Merge branch 'main' into Downgrade-CI

.github/workflows/CompatHelper.yml

@@ -15,7 +15,7 @@ jobs:
         run: which julia
         continue-on-error: true
       - name: Install Julia, but only if it is not already available in the PATH
-        uses: julia-actions/setup-julia@v1
+        uses: julia-actions/setup-julia@v2
         with:
           version: '1'
           arch: ${{ runner.arch }}

.github/workflows/ci.yml

@@ -42,7 +42,7 @@ jobs:
       - uses: actions/checkout@v4
         with:
           persist-credentials: false
-      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/setup-julia@v2
         with:
           show-versioninfo: true
           version: ${{ matrix.version }}

.github/workflows/doc-preview-cleanup.yml

@@ -0,0 +1,33 @@
+name: Doc Preview Cleanup
+
+on:
+  pull_request:
+    types: [closed]
+
+# Ensure that only one "Doc Preview Cleanup" workflow is force pushing at a time
+concurrency:
+  group: doc-preview-cleanup
+  cancel-in-progress: false
+
+jobs:
+  doc-preview-cleanup:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - name: Checkout gh-pages branch
+        uses: actions/checkout@v4
+        with:
+          ref: gh-pages
+      - name: Delete preview and history + push changes
+        run: |
+          if [ -d "${preview_dir}" ]; then
+              git config user.name "Documenter.jl"
+              git config user.email "[email protected]"
+              git rm -rf "${preview_dir}"
+              git commit -m "delete preview"
+              git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
+              git push --force origin gh-pages-new:gh-pages
+          fi
+        env:
+          preview_dir: previews/PR${{ github.event.number }}

.github/workflows/documentation.yml

@@ -1,32 +1,35 @@
-name: Documenter
+name: Documentation
 
 on:
   push:
-    tags:
-      - '*'
     branches:
-      - 'main'
+      - main
+    tags: '*'
   pull_request:
-    branches:
-      - 'main'
 
 concurrency:
   # Skip intermediate builds: always.
   # Cancel intermediate builds: only if it is a pull request build.
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
 jobs:
-  Documenter:
+  build:
     permissions:
       contents: write
+      pull-requests: read
       statuses: write
-    name: Documentation
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: '1.10'
       - uses: julia-actions/cache@v1
-      - uses: julia-actions/julia-buildpkg@latest 
-      - uses: julia-actions/julia-docdeploy@latest
+      - name: Install dependencies
+        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - name: Build and deploy
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key
+        run: julia --project=docs/ docs/make.jl

docs/make.jl

@@ -13,7 +13,8 @@ makedocs(;
     modules=[CriticalTransitions],
     doctest=false,
     format = Documenter.HTML(
-        prettyurls = get(ENV, "CI", nothing) == "true",
+        canonical="https://juliadynamics.github.io/CriticalTransitions.jl/",
+        prettyurls = true,
         mathengine = Documenter.MathJax2()
         ),
     linkcheck = true,
@@ -34,9 +35,10 @@ makedocs(;
         "Predefined systems" => "man/systems.md",
         "Development stage" => "man/dev.md"
     ],
-    plugins=[bib],
+    plugins=[bib]
 )
 
 deploydocs(
-    repo = "github.com/juliadynamics/CriticalTransitions.jl.git",
+    repo = "github.com/JuliaDynamics/CriticalTransitions.jl.git",
+    push_preview = false
 )

systems/fitzhughnagumo.jl

@@ -3,7 +3,6 @@ Dynamical systems specification file
 """
 
 # fitzhugh_nagumo model
-
 """
     fitzhugh_nagumo!(du, u, p, t)
 In-place definition of the FitzHugh-Nagumo system.
@@ -41,32 +40,32 @@ FitzHughNagumo!(u,p,t) = fitzhugh_nagumo!(u,p,t)
 
 """
     fhn_ϵσ(ϵ,σ)
-A shortcut command for returning a StochSystem of the FitzHugh Nagumo system in a default setup with additive isotropic noise. 
-    
+A shortcut command for returning a StochSystem of the FitzHugh Nagumo system in a default setup with additive isotropic noise.
+
 This setup fixes the parameters β = 3, α =  γ = κ = 1, I = 0 and leaves the value of the time-scale parameter ϵ as a function argument. The prescribed noise process is additive and isotropic: the variables are peturbed by independently drawn identical Gaussian white noise realisations, with standard deviation σ (the other function argument).
 """
-function fhn_ϵσ(ϵ, σ) # a convenient two-parameter version of the FitzHugh Nagumo system 
+function fhn_ϵσ(ϵ, σ) # a convenient two-parameter version of the FitzHugh Nagumo system
     # defining the StochSystem
     f(u,p,t) = fitzhugh_nagumo(u,p,t);
     β = 3; α = γ = κ = 1; I = 0; # standard parameters without ϵ (time-scale separation parameter)
     pf_wo_ϵ = [β, α, γ, κ, I]; # parameter vector without ϵ
     dim = 2;
     g = idfunc;
-    pg = nothing; 
+    pg = nothing;
     Σ = [1 0; 0 1];
     process = "WhiteGauss";
     StochSystem(f, vcat([ϵ], pf_wo_ϵ), dim, σ, g, pg, Σ, process)
 end;
 
-function fhn_ϵσ_backward(ϵ, σ) # a convenient two-parameter version of the FitzHugh Nagumo system 
+function fhn_ϵσ_backward(ϵ, σ) # a convenient two-parameter version of the FitzHugh Nagumo system
     # defining the StochSystem
     f(u,p,t) = -fitzhugh_nagumo(u,p,t);
     β = 3; α = γ = κ = 1; I = 0; # standard parameters without ϵ (time-scale separation parameter)
     pf_wo_ϵ = [β, α, γ, κ, I]; # parameter vector without ϵ
     dim = 2;
     g = idfunc;
-    pg = nothing; 
+    pg = nothing;
     Σ = [1 0; 0 1];
     process = "WhiteGauss";
     StochSystem(f, vcat([ϵ], pf_wo_ϵ), dim, σ, g, pg, Σ, process)
-end;
+end;