ChaosTools, Attractors
+using DynamicalSystemsBase
 
 project_toml = Pkg.TOML.parsefile(joinpath(@__DIR__, "..", "Project.toml"))
 package_version = project_toml["version"]
@@ -45,10 +46,12 @@ makedocs(;
         CriticalTransitions.DiffEqNoiseProcess,
         Base.get_extension(CriticalTransitions, :ChaosToolsExt),
         Base.get_extension(CriticalTransitions, :CoupledSDEsBaisin),
+        DynamicalSystemsBase,
+        Base.get_extension(DynamicalSystemsBase, :StochasticSystemsBase),
     ],
     doctest=false,
     format=Documenter.HTML(; html_options...),
-    warnonly=[:missing_docs],
+    warnonly=[:missing_docs, :linkcheck, :cross_references],
     pages=pages,
     plugins=[bib, links],
 )

docs/pages.jl

@@ -5,7 +5,7 @@ pages = [
     "Tutorial" => "tutorial.md",
     "Manual" => Any[
         "Define a CoupledSDEs system" => "man/CoupledSDEs.md",
-        "Stability analysis" => "man/systemanalysis.md",
+        #"Stability analysis" => "man/systemanalysis.md",
         "Simulating the system" => "man/simulation.md",
         "Sampling transitions" => "man/sampling.md",
         "Large deviation theory" => "man/largedeviations.md",

docs/src/index.md

@@ -7,10 +7,9 @@ Building on [DynamicalSystems.jl](https://juliadynamics.github.io/DynamicalSyste
 ![CT.jl infographic](./figs/CTjl_structure_v0.3_small.jpeg)
 
 !!! info "Current features"
-    * **Stability analysis**: Fixed points, linear stability, basins of attraction, edge tracking
-    * **Stochastic simulation**: Gaussian noise, uncorrelated and correlated, additive and multiplicative
-    * **Transition path sampling**: Ensemble sampling by direct simulation and Pathspace Langevin MCMC
-    * **Large deviation theory**: Action functionals and minimization algorithms (MAM, gMAM)
+    * **Stochastic simulation** made easy: Gaussian noise, uncorrelated and correlated, additive and multiplicative
+    * **Transition path sampling**: Parallelized ensemble rejection sampling
+    * **Large deviation theory** tools: Action functionals and minimization algorithms (MAM, gMAM)
 
 !!! ukw "Planned features"
     * **Rare event simulation**: importance sampling, AMS