Merge branch 'main' of https://github.com/JuliaDynamics/CriticalTrans…

…itions.jl

.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@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

.github/workflows/downgrade.yml

@@ -0,0 +1,42 @@
+name: Downgrade
+on:
+  push:
+    tags:
+      - '*'
+    branches:
+      - 'main'
+  pull_request:
+    branches:
+      - 'main'
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 60
+    permissions: # needed to allow julia-actions/cache to proactively delete old caches that it has created
+      actions: write
+      contents: read
+    strategy:
+      matrix:
+        version:
+          - '1.10'
+          # - '1.9'
+          # - 'nightly'
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          persist-credentials: false
+      - uses: julia-actions/setup-julia@v2
+        with:
+          show-versioninfo: true
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: julia-actions/julia-downgrade-compat@v1
+        with:
+          skip: Pkg,TOML
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1

Project.toml

@@ -12,7 +12,7 @@ DiffEqNoiseProcess = "77a26b50-5914-5dd7-bc55-306e6241c503"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 DrWatson = "634d3b9d-ee7a-5ddf-bec9-22491ea816e1"
 DynamicalSystemsBase = "6e36e845-645a-534a-86f2-f5d4aa5a06b4"
-Formatting = "59287772-0a20-5a39-b81b-1366585eb4c0"
+Format = "1fa38f19-a742-5d3f-a2b9-30dd87b9d5f8"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
 IntervalRootFinding = "d2bf35a9-74e0-55ec-b149-d360ff49b807"
@@ -30,33 +30,33 @@ StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
 Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 
 [compat]
-DynamicalSystemsBase = "3"
-Optim = "1"
-Reexport = "1"
-ForwardDiff = "0.10"
-JLD2 = "0.4"
-DiffEqNoiseProcess = "5"
-Dierckx = "0.5"
-HDF5 = "0.17"
-Formatting = "0.4"
-IntervalRootFinding = "0.5"
-DrWatson = "2"
-StaticArrays = "1"
-Attractors = "1"
-Symbolics = "5"
-DocStringExtensions = "0.9"
-Statistics = "1"
-ProgressBars = "1"
-StochasticDiffEq = "6"
-ProgressMeter = "1"
-ChaosTools = "3"
-OrdinaryDiffEq = "6"
-julia = "1.4"
+Attractors = "1.15.0"
+ChaosTools = "3.1.2"
+Dierckx = "0.5.3"
+DiffEqNoiseProcess = "5.21.0"
+DocStringExtensions = "0.9.3"
+DrWatson = "2.14.1"
+DynamicalSystemsBase = "3.7.1"
+Format = "1"
+ForwardDiff = "0.10.36"
+HDF5 = "0.17.1"
+IntervalRootFinding = "0.5.11"
+JLD2 = "0.4.46"
+Optim = "1.9.3"
+OrdinaryDiffEq = "6.74.1"
+ProgressBars = "1.5.1"
+ProgressMeter = "1.10.0"
+Reexport = "1.2.2"
+StaticArrays = "1.9.3"
+Statistics = "1.10.0"
+StochasticDiffEq = "6.65.1"
+Symbolics = "5.26.0"
+julia = "1.9"
 
 [extras]
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 IntervalRootFinding = "d2bf35a9-74e0-55ec-b149-d360ff49b807"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
 test = ["Test", "Random", "IntervalRootFinding"]

docs/make.jl

@@ -14,7 +14,7 @@ makedocs(;
     doctest=false,
     format = Documenter.HTML(
         canonical="https://juliadynamics.github.io/CriticalTransitions.jl/",
-        prettyurls = get(ENV, "CI", nothing) == "true",
+        prettyurls = true,
         mathengine = Documenter.MathJax2()
         ),
     linkcheck = true,
@@ -39,6 +39,6 @@ makedocs(;
 )
 
 deploydocs(
-    repo = "github.com/juliadynamics/CriticalTransitions.jl.git",
+    repo = "github.com/JuliaDynamics/CriticalTransitions.jl.git",
     push_preview = false
 )

src/CriticalTransitions.jl

@@ -7,7 +7,7 @@ using Reexport
 @reexport using StochasticDiffEq
 @reexport using DiffEqNoiseProcess
 @reexport using LinearAlgebra
-using Formatting, Dates, JLD2, HDF5, ProgressBars, ProgressMeter, DocStringExtensions
+using Format, Dates, JLD2, HDF5, ProgressBars, ProgressMeter, DocStringExtensions
 using Attractors
 using ChaosTools
 using IntervalRootFinding
@@ -82,7 +82,7 @@ export saddles_idx, repellers_idx, attractors_idx
 export additive_idx, additive_idx!
 export multiplicative_idx, multiplicative_idx!
 export FitzHughNagumoSPDE, fhn_pathspace_sampling
-export langevinmcmc_spde, symbolise_spde, stochastic_bridge 
+export langevinmcmc_spde, symbolise_spde, stochastic_bridge
 export jacobian
 export residence_time, residence_times, ResTimes, temporal, runandsavetimes, get_res_times
 export exit_time, exit_times