docs: fix links

JuliaDynamics · Dec 28, 2024 · 8635398 · 8635398
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diff --git a/docs/make.jl b/docs/make.jl
@@ -5,6 +5,10 @@ using Pkg
 
 using CriticalTransitions, ChaosTools, Attractors
 using DynamicalSystemsBase
+StochasticSystemsBase = Base.get_extension(DynamicalSystemsBase, :StochasticSystemsBase)
+ChaosToolsExt = Base.get_extension(CriticalTransitions, :ChaosToolsExt)
+CoupledSDEsBasin = Base.get_extension(CriticalTransitions, :CoupledSDEsBasin)
+
 
 project_toml = Pkg.TOML.parsefile(joinpath(@__DIR__, "..", "Project.toml"))
 package_version = project_toml["version"]
@@ -13,6 +17,7 @@ authors = join(project_toml["authors"], ", ") * " and contributors"
 github = "https://github.com/juliadynamics/CriticalTransitions.jl"
 
 links = InterLinks(
+    "DynamicalSystemsBase" => "https://juliadynamics.github.io/DynamicalSystemsBase.jl/dev/",
 # "DiffEqNoiseProcess" => "https://docs.sciml.ai/DiffEqNoiseProcess/stable/",
 # "DifferentialEquations" => "https://docs.sciml.ai/DiffEqDocs/stable/",
 # "StochasticDiffEq" => "https://docs.sciml.ai/DiffEqDocs/stable/",
@@ -41,12 +46,12 @@ makedocs(;
     repo=Documenter.Remotes.GitHub("JuliaDynamics", "CriticalTransitions.jl"),
     modules=[
         CriticalTransitions,
-        CriticalTransitions.DiffEqNoiseProcess,
         Base.get_extension(CriticalTransitions, :ChaosToolsExt),
         Base.get_extension(CriticalTransitions, :CoupledSDEsBasin),
-        DynamicalSystemsBase,
         Base.get_extension(DynamicalSystemsBase, :StochasticSystemsBase),
+        # DynamicalSystemsBase
     ],
+    checkdocs_ignored_modules=[DynamicalSystemsBase, CriticalTransitions.CTLibrary],
     pages=pages,
     linkcheck=true,
     pagesonly=true,

diff --git a/docs/pages.jl b/docs/pages.jl
@@ -9,7 +9,7 @@ pages = [
     ],
     "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",

diff --git a/docs/src/examples/gMAM_Maierstein.md b/docs/src/examples/gMAM_Maierstein.md
@@ -16,7 +16,7 @@ Let us explore the features of [CriticalTransitions.jl](https://github.com/Julia
 
 ## Maier-stein model
 
-The [Maier-Stein model](https://link.springer.com/article/10.1007/BF02183736) (J. Stat. Phys 83, 3–4 (1996)) is commonly used in the field of nonlinear dynamics for benchmarking Large Deviation Theory (LDT) techniques, e.g., stoachastic transitions between different stable states. It is a simple model that describes the dynamics of a system with two degrees of freedom ``u`` and ``v``, and is given by the following set of ordinary differential equations:
+The [Maier-Stein model](https://doi.org/10.1007/BF02183736) (J. Stat. Phys 83, 3–4 (1996)) is commonly used in the field of nonlinear dynamics for benchmarking Large Deviation Theory (LDT) techniques, e.g., stoachastic transitions between different stable states. It is a simple model that describes the dynamics of a system with two degrees of freedom ``u`` and ``v``, and is given by the following set of ordinary differential equations:
 ```math
 \begin{aligned}
     \dot{u} &= u-u^3 - \beta*u*v^2\\
@@ -229,7 +229,7 @@ yy = 0.3 .* (-xx .^ 2 .+ 1)
 init = Matrix([xx yy]')
 ```
 
-`geometric_min_action_method` computes the minimizer of the Freidlin-Wentzell action using the geometric minimum action method (gMAM), to find the minimum action path (instanton) between an initial state x_i and final state x_f. The Minimum Action Method (MAM) is a more traditional approach, while the Geometric Minimum Action Method (gMAM) is a blend of the original MAM and the [string method](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.66.052301).
+`geometric_min_action_method` computes the minimizer of the Freidlin-Wentzell action using the geometric minimum action method (gMAM), to find the minimum action path (instanton) between an initial state x_i and final state x_f. The Minimum Action Method (MAM) is a more traditional approach, while the Geometric Minimum Action Method (gMAM) is a blend of the original MAM and the [string method](https://doi.org/10.1103/PhysRevB.66.052301).
 
 ```@example GMAM
 gm = geometric_min_action_method(sys, init, maxiter=500; show_progress=false)

diff --git a/docs/src/examples/tutorial.md b/docs/src/examples/tutorial.md
@@ -77,7 +77,7 @@ sim = trajectory(sys, 100, fp1)
 
 In the keyword arguments, we have specified at which interval the solution is saved. Further keyword arguments can be used to change the solver (the default is `SOSRA()` for stochastic integration) and other settings.
 
-The simulated trajectory is stored in `sim` in the usual output format of the [`solve`](https://docs.sciml.ai/DiffEqDocs/stable/basics/common_solver_opts/#CommonSolve.solve-Tuple%7BSciMLBase.AbstractDEProblem,%20Vararg%7BAny%7D%7D) method of DifferentialEquations.jl, including the solution `sim.u` and the vector of time points `sim.t`. The solution can also be accessed as a matrix `sim[i, t]`, where `i` is the `i`-th component of `u` and `t` the time index.
+The simulated trajectory is stored in `sim` in the usual output format of the [`solve`](https://docs.sciml.ai/DiffEqDocs/stable/basics/common_solver_opts/) method of DifferentialEquations.jl, including the solution `sim.u` and the vector of time points `sim.t`. The solution can also be accessed as a matrix `sim[i, t]`, where `i` is the `i`-th component of `u` and `t` the time index.
 
 Let's plot the result. Did the trajectory transition to the other attractor?
 

diff --git a/docs/src/man/sampling.md b/docs/src/man/sampling.md
@@ -1,5 +1,9 @@
 # Sampling transitions
 
+```@docs
+TransitionEnsemble
+```
+
 ## ... by direct simulation
 These functions generate noise-induced transitions between an initial and final state.
 

diff --git a/docs/src/man/simulation.md b/docs/src/man/simulation.md
@@ -1,16 +1,9 @@
 # Simulating the system
 
 We provide two main functions to simulate a [`CoupledSDEs`](@ref) forward in time:
-* [`trajectory`](@ref), which integrates the stochastic `CoupledSDEs` system forward in time
+* [`DynamicalSystemsBase.trajectory`](@extref), which integrates the stochastic `CoupledSDEs` system forward in time
 * [`deterministic_orbit`](@ref), which integrates only the deterministic part of the `CoupledSDEs` system 
 
-## Stochastic dynamics
-
-```@docs
-trajectory
-```
-
-## Deterministic dynamics
 
 ```@docs
 deterministic_orbit

diff --git a/docs/src/man/systemanalysis.md b/docs/src/man/systemanalysis.md
@@ -4,7 +4,6 @@ To use the following functionalities, you need to load `ChoasTools.jl` and `Attr
 
 ## Fixed points
 ```@docs
-equilib(sys::CoupledSDEs, state; kwargs...)
 fixedpoints
 ```
 
@@ -16,4 +15,11 @@ introduced by [Battelino et al. (1988)](https://doi.org/10.1016/0167-2789(88)900
 ```@docs
 edgetracking
 bisect_to_edge
+```
+
+## Baisin of attraction
+```@docs
+basinboundary
+basboundary
+basins
 ```
diff --git a/docs/src/man/utils.md b/docs/src/man/utils.md
@@ -3,12 +3,16 @@
 ## `CoupledSDEs` utility functions
 
 ```@docs
-covariance_matrix
-diffusion_matrix
-dynamic_rule
+solver
+StochasticSystemsBase.covariance_matrix
+StochasticSystemsBase.diffusion_matrix
 noise_process
-current_state
-set_state!
 drift
 div_drift
+```
+
+## More
+
+```@docs
+intervals_to_box
 ```
diff --git a/src/CriticalTransitions.jl b/src/CriticalTransitions.jl
@@ -69,21 +69,19 @@ using .CTLibrary
 # Core types
 export CoupledSDEs, CoupledODEs, noise_process, covariance_matrix, diffusion_matrix
 export dynamic_rule, current_state, set_state!, trajectory
+export drift, div_drift, solver
 
 export sgmam, SgmamSystem
+export fw_action, om_action, action, geometric_action
+export min_action_method, geometric_min_action_method, string_method
+export MinimumActionPath
 
-# Methods
-export drift, div_drift, solver
 export deterministic_orbit
 export transition, transitions
+export TransitionEnsemble
+
 export basins, basinboundary, basboundary
 export intervals_to_box
-export fw_action, om_action, action, geometric_action
-export min_action_method, geometric_min_action_method
-export MinimumActionPath
-export string_method
-export covariance_matrix, diffusion_matrix
-# export edgetracking, bisect_to_edge, AttractorsViaProximity
 
 # Error hint for extensions stubs
 function __init__()