CompatHelper: bump compat for Interpolations to 0.16, (keep existing compat) (#169)

* CompatHelper: bump compat for Interpolations to 0.16, (keep existing compat)

* changed example menu headings

* fixed ModelingToolkit test

* bump version number

* tried to fix github-actions

* bump DiffEqNoiseProcess version hoping to fix downgrade CI

* disable downgrade.yml running after push

* updated docs

* bump version number

---------

Co-authored-by: CompatHelper Julia <compathelper_noreply@julialang.org>
Co-authored-by: reykboerner <reyk.boerner@reading.ac.uk>

Author: 3 people

.github/workflows/ci.yml

@@ -2,8 +2,6 @@ name: CI
 
 on:
   push:
-    tags:
-      - '*'
     branches:
       - 'main'
   pull_request:
@@ -27,8 +25,9 @@ jobs:
     strategy:
       matrix:
         version:
-          - 'pre'
           - '1.10'
+          - '1.11'
+          #- 'pre'
           # - '1.9'
           # - 'nightly'
         os:
@@ -53,6 +52,10 @@ jobs:
           arch: ${{ matrix.arch }}
       - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-buildpkg@v1
+
+      - name: Instantiate Julia environment
+        run: julia --project=. -e 'using Pkg; Pkg.instantiate()'
+      
       - uses: julia-actions/julia-runtest@v1
       # - uses: julia-actions/julia-processcoverage@v1
       # - uses: codecov/codecov-action@v4

.github/workflows/downgrade.yml

@@ -1,13 +1,12 @@
 name: Downgrade
 on:
-  push:
-    tags:
-      - '*'
-    branches:
-      - 'main'
-  pull_request:
-    branches:
-      - 'main'
+  workflow_dispatch:
+  #push:
+  #  branches:
+  #    - 'main'
+  #pull_request:
+  #  branches:
+  #    - 'main'
 jobs:
   test:
     name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}
@@ -19,7 +18,7 @@ jobs:
     strategy:
       matrix:
         version:
-          - '1.10'
+          - '1.11'
           # - '1.9'
           # - 'nightly'
         os:
@@ -39,4 +38,8 @@ jobs:
         with:
           skip: Pkg,TOML
       - uses: julia-actions/julia-buildpkg@v1
+
+      - name: Instantiate Julia environment
+        run: julia --project=. -e 'using Pkg; Pkg.instantiate()'
+
       - uses: julia-actions/julia-runtest@v1

Project.toml

@@ -2,7 +2,7 @@ name = "CriticalTransitions"
 uuid = "251e6cd3-3112-48a5-99dd-66efcfd18334"
 authors = ["Reyk Börner, Orjan Ameye, Ryan Deeley, Raphael Römer"]
 repo = "https://github.com/juliadynamics/CriticalTransitions.jl.git"
-version = "0.5.0"
+version = "0.6.0"
 
 [deps]
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
@@ -32,8 +32,8 @@ DelaunayTriangulation = "927a84f5-c5f4-47a5-9785-b46e178433df"
 StateSpaceSets = "40b095a5-5852-4c12-98c7-d43bf788e795"
 
 [extensions]
-ChaosToolsExt = ["ChaosTools"]
 AttractorsExt = ["Attractors"]
+ChaosToolsExt = ["ChaosTools"]
 DistMesh2D = ["DelaunayTriangulation"]
 
 [compat]
@@ -44,7 +44,7 @@ DelaunayTriangulation = "1.6"
 DocStringExtensions = "0.9.3"
 DynamicalSystemsBase = "3.13"
 Format = "1"
-Interpolations = "0.15.1"
+Interpolations = "0.15.1, 0.16"
 IntervalArithmetic = "0.22.22"
 LinearSolve = "2.37.0, 3"
 Optimization = "4"

README.md

@@ -21,16 +21,16 @@ using CriticalTransitions
 
 function fitzhugh_nagumo(u, p, t)
     x, y = u
-    ϵ, β, α, γ, κ, I = p
+    ϵ, β = p
 
-    dx = (-α * x^3 + γ * x - κ * y + I) / ϵ
-    dy = -β * y + x
+    dx = (-x^3 + x - y)/ϵ
+    dy = -β*y + x
 
     return SVector{2}([dx, dy])
 end
 
 # System parameters
-params = [1., 3., 1., 1., 1., 0.]
+params = [0.1, 3.0]
 noise_strength = 0.02
 initial_state = zeros(2)
 
@@ -52,4 +52,4 @@ Developers: Reyk Börner, Ryan Deeley, Raphael Römer and Orjan Ameye
 
 Thanks to Jeroen Wouters, Calvin Nesbitt, Tobias Grafke, George Datseris and Oliver Mehling
 
-This work is part of the [CriticalEarth](https://www.criticalearth.eu) project.
+This package was created as part of the [CriticalEarth](https://www.criticalearth.eu) project.

docs/pages.jl

@@ -4,9 +4,9 @@ pages = [
     "Quickstart" => "quickstart.md",
     "Tutorial" => "examples/tutorial.md",
     "Examples" => Any[
-        "Anlyses of the Maier-Stein system" => "examples/gMAM_Maierstein.md",
-        "sgMAM for the Kerr Parametric Oscillator" => "examples/sgMAM_KPO.md",
-        "Transition Path Theory using finite element method" => "examples/duffing_TPT.md",
+        "Maier-Stein system: Noise-induced transitions and instantons" => "examples/gMAM_Maierstein.md",
+        "Kerr Parametric Oscillator: Simple gMAM" => "examples/sgMAM_KPO.md",
+        "Duffing Oscillator: Transition path theory" => "examples/duffing_TPT.md",
     ],
     "Manual" => Any[
         "Define a CoupledSDEs system" => "man/CoupledSDEs.md",

docs/src/quickstart.md

@@ -1,20 +1,17 @@
 # Quickstart
 
 ## Installation
-As this module is not published yet, there are two ways to access it:
+Although the package is not yet registered, you can install it from Github via the Julia package manager:
+```julia
+using Pkg; Pkg.add('https://github.com/juliadynamics/CriticalTransitions.jl.git')
+```
 
-* **Option 1 (recommended): Install from GitHub**
-    1. Enter the Julia package manager by typing `]` in the REPL: `julia> ]`
-    2. type `add https://github.com/juliadynamics/CriticalTransitions.jl.git`
-* **Option 2: Load module locally**
-    1. Clone the repo: `git clone https://github.com/juliadynamics/CriticalTransitions.jl.git`
-    2. In Julia, include the module file: `include("PATH/src/CriticalTransitions.jl")`, where `PATH` is the relative path to the repo you just cloned
-    3. Load the module: `using .CriticalTransitions`
+The package is currently tested to be compatible with Julia versions `1.10` and `1.11`.
 
 ## Basic usage
 The general workflow of `CriticalTransitions` essentially follows two steps:
 
-1. Define your system (see [Define a CoupledSDEs system](@ref))
+1. Define your system as a `CoupledSDEs` (see [Define a CoupledSDEs system](@ref))
 2. Investigate the system by calling methods (see [Methods](@ref))
 
 !!! info "New system type: RateSystem"
@@ -26,5 +23,5 @@ Currently the following functions are implemented to analyze a [`CoupledSDEs`](@
 corresponding sample transition paths.
 
 ```@index
-Pages = ["man/simulation.md", "man/sampling.md", "man/largedeviations.md"]
+Pages = ["man/systemanalysis.md", "man/simulation.md", "man/sampling.md", "man/largedeviations.md", "man/utils.md"]
 ```

test/ModelingToolkit.jl

@@ -27,7 +27,7 @@ using StochasticDiffEq: LambaEulerHeun
         (s * x * z)-s * z 0
     ]
 
-    sys2 = SDESystem(drift_eqs, diffusion_eqs, t, sts, ps; name=:sys1)
+    sys2 = structural_simplify(SDESystem(drift_eqs, diffusion_eqs, t, sts, ps; name=:sys1))
     @test sys1 == sys2
 
     prob = SDEProblem(sys1, sts .=> [1.0, 0.0, 0.0], (0.0, 100.0), ps .=> (10.0, 26.0))

test/Project.toml

@@ -28,9 +28,9 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Aqua = "0.8.7"
 Attractors = "1.19.12"
 ChaosTools = "3.2.1"
-DiffEqNoiseProcess = "5.22"
+DiffEqNoiseProcess = "5.24"
 ExplicitImports = "1.9"
-JET = "0.9.9"
+JET = "0.9.18"
 ModelingToolkit = "9.25"
 Optimization = "4"
 OptimizationOptimJL = "0.4.1"