!!! remove requires.jl

bifurcationkit · Aug 16, 2024 · 0e6ca9a · 0e6ca9a
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diff --git a/News.md b/News.md
@@ -6,6 +6,9 @@ All notable changes to this project will be documented in this file (hopefully).
 ## Near future
 - Setfield.jl has been changed to Accessors.jl
 
+## [0.3.7]
+- remove `Requires.jl` and use extensions. This requires julia>=1.9
+
 ## [0.3.5]
 - add field `save_solution` to `BifurcationProblem`. Allows to save problem state along with the current solution. Useful for periodic orbits for example where we can save the phase condition and the mesh when the latter is adapted.
 

diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "BifurcationKit"
 uuid = "0f109fa4-8a5d-4b75-95aa-f515264e7665"
 authors = ["Romain Veltz <[email protected]>"]
-version = "0.3.6"
+version = "0.3.7"
 
 [deps]
 ArnoldiMethod = "ec485272-7323-5ecc-a04f-4719b315124d"
@@ -22,7 +22,6 @@ Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
 RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
-Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 Setfield = "efcf1570-3423-57d1-acb7-fd33fddbac46"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
@@ -42,14 +41,23 @@ LinearMaps = "2.7, ^3.0"
 OrdinaryDiffEq = "^6.33"
 Parameters = "0.12.3"
 PreallocationTools = "0.4.1"
-RecipesBase = "1.0, 1.1"
+RecipesBase = "1.0, 1.1, 1.3"
 RecursiveArrayTools = "^2.3, ^2.4, ^2.8, ^2.9, ^3"
 Reexport = "1.2.2"
-Requires = "1.1.2"
 SciMLBase = "^1, ^2"
 Setfield = "0.5.0, 0.7.0, 0.8.0, ^1.1"
 StructArrays = "0.4, ^0.6"
-julia = "1.5"
+julia = "1.9"
+
+[weakdeps]
+JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
+Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
+
+[extensions]
+JLD2Ext = "JLD2"
+PlotsExt = "Plots"
+GLMakieExt = "GLMakie"
 
 [extras]
 AbstractDifferentiation = "c29ec348-61ec-40c8-8164-b8c60e9d9f3d"

diff --git a/examples/COModel.jl b/examples/COModel.jl
@@ -27,7 +27,7 @@ br = @time continuation(prob, PALC(), opts_br;
     normC = norminf,
     bothside = true)
 
-BK.plot(br, plotfold=false, )#markersize=4, legend=:topright, ylims=(0,0.16))
+BK.plot(br)#markersize=4, legend=:topright, ylims=(0,0.16))
 ####################################################################################################
 # periodic orbits
 function plotSolution(x, p; k...)
@@ -42,7 +42,7 @@ end
 function plotSolution(ax, x, p; ax1 = nothing, k...)
     @info "plotsol Makie"
     xtt = BK.get_periodic_orbit(p.prob, x, p.p)
-    lines!(ax1, br; putspecialptlegend = false)
+    lines!(ax1, br)
     lines!(ax, xtt.t, xtt[1,:]; k...)
     lines!(ax, xtt.t, xtt[2,:]; k...)
     lines!(ax, xtt.t, xtt[3,:]; k...)
@@ -99,7 +99,7 @@ brpo = @time continuation(br, 5, opts_po_cont,
     args_po...
     )
 
-BK.plot(br, brpo, putspecialptlegend = false, branchlabel = ["eq","max"])
+BK.plot(br, brpo, branchlabel = ["eq","max"])
 xlims!((1.037, 1.055))
 scatter!(br)
 plot!(brpo.param, brpo.min, label = "min", xlims = (1.037, 1.055))

diff --git a/ext/GLMakieExt/GLMakieExt.jl b/ext/GLMakieExt/GLMakieExt.jl
@@ -0,0 +1,29 @@
+module GLMakieExt
+    using GLMakie, BifurcationKit
+    import BifurcationKit: plot, 
+                           plot!,
+                           hasbranch,
+                           plot_branch_cont,
+                           plot_periodic_potrap,
+                           plot_periodic_shooting!,
+                           plot_periodic_shooting,
+                           plot_eigenvals,
+                           compute_eigenelements,
+                           get_lens_symbol,
+                           _getfirstusertype,
+                           ContResult,
+                           DCResult,
+                           AbstractBranchResult,
+                           get_plot_vars,
+                           get_axis_labels,
+                           _hasstability,
+                           filter_bifurcations,
+                           get_color,
+                           colorbif,
+                           get_plot_backend,
+                           BK_Makie
+
+    # TODO block precompilation
+    get_plot_backend() = BK_Makie()
+    include("plot.jl")
+end
diff --git a/src/plotting/RecipesMakie.jl → ext/GLMakieExt/plot.jl b/src/plotting/RecipesMakie.jl → ext/GLMakieExt/plot.jl
@@ -1,5 +1,5 @@
-# https://github.com/SciML/SciMLBase.jl/issues/427
-# https://github.com/VarLad/SciMLMakie.jl
+using GLMakie: Point2f0
+
 function GLMakie.convert_arguments(::PointBased, contres::AbstractBranchResult, vars = nothing, applytoY = identity, applytoX = identity)
     ind1, ind2 = get_plot_vars(contres, vars)
     return ([Point2f0(i, j) for (i, j) in zip(map(applytoX, getproperty(contres.branch, ind1)), map(applytoY, getproperty(contres.branch, ind2)))],)
@@ -35,72 +35,72 @@ function plot!(ax1, contres::AbstractBranchResult;
     end
     ax1.xlabel = xlab
     ax1.ylabel = ylab
-
+    
     # display bifurcation points
     bifpt = filter(x -> (x.type != :none) && (x.type != :endpoint) && (plotfold || x.type != :fold) && (x.idx <= length(contres)-1), contres.specialpoint)
     if length(bifpt) >= 1 && plotspecialpoints #&& (ind1 == :param)
         if filterspecialpoints == true
             bifpt = filterBifurcations(bifpt)
         end
         scatter!(ax1, 
-            [applytoX(getproperty(contres[pt.idx], ind1)) for pt in bifpt],
-            [applytoY(getproperty(contres[pt.idx], ind2)) for pt in bifpt];
-            marker = map(x -> (x.status == :guess) && (plotcirclesbif==false) ? :rect : :circle, bifpt), 
-            markersize = 10, 
-            color = map(x -> colorbif[x.type], bifpt),
-            )
+        [applytoX(getproperty(contres[pt.idx], ind1)) for pt in bifpt],
+        [applytoY(getproperty(contres[pt.idx], ind2)) for pt in bifpt];
+        marker = map(x -> (x.status == :guess) && (plotcirclesbif==false) ? :rect : :circle, bifpt), 
+        markersize = 10, 
+        color = map(x -> colorbif[x.type], bifpt),
+        )
     end
-
+    
     # add legend for bifurcation points
     if putspecialptlegend && length(bifpt) >= 1
         bps = unique(x -> x.type, [pt for pt in bifpt if (pt.type != :none && (plotfold || pt.type != :fold))])
         (length(bps) == 0) && return
         for pt in bps
             scatter!(ax1, 
-                [applytoX(getproperty(contres[pt.idx], ind1))], 
-                [applytoY(getproperty(contres[pt.idx], ind2))];
-                color = get_color(pt.type),
-                markersize = 10,
-                label = "$(pt.type)")
+            [applytoX(getproperty(contres[pt.idx], ind1))], 
+            [applytoY(getproperty(contres[pt.idx], ind2))];
+            color = get_color(pt.type),
+            markersize = 10,
+            label = "$(pt.type)")
         end
-        # GLMakie.axislegend(ax1, merge = true, unique = true)
+        GLMakie.axislegend(ax1, merge = true, unique = true)
     end
     ax1
 end
 
 function plot_branch_cont(contres::ContResult,
-        state,
-        iter,
-        plotuserfunction;
-        plotfold = false,
-        plotstability = true,
-        plotspecialpoints = true,
-        putspecialptlegend = true,
-        filterspecialpoints = false,
-        linewidthunstable = 1.0,
-        linewidthstable = 3.0linewidthunstable,
-        plotcirclesbif = true,
-        applytoY = identity,
-        applytoX = identity)
+                        state,
+                        iter,
+                        plotuserfunction;
+                        plotfold = false,
+                        plotstability = true,
+                        plotspecialpoints = true,
+                        putspecialptlegend = true,
+                        filterspecialpoints = false,
+                        linewidthunstable = 1.0,
+                        linewidthstable = 3.0linewidthunstable,
+                        plotcirclesbif = true,
+                        applytoY = identity,
+                        applytoX = identity)
     sol = getsolution(state)
     if length(contres) == 0; return ; end
-
+    
     # names for axis labels
     ind1, ind2 = get_plot_vars(contres, nothing)
     xlab, ylab = get_axis_labels(ind1, ind2, contres)
-
+    
     # stability linewidth
     linewidth = linewidthunstable
     if _hasstability(contres) && plotstability
         linewidth = map(x -> isodd(x) ? linewidthstable : linewidthunstable, contres.stable)
     end
-
+    
     fig = Figure(size = (1200, 700))
     ax1 = fig[1:2, 1] = Axis(fig, xlabel = String(xlab), ylabel = String(ylab), tellheight = true)
-
+    
     ax2 = fig[1, 2] = Axis(fig, xlabel = "step [$(state.step)]", ylabel = String(xlab))
     lines!(ax2, contres.step, contres.param, linewidth = linewidth)
-
+    
     if compute_eigenelements(iter)
         eigvals = contres.eig[end].eigenvals
         ax_ev = fig[3, 1:2] = Axis(fig, xlabel = "ℜ", ylabel = "ℑ")
@@ -113,23 +113,23 @@ function plot_branch_cont(contres::ContResult,
         end
         lines!(ax_ev, [0, 0], [maxIm, minIm], color = :blue, linewidth = linewidthunstable)
     end
-
+    
     # plot arrow to indicate the order of computation
     if length(contres) > 1
         x = contres.branch[end].param
         y = getproperty(contres.branch,1)[end]
         u = contres.branch[end].param - contres.branch[end-1].param
-        v = getproperty(contres.branch,1)[end]-getproperty(contres.branch,1)[end-1]
+        v = getproperty(contres.branch,1)[end] - getproperty(contres.branch,1)[end-1]
         GLMakie.arrows!(ax1, [x], [y], [u], [v], color = :green, arrowsize = 20,)
     end
-
+    
     plot!(ax1, contres; plotfold, plotstability, plotspecialpoints, putspecialptlegend, filterspecialpoints, linewidthunstable, linewidthstable, plotcirclesbif, applytoY, applytoX)
-
+    
     if isnothing(plotuserfunction) == false
         ax_perso = fig[2, 2] = Axis(fig, tellheight = true)
         plotuserfunction(ax_perso, sol.u, sol.p; ax1 = ax1)
     end
-
+    
     display(fig)
     fig
 end
@@ -142,30 +142,25 @@ function plot(contres::AbstractBranchResult; kP...)
 
     fig = Figure()
     ax1 = fig[1, 1] = Axis(fig, xlabel = String(xlab), ylabel = String(ylab), tellheight = true)
-
-    plot!(ax1, contres; kP...)
 
+    plot!(ax1, contres; kP...)
     display(fig)
     fig, ax1
 end
 
+plot(brdc::DCResult; kP...) = plot(brdc.branches...; kP...)
+
 function plot(brs::AbstractBranchResult...; 
-        branchlabel = fill("", length(brs)),
-        kP...)
+                branchlabel = ["$i" for i=1:length(brs)],
+                kP...)
     if length(brs) == 0; return ;end
     fig = Figure()
     ax1 = fig[1, 1] = Axis(fig)
 
     for (id, contres) in pairs(brs)
-
-        ind1, ind2 = get_plot_vars(contres, nothing)
-        xlab, ylab = get_axis_labels(ind1, ind2, contres)
-
         plot!(ax1, contres; branchlabel = branchlabel[id], kP...)
-
     end
-    # GLMakie.axislegend(ax1, merge = true, unique = true)
-
+    GLMakie.axislegend(ax1, merge = true, unique = true)
     display(fig)
     fig, ax1
 end
@@ -218,7 +213,7 @@ end
 function plot(bd::BifDiagNode; code = (), level = (-Inf, Inf), k...)
     if ~hasbranch(bd); return; end
 
-    fig = Figure(size = (1200, 700))
+    fig = Figure()
     ax = fig[1, 1] = Axis(fig)
 
     _plot_bifdiag_makie!(ax, bd; code, level, k...)
@@ -244,4 +239,4 @@ function _plot_bifdiag_makie!(ax, bd::Vector{BifDiagNode}; code = (), level = (-
         _plot_bifdiag_makie!(ax, b; code, level, k... )
     end
 end
-####################################################################################################
+####################################################################################################
diff --git a/ext/JLD2Ext/JLD2Ext.jl b/ext/JLD2Ext/JLD2Ext.jl
@@ -0,0 +1,5 @@
+module JLD2Ext
+    using JLD2, BifurcationKit
+    import BifurcationKit: save_to_file, AbstractContinuationIterable, ContResult
+    include("save.jl")
+end
diff --git a/ext/JLD2Ext/save.jl b/ext/JLD2Ext/save.jl
@@ -0,0 +1,50 @@
+"""
+Save solution / data in JLD2 file
+- `filename` is for example "example.jld2"
+- `sol` is the solution
+- `p` is the parameter
+- `i` is the index of the solution to be saved
+"""
+function save_to_file(iter::AbstractContinuationIterable, sol, p, i::Int64, br::ContResult)
+    if iter.contparams.save_to_file == false; return nothing; end
+    filename = iter.filename
+    # this allows to save two branches forward/backward in case
+    # bothside = true is passed to continuation
+    fd = iter.contparams.ds >=0 ? "fw" : "bw"
+
+    # create a group in the JLD format
+    jldopen(filename*".jld2", "a+") do file
+        if haskey(file, "sol-$fd-$i")
+            delete!(file, "sol-$fd-$i")
+        end
+        mygroup = JLD2.Group(file, "sol-$fd-$i")
+        mygroup["sol"] = sol
+        mygroup["param"] = p
+    end
+
+    jldopen(filename*"-branch.jld2", "a+") do file
+        if haskey(file, "branch"*fd)
+            delete!(file, "branch"*fd)
+        end
+        file["branch"*fd] = br
+    end
+end
+
+# final save of branch, in case bothsided = true is used
+function save_to_file(iter::AbstractContinuationIterable, br::ContResult)
+    if iter.contparams.save_to_file == false; return nothing; end
+    filename = iter.filename
+
+    jldopen(filename*"-branch.jld2", "a+") do file
+        if haskey(file, "branchfw")
+            delete!(file, "branchfw")
+        end
+        if haskey(file, "branchbw")
+            delete!(file, "branchbw")
+        end
+        if haskey(file, "branch")
+            delete!(file, "branch")
+        end
+        file["branch"] = br
+    end
+end
diff --git a/ext/PlotsExt/PlotsExt.jl b/ext/PlotsExt/PlotsExt.jl
@@ -0,0 +1,22 @@
+module PlotsExt
+    using Plots, BifurcationKit
+    import BifurcationKit: plot_branch_cont,
+                           plot_periodic_potrap,
+                           plot_periodic_shooting!,
+                           plot_periodic_shooting,
+                           plot_eigenvals,
+                           compute_eigenelements,
+                           get_lens_symbol,
+                           _getfirstusertype,
+                           ContResult,
+                           DCResult,
+                           AbstractBranchResult,
+                           get_plot_vars,
+                           get_axis_labels,
+                           _hasstability,
+                           filter_bifurcations,
+                           get_color,
+                           AbstractResult
+
+    include("plot.jl")
+end