remove systems and dev from docs

docs/make.jl

@@ -38,6 +38,8 @@ makedocs(;
     linkcheck=true,
     modules=[
         CriticalTransitions,
+        # CriticalTransitions.StochasticDiffEq,
+        CriticalTransitions.DiffEqNoiseProcess,
         Base.get_extension(CriticalTransitions, :ChaosToolsExt),
         Base.get_extension(CriticalTransitions, :CoupledSDEsBaisin),
     ],

docs/pages.jl

@@ -11,7 +11,7 @@ pages = [
         "Large deviation theory" => "man/largedeviations.md",
         "Utilities" => "man/utils.md",
     ],
-    "Predefined systems" => "man/systems.md",
-    "Development stage" => "man/dev.md",
+    # "Predefined systems" => "man/systems.md",
+    # "Development stage" => "man/dev.md",
 ]
 #! format: on

src/CoupledSDEs.jl

@@ -52,7 +52,9 @@ If you want to specify a solver, do so by using the keyword `alg`, e.g.:
 `diffeq = (alg = Tsit5(), reltol = 1e-6)`. This requires you to have been first
 `using OrdinaryDiffEq` to access the solvers. The default `diffeq` is:
 
+```julia
 $(DynamicalSystemsBase.DEFAULT_DIFFEQ)
+```
 
 `diffeq` keywords can also include `callback` for [event handling
 ](http://docs.juliadiffeq.org/latest/features/callback_functions.html).

src/largedeviations/action.jl

@@ -13,7 +13,7 @@ Returns a single number, which is the value of the action functional
 
 where ``\\phi_t`` denotes the path in state space, ``b`` the drift field, and ``T`` the
 total time of the path. The subscript ``Q`` refers to the
-generalized norm ``||a||_Q^2 := \\langle a, Q^{-1} b \\rangle`` (see [`anorm`](@ref)). Here
+generalized norm ``||a||_Q^2 := \\langle a, Q^{-1} b \\rangle`` (see `anorm``). Here
 ``Q`` is the noise covariance matrix `sys.Σ`.
 
 ## Keyword arguments
@@ -53,7 +53,7 @@ Returns a single number, which is the value of the action functional
 
 where ``\\phi_t`` denotes the path in state space, ``b`` the drift field, ``T`` the total
 time of the path, and ``\\sigma`` the noise strength. The subscript ``Q`` refers to the
-generalized norm ``||a||_Q^2 := \\langle a, Q^{-1} b \\rangle`` (see [`anorm`](@ref)). Here
+generalized norm ``||a||_Q^2 := \\langle a, Q^{-1} b \\rangle`` (see `anorm``). Here
 ``Q`` is the noise covariance matrix.
 
 ## Keyword arguments
@@ -112,7 +112,7 @@ by the integral
 
 where ``s`` is the arclength coordinate, ``L`` the arclength, ``b`` the drift field, and the
 subscript ``Q`` refers to the generalized dot product ``\\langle a, b \\rangle_Q := a^{\\top}
-\\cdot Q^{-1} b`` (see [`anorm`](@ref)). Here ``Q`` is the noise covariance matrix `sys.Σ`.
+\\cdot Q^{-1} b`` (see `anorm``). Here ``Q`` is the noise covariance matrix `sys.Σ`.
 
 ## Keyword arguments
 * `cov_inv = nothing`: Inverse of the covariance matrix ``\\Sigma``.

src/utils.jl

@@ -65,52 +65,50 @@ function intervals_to_box(bmin::Vector, bmax::Vector)
     return box
 end;
 
-function additive_idx!(du, u, p, t, idx)
-    du[idx] = 1.0
-    return nothing
-end;
+# function additive_idx!(du, u, p, t, idx)
+#     du[idx] = 1.0
+#     return nothing
+# end;
 
-function additive_idx(u, p, t, idx)
-    du = zeros(length(u))
-    du[idx] = 1.0
-    return SVector{length(u)}(du)
-end;
+# function additive_idx(u, p, t, idx)
+#     du = zeros(length(u))
+#     du[idx] = 1.0
+#     return SVector{length(u)}(du)
+# end;
 
-function multiplicative_idx!(du, u, p, t, idx)
-    return du[idx] = u[idx]
-end;
+# function multiplicative_idx!(du, u, p, t, idx)
+#     return du[idx] = u[idx]
+# end;
 
-function multiplicative_idx(u, p, t, idx)
-    du = zeros(length(u))
-    du[idx] = u[idx]
-    return SVector{length(u)}(du)
-end
+# function multiplicative_idx(u, p, t, idx)
+#     du = zeros(length(u))
+#     du[idx] = u[idx]
+#     return SVector{length(u)}(du)
+# end
 
-function multiplicative_first!(du, u, p, t)
-    return du[1] = u[1]
-end;
+# function multiplicative_first!(du, u, p, t)
+#     return du[1] = u[1]
+# end;
 
-function multiplicative_first(u, p, t)
-    du = zeros(length(u))
-    du[1] = u[1]
+# function multiplicative_first(u, p, t)
+#     du = zeros(length(u))
+#     du[1] = u[1]
 
-    return SVector{length(u)}(du)
-end;
+#     return SVector{length(u)}(du)
+# end;
 
-function additive_first!(du, u, p, t)
-    return du[1] = 1
-end;
+# function additive_first!(du, u, p, t)
+#     return du[1] = 1
+# end;
 
-function additive_first(u, p, t)
-    du = zeros(length(u))
-    du[1] = 1
+# function additive_first(u, p, t)
+#     du = zeros(length(u))
+#     du[1] = 1
 
-    return SVector{length(u)}(du)
-end;
+#     return SVector{length(u)}(du)
+# end;
 
 """
-$(TYPEDSIGNATURES)
-
 Calculates the generalized ``A``-norm of the vector `vec`,
 ``||v||_A := \\sqrt(v^\\top \\cdot A \\cdot v)``,
 where `A` is a square matrix of dimension `(length(vec) x length(vec))`.