update for [email protected]

Project.toml

@@ -14,16 +14,16 @@ RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 Setfield = "efcf1570-3423-57d1-acb7-fd33fddbac46"
 
+
 [compat]
-julia = "1.7"
-BifurcationKit = "0.3"
-DocStringExtensions = "0.9"
-ForwardDiff = "0.10.36"
-NonlinearEigenproblems = "1.1.1"
+BifurcationKit = "^0.3.5"
+DocStringExtensions = "^0.9"
+ForwardDiff = "^0.10"
+NonlinearEigenproblems = "^1.0.1"
 Parameters = "0.12.3"
-RecursiveArrayTools = "2.38.10"
-SciMLBase = "1.98.1"
-Setfield = "^1.1"
+RecursiveArrayTools = "^2.3, ^2.4, ^2.8, ^2.9, ^3"
+SciMLBase = "^1, ^2"
+julia = "1.9"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

docs/Project.toml

@@ -1,20 +1,14 @@
 [deps]
 BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665"
 DDEBifurcationKit = "954e4062-bdb8-4e3f-9eee-d47105dd3e65"
-DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
-SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
-Setfield = "efcf1570-3423-57d1-acb7-fd33fddbac46"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [compat]
-BifurcationKit = "0.3"
-DifferentialEquations = "6.19.0, 7.1.0"
-Documenter = "0.27"
-Setfield = "0.5.0, 0.7.0, 0.8.0, 1"
-julia = "1"
+BifurcationKit = "^0.3.4"
+Documenter = "^1.0"
+julia = "1.10"

docs/make.jl

@@ -1,15 +1,21 @@
 using Pkg
+cd(@__DIR__)
+pkg" activate ."
 
-using Documenter, DDEBifurcationKit, Setfield, BifurcationKit
+pkg"dev DDEBifurcationKit BifurcationKit"
 # using DocThemeIndigo
 ENV["GKSwstype"] = "100"
 
+using Documenter, DDEBifurcationKit, BifurcationKit
+
 # to display progress
 # ENV["JULIA_DEBUG"] = Documenter
 
-makedocs(doctest = false,
+makedocs(
+	modules = [DDEBifurcationKit],
+	doctest = false,
 	sitename = "Bifurcation Analysis of DDEs in Julia",
-	format = Documenter.HTML(collapselevel = 1,assets = ["assets/indigo.css"]),
+	format = Documenter.HTML(collapselevel = 1, assets = ["assets/indigo.css"]),
 	# format = DocumenterLaTeX.LaTeX(),
 	authors = "Romain Veltz",
 	pages = Any[
@@ -51,5 +57,6 @@ makedocs(doctest = false,
 
 deploydocs(
 	repo = "github.com/bifurcationkit/DDEBifurcationKit.jl.git",
+	push_preview = true,
 	devbranch = "main"
 )

docs/src/tutorials/dde/Humphries.md

@@ -14,12 +14,12 @@ $$x^{\prime}(t)=-\gamma x(t)-\kappa_1 x\left(t-a_1-c x(t)\right)-\kappa_2 x\left
 We first instantiate the model
 
 ```@example TUTHumphries
-using Revise, DDEBifurcationKit, Parameters, Plots
+using Revise, DDEBifurcationKit, Plots
 using BifurcationKit
 const BK = BifurcationKit
 
 function humpriesVF(x, xd, p)
-   @unpack κ1,κ2,γ,a1,a2,c = p
+   (;κ1,κ2,γ,a1,a2,c) = p
    [
       -γ * x[1] - κ1 * xd[1][1] - κ2 * xd[2][1]
    ]
@@ -60,7 +60,7 @@ We tell the solver to consider br.specialpoint[2] and continue it.
 
 ```@example TUTHumphries
 brhopf = continuation(br, 2, (@lens _.κ2),
-         setproperties(br.contparams, detect_bifurcation = 2, dsmax = 0.04, max_steps = 230, p_max = 5., p_min = -1.,ds = -0.02);
+         ContinuationPar(br.contparams, detect_bifurcation = 2, dsmax = 0.04, max_steps = 230, p_max = 5., p_min = -1.,ds = -0.02);
          verbosity = 0, plot = false,
          # we disable detection of Bautin bifurcation as the
          # Hopf normal form is not implemented for SD-DDE

docs/src/tutorials/dde/HutchinsonDiff.md

@@ -11,20 +11,20 @@ $$\begin{aligned}
 & \frac{\partial u(t, x)}{\partial x}=0, x=0, \pi
 \end{aligned}$$
 
-where $a>0,d>0$. 
+where $a>0, d>0$. 
 
 ## Problem discretization
 
 We start by discretizing the above PDE based on finite differences.
 
 ```@example TUTHut
-using Revise, DDEBifurcationKit, Parameters, LinearAlgebra, Plots, SparseArrays
+using Revise, DDEBifurcationKit, Plots, SparseArrays
 using BifurcationKit
 const BK = BifurcationKit
 
 function Hutchinson(u, ud, p)
-   @unpack a,d,Δ = p
-   d .* (Δ*u) .- a .* ud[1] .* (1 .+ u)
+   (; a, d, Δ) = p
+   d .* (Δ * u) .- a .* ud[1] .* (1 .+ u)
 end
 
 delaysF(par) = [1.]
@@ -38,16 +38,8 @@ We can now instantiate the model
 # discretisation
 Nx = 200; Lx = pi/2;
 X = -Lx .+ 2Lx/Nx*(0:Nx-1) |> collect
-
-function DiffOp(N, lx; order = 2)
-	hx = 2lx/N
-	Δ = spdiagm(0 => -2ones(N), 1 => ones(N-1), -1 => ones(N-1) )
-	Δ[1,1]=-1; Δ[end,end]=-1
-	Δ = Δ / hx^2
-	return Δ
-end
-
-Δ = DiffOp(Nx, Lx)
+h = 2Lx/Nx
+Δ = spdiagm(0 => -2ones(Nx), 1 => ones(Nx-1), -1 => ones(Nx-1) ) / h^2; Δ[1,1]=Δ[end,end]=-1/h^2
 nothing #hide
 ```
 
@@ -82,7 +74,7 @@ We show how to specify the jacobian and speed up the code a lot.
 ```@example TUTHut
 # analytical jacobian
 function JacHutchinson(u, p)
-   @unpack a,d,Δ = p
+   (;a, d, Δ) = p
    # we compute the jacobian at the steady state
    J0 = d * Δ .- a .* Diagonal(u)
    J1 = -a .* Diagonal(1 .+ u)
@@ -98,6 +90,4 @@ br
 ```
 
 
-
-
 ## References

docs/src/tutorials/dde/neuron.md

@@ -17,12 +17,12 @@ $$\left\{\begin{array}{l}
 We first instantiate the model
 
 ```@example TUTneuron
-using Revise, DDEBifurcationKit, Parameters, LinearAlgebra, Plots
+using Revise, DDEBifurcationKit, Plots
 using BifurcationKit
 const BK = BifurcationKit
 
 function neuronVF(x, xd, p)
-   @unpack κ, β, a12, a21, τs, τ1, τ2 = p
+   (; κ, β, a12, a21, τs, τ1, τ2) = p
    [
       -κ * x[1] + β * tanh(xd[3][1]) + a12 * tanh(xd[2][2]),
       -κ * x[2] + β * tanh(xd[3][2]) + a21 * tanh(xd[1][1])
@@ -61,14 +61,14 @@ We follow the Hopf points in the parameter plane $(a_{21},\tau_s)$. We tell the
 ```@example TUTneuron
 # continuation of the first Hopf point
 brhopf = continuation(br, 3, (@lens _.a21),
-         setproperties(br.contparams, detect_bifurcation = 1, dsmax = 0.04, max_steps = 230, p_max = 15., p_min = -1.,ds = -0.02);
+         ContinuationPar(br.contparams, detect_bifurcation = 1, dsmax = 0.04, max_steps = 230, p_max = 15., p_min = -1.,ds = -0.02);
          detect_codim2_bifurcation = 2,
          # bothside = true,
          start_with_eigen = true)
 
 # continuation of the second Hopf point
 brhopf2 = continuation(br, 2, (@lens _.a21),
-         setproperties(br.contparams, detect_bifurcation = 1, dsmax = 0.1, max_steps = 56, p_max = 15., p_min = -1.,ds = -0.01, n_inversion = 4);
+         ContinuationPar(br.contparams, detect_bifurcation = 1, dsmax = 0.1, max_steps = 56, p_max = 15., p_min = -1.,ds = -0.01, n_inversion = 4);
          detect_codim2_bifurcation = 2,
          start_with_eigen = true,
          bothside=true)
@@ -82,7 +82,7 @@ We change the continuation parameter and study the bifurcations as function of $
 
 ```@example TUTneuron
 prob2 = ConstantDDEBifProblem(neuronVF, delaysF, x0, pars, (@lens _.a21))
-br2 = BK.continuation(prob2, PALC(), setproperties(opts, ds = 0.1, p_max = 3., n_inversion=8); verbosity = 0, plot = false, normC = norminf)
+br2 = BK.continuation(prob2, PALC(), ContinuationPar(opts, ds = 0.1, p_max = 3., n_inversion=8); verbosity = 0, plot = false, normC = norminf)
 ```
 
 We then compute the branch of periodic orbits from the Hopf bifurcation points using orthogonal collocation.

docs/src/tutorials/dde/neuronV2.md

@@ -19,13 +19,13 @@ where $g(z)=[\tanh (z-1)+\tanh (1)] \cosh (1)^2$.
 We first instantiate the model
 
 ```@example TUTneuron2
-using Revise, DDEBifurcationKit, Parameters, Plots
+using Revise, DDEBifurcationKit, Plots
 using BifurcationKit
 const BK = BifurcationKit
 
 g(z) = (tanh(z − 1) + tanh(1))*cosh(1)^2
 function neuron2VF(x, xd, p)
-   @unpack a,b,c,d = p
+   (; a,b,c,d) = p
    [
       -x[1] - a * g(b*xd[1][1]) + c * g(d*xd[2][2]),
       -x[2] - a * g(b*xd[1][2]) + c * g(d*xd[2][1])
@@ -66,14 +66,14 @@ We follow the Hopf points in the parameter plane $(a,c)$. We tell the solver to
 ```@example TUTneuron2
 # continuation of the first Hopf point
 brhopf = continuation(br, 1, (@lens _.c),
-         setproperties(br.contparams, detect_bifurcation = 1, dsmax = 0.01, max_steps = 100, p_max = 1.1, p_min = -0.1,ds = 0.01, n_inversion = 2);
+         ContinuationPar(br.contparams, detect_bifurcation = 1, dsmax = 0.01, max_steps = 100, p_max = 1.1, p_min = -0.1,ds = 0.01, n_inversion = 2);
          verbosity = 0,
          detect_codim2_bifurcation = 2,
          bothside = true,
          start_with_eigen = true)
 
 brhopf2 = continuation(br, 2, (@lens _.c),
-         setproperties(br.contparams, detect_bifurcation = 1, dsmax = 0.01, max_steps = 100, p_max = 1.1, p_min = -0.1,ds = -0.01);
+         ContinuationPar(br.contparams, detect_bifurcation = 1, dsmax = 0.01, max_steps = 100, p_max = 1.1, p_min = -0.1,ds = -0.01);
          verbosity = 0,
          detect_codim2_bifurcation = 2,
          bothside = true,
@@ -89,15 +89,15 @@ We follow the Fold points in the parameter plane $(a, c)$. We tell the solver to
 
 ```@example TUTneuron2
 prob2 = ConstantDDEBifProblem(neuron2VF, delaysF, x0, (@set pars.a = 0.12), (@lens _.c))
-br2 = continuation(prob2, PALC(), setproperties(opts, p_max = 1.22);)
+br2 = continuation(prob2, PALC(), ContinuationPar(opts, p_max = 1.22);)
 
 
 # change tolerance for avoiding error computation of the EV
 opts_fold = br.contparams
 @set! opts_fold.newton_options.eigsolver.σ = 1e-7
 
 brfold = continuation(br2, 3, (@lens _.a),
-         setproperties(opts_fold; detect_bifurcation = 1, dsmax = 0.01, max_steps = 70, p_max = 0.6, p_min = -0.6,ds = -0.01, n_inversion = 2, tol_stability = 1e-6);
+         ContinuationPar(opts_fold; detect_bifurcation = 1, dsmax = 0.01, max_steps = 70, p_max = 0.6, p_min = -0.6,ds = -0.01, n_inversion = 2, tol_stability = 1e-6);
          verbosity = 1, plot = true,
          detect_codim2_bifurcation = 2,
          update_minaug_every_step = 1,

examples/HutchinsonDiffusion.jl

@@ -3,18 +3,15 @@ cd(@__DIR__)
 cd("..")
 # using Pkg, LinearAlgebra, Test
 # pkg"activate ."
-using Revise, DDEBifurcationKit, Parameters, Setfield, LinearAlgebra, Plots, SparseArrays
+using Revise, DDEBifurcationKit, LinearAlgebra, Plots, SparseArrays
 using BifurcationKit
 const BK = BifurcationKit
 const DDEBK = DDEBifurcationKit
 
-# sup norm
-norminf(x) = norm(x, Inf)
-
 using DiffEqOperators
 
 function Hutchinson(u, ud, p)
-   @unpack a,d,Δ = p
+   (;a,d,Δ) = p
    d .* (Δ*u) .- a .* ud[1] .* (1 .+ u)
 end
 
@@ -42,7 +39,7 @@ hopfpt = BK.getNormalForm(br, 1)
 ################################################################################
 # case where we specify the jacobian
 function JacHutchinson(u, p)
-   @unpack a,d,Δ = p
+	(;a,d,Δ) = p
    # we compute the jacobian at the steady state
    J0 = d * Δ .- a .* Diagonal(u)
    J1 = -a .* Diagonal(1 .+ u)

examples/delayed-log.jl

@@ -2,15 +2,15 @@ cd(@__DIR__)
 cd("..")
 # using Pkg, LinearAlgebra, Test
 # pkg"activate ."
-using Revise, DDEBifurcationKit, Parameters, Setfield, LinearAlgebra
+using Revise, DDEBifurcationKit, LinearAlgebra
 using BifurcationKit
 const BK = BifurcationKit
 const DDEBK = DDEBifurcationKit
 
 using Plots
 
 function delayedlogVF(x, xd, p)
-   @unpack λ = p
+   (;λ) = p
    y = xd[1][1]
    [
       (λ - y) * x[1]
@@ -54,6 +54,7 @@ args_po = (    record_from_solution = (x, p) -> begin
 		plot!(xtt.t, xtt[1,:]; label = "V1", k...)
 		plot!(br; subplot = 1, putspecialptlegend = false)
 		end,
+	normC = norminf)
 
 probpo = PeriodicOrbitOCollProblem(40, 4; N = 1)
 	# probpo = PeriodicOrbitTrapProblem(M = 2000, jacobian = :DenseAD, N = 2)

examples/humpries.jl

@@ -1,16 +1,16 @@
 cd(@__DIR__)
-cd("..")
-# using Pkg, LinearAlgebra, Test
-# pkg"activate ."
+# cd("..")
+using Pkg, LinearAlgebra, Test
+pkg"activate ."
 
 # https://ddebiftool.sourceforge.net/demos/neuron/html/demo1_stst.html
-using Revise, DDEBifurcationKit, Parameters, Setfield, LinearAlgebra, Plots
+using Revise, DDEBifurcationKit, LinearAlgebra, Plots
 using BifurcationKit
 const BK = BifurcationKit
 const DDEBK = DDEBifurcationKit
 
 function humpriesVF(x, xd, p)
-   @unpack κ1,κ2,γ,a1,a2,c = p
+   (; κ1, κ2, γ, a1, a2, c) = p
    [
       -γ * x[1] - κ1 * xd[1][1] - κ2 * xd[2][1]
    ]
@@ -24,11 +24,12 @@ function delaysF(x, par)
 end
 
 
-pars = (κ1=0.,κ2=2.3,a1=1.3,a2=6,γ=4.75,c=1.)
+pars = (κ1=0., κ2=2.3, a1=1.3, a2=6, γ=4.75, c=1.)
 x0 = zeros(1)
 
 prob = DDEBK.SDDDEBifProblem(humpriesVF, delaysF, x0, pars, (@lens _.κ1))
 
+
 optn = NewtonPar(verbose = true, eigsolver = DDE_DefaultEig())
 opts = ContinuationPar(p_max = 13., p_min = 0., newton_options = optn, ds = -0.01, detect_bifurcation = 3, nev = 3, )
 
@@ -37,7 +38,7 @@ br = continuation(prob, PALC(), opts; verbosity = 1, plot = true, bothside = tru
 plot(br)
 ################################################################################
 brhopf = continuation(br, 2, (@lens _.κ2),
-         setproperties(br.contparams, detect_bifurcation = 2, dsmax = 0.04, max_steps = 230, p_max = 5., p_min = -1.,ds = -0.02);
+         ContinuationPar(br.contparams, detect_bifurcation = 2, dsmax = 0.04, max_steps = 230, p_max = 5., p_min = -1.,ds = -0.02);
          verbosity = 2, plot = true,
          detect_codim2_bifurcation = 0,
          bothside = true,
@@ -103,7 +104,7 @@ function h0(p, t)
      t ≤ 0 || error("history function is only implemented for t ≤ 0")
      0 .+ 0.03sin(t)
  end
-prob_de = DDEProblem(humpriesVF_DE2,h0,(0.,10200.),setproperties(pars, κ1 = br.specialpoint[2].param + 0.01); dependent_lags=((x,par,t)->par.a1 + par.c * x, (x,par,t)->par.a2 + par.c * x))
+prob_de = DDEProblem(humpriesVF_DE2,h0,(0.,10200.),ContinuationPar(pars, κ1 = br.specialpoint[2].param + 0.01); dependent_lags=((x,par,t)->par.a1 + par.c * x, (x,par,t)->par.a2 + par.c * x))
 alg = MethodOfSteps(Rosenbrock23())
 sol = solve(prob_de,alg)
 plot(plot(sol, xlims = (sol.t[end]-30,sol.t[end])), plot(sol))