Fix docs

.github/dependabot.yml

@@ -0,0 +1,10 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    open-pull-requests-limit: 50
+    labels:
+      - "dependencies"
+      - "github-actions"

.github/workflows/CompatHelper.yml

@@ -0,0 +1,44 @@
+name: CompatHelper
+on:
+  schedule:
+    - cron: 0 0 * * *
+  workflow_dispatch:
+permissions:
+  contents: write
+  pull-requests: write
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check if Julia is already available in the PATH
+        id: julia_in_path
+        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
+        with:
+          version: '1'
+          arch: ${{ runner.arch }}
+        if: steps.julia_in_path.outcome != 'success'
+      - name: "Add the General registry via Git"
+        run: |
+          import Pkg
+          ENV["JULIA_PKG_SERVER"] = ""
+          Pkg.Registry.add("General")
+        shell: julia --color=yes {0}
+      - name: "Install CompatHelper"
+        run: |
+          import Pkg
+          name = "CompatHelper"
+          uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
+          version = "3"
+          Pkg.add(; name, uuid, version)
+        shell: julia --color=yes {0}
+      - name: "Run CompatHelper"
+        run: |
+          import CompatHelper
+          CompatHelper.main()
+        shell: julia --color=yes {0}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/ci.yml

@@ -4,10 +4,10 @@ on:
     tags:
       - '*'
     branches:
-      - 'master'
+      - 'main'
   pull_request:
     branches:
-      - 'master'
+      - 'main'
 concurrency:
   # Skip intermediate builds: always.
   # Cancel intermediate builds: only if it is a pull request build.

.github/workflows/documentation.yml

@@ -1,26 +1,23 @@
-name: Documentation
+name: Documenter
 
 on:
   push:
-    branches:
-      - main # update to match your development branch (master, main, dev, trunk, ...)
-    tags: '*'
+    branches: main
+    tags: [v*]
   pull_request:
 
 jobs:
-  build:
+  Documenter:
     permissions:
       contents: write
+      statuses: write
+    name: Documentation
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
-        with:
-          version: '1.8'
-      - name: Install dependencies
-        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
-      - name: Build and deploy
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@latest 
+      - uses: julia-actions/julia-docdeploy@latest
         env:
-          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_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -9,6 +9,7 @@ docs/build/
 /ryan/  
 .vscode/
 /Manifest.toml
+docs/Manifest.toml
 dev/levy.jl
 .JuliaFormatter.toml
 reyk_local/

README.md

@@ -35,4 +35,4 @@ 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://criticalearth.eu) project.
+This work is part of the [CriticalEarth](https://www.criticalearth.eu) project.

dev/RateSys1.jl

@@ -6,21 +6,21 @@ State = Union{Vector, SVector}
 # Define RateSystem
 """
     RateSystem(f, pf, dim, σ, g, pg, Σ, process)
-Defines a stochastic dynamical system with a rate dependent shift in `CriticalTransitions.jl`. See [documentation](https://reykboerner.github.io/CriticalTransitions.jl/dev/man/stochsystem/).
+Defines a stochastic dynamical system with a rate dependent shift in `CriticalTransitions.jl`. See [documentation](https://juliadynamics.github.io/CriticalTransitions.jl/dev/man/stochsystem/).
 """
 struct RateSystem
     # i think it would maybe be helpful to define a few more fields:
     # gL::Function, a function describing the noise functions of the time-dependent functions
     # dim2::Int64, gives the number of time-dependent functions
     # Σ₂::CovMatrix, gives the covariance matrix of the time-dependent parameters
     f::Function                 # vector of functions describing the derivatives of each state variable
-    pf::Parameters              # parameters for the derivatives of the state variables 
+    pf::Parameters              # parameters for the derivatives of the state variables
     td_inds::Vector{Bool}       # a boolean vector indicating which parameters are time-dependent
     L::Function                 # vector of functions describing the derivatives of each time-dependent parameter
     pL::Parameters              # parameters for the derivatives of the parameter variables
     T_trans::Float64            # the length of time before ramping begins
     T_shift::Float64            # the length of time where the specified parameters evolve
-    dim::Int64                  
+    dim::Int64
     σ::Float64
     g::Function
     pg::Parameters
@@ -59,7 +59,7 @@ function simulate(sys::RateSystem, init::State;
     func(u,p,t) = fL(u,p,t,sys)
 
     prob = SDEProblem(func, σg(sys), init, (0, tmax), p(sys), noise=stochprocess(sys))
-    
+
     solve(prob, solver; dt=dt, callback=callback, progress=progress, kwargs...)
 
 end;
@@ -77,7 +77,7 @@ This function integrates `sys.f` forward in time, using the [`ODEProblem`](https
 * `callback=nothing`: callback condition
 * `kwargs...`: keyword arguments for `solve(ODEProblem)`
 
-For more info, see [`ODEProblem`](https://diffeq.sciml.ai/stable/types/ode_types/#SciMLBase.ODEProblem). 
+For more info, see [`ODEProblem`](https://diffeq.sciml.ai/stable/types/ode_types/#SciMLBase.ODEProblem).
 For stochastic integration, see [`simulate`](@ref).
 
 > Warning: This function has only been tested for the `Euler()` solver.
@@ -88,7 +88,7 @@ function relax(sys::RateSystem, init::State;
     solver=Euler(),
     callback=nothing,
     kwargs...)
-    
+
     func(u,p,t) = fL(u,p,t,sys)
 
     prob = ODEProblem(func, init, (0, tmax), p(sys))
@@ -138,7 +138,7 @@ end
     gauss(sys::RateSystem)
 Returns a Wiener process with dimension `length(sys.u)` and covariance matrix `sys.Σ`.
 
-This function is based on the [`CorrelatedWienerProcess`](https://noise.sciml.ai/stable/noise_processes/#DiffEqNoiseProcess.CorrelatedWienerProcess) of [`DiffEqNoiseProcess.jl`](https://noise.sciml.ai/stable/), a component of `DifferentialEquations.jl`. The initial condition of the process is set to the zero vector at `t=0`.
+This function is based on the [`CorrelatedWienerProcess`](https://docs.sciml.ai/DiffEqNoiseProcess/stable/noise_processes/#DiffEqNoiseProcess.CorrelatedWienerProcess) of [`DiffEqNoiseProcess.jl`](https://docs.sciml.ai/DiffEqNoiseProcess/stable/), a component of `DifferentialEquations.jl`. The initial condition of the process is set to the zero vector at `t=0`.
 """
 function gauss(sys::RateSystem)
     Σ₂ = zeros(sum(sys.td_inds),sum(sys.td_inds)); # the covariance matrix of the time-dependent parameters, fixed to zero for now
@@ -154,7 +154,7 @@ end;
 function fL(u,p,t,sys::RateSystem)
 
     pf = p[1][1:length(sys.pf)];
-    pL = p[1][length(sys.pf)+1:end]; 
+    pL = p[1][length(sys.pf)+1:end];
 
     #stationary = 0..t_trans ∪ t_trans+t_shift..Inf
     #du = t in stationary ? hcat(sys.f(u,p,t),zeros(length(sys.pf)) : hcat(sys.f(u,p,t),sys.L(u,p,t))
@@ -166,9 +166,9 @@ function fL(u,p,t,sys::RateSystem)
     pf[sys.td_inds] = param_vars; # modifying the vector of fixed parameters to account for the current values of the time-dependent parameters
 
     nonstationary = sys.T_trans..sys.T_trans+sys.T_shift; # the time-interval of the ramping period
-    
+
     du = t in nonstationary ? vcat(sys.f(state_vars,[pf],t),sys.L(param_vars,[pL],t)) : vcat(sys.f(state_vars,[pf],t),SVector{sum(sys.td_inds)}(zeros(sum(sys.td_inds))))
 
 end;
 
-stochtorate(sys::StochSystem,td_inds::Vector{Bool},L::Function,pL::Vector,T_trans::Float64,T_shift::Float64)=RateSystem(sys.f,sys.pf,td_inds,L,pL,T_trans,T_shift,length(sys.u),sys.σ,sys.g,sys.pg,sys.Σ,sys.process)
+stochtorate(sys::StochSystem,td_inds::Vector{Bool},L::Function,pL::Vector,T_trans::Float64,T_shift::Float64)=RateSystem(sys.f,sys.pf,td_inds,L,pL,T_trans,T_shift,length(sys.u),sys.σ,sys.g,sys.pg,sys.Σ,sys.process)