diff --git a/docs/Project.toml b/docs/Project.toml index a19926fc..d0bbef2c 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -6,6 +6,7 @@ GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306" MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" +Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" PencilFFTs = "4a48f351-57a6-4416-9ec4-c37015456aae" Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7" @@ -14,4 +15,5 @@ RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" [compat] -Documenter = "0.27" +Documenter = "1" +Makie = "0.19.9" diff --git a/docs/examples/navier_stokes.jl b/docs/examples/navier_stokes.jl index 987515bf..ee99cd85 100644 --- a/docs/examples/navier_stokes.jl +++ b/docs/examples/navier_stokes.jl @@ -120,11 +120,13 @@ end let fig = Figure(resolution = (700, 600)) ax = Axis3(fig[1, 1]; aspect = :data, xlabel = "x", ylabel = "y", zlabel = "z") - vnorm = vecnorm(v⃗₀) + vnorm = parent(vecnorm(v⃗₀)) # use `parent` because Makie doesn't like custom array types... ct = contour!( ax, grid.x, grid.y, grid.z, vnorm; alpha = 0.2, levels = 4, - colormap = :viridis, colorrange = (0.0, 1.0), + colormap = :viridis, + colorrange = (0.0, 1.0), + highclip = (:red, 0.2), lowclip = (:green, 0.2), ) cb = Colorbar(fig[1, 2], ct; label = "Velocity magnitude") fig @@ -233,11 +235,12 @@ curl_fourier!(ω̂s, v̂s, grid_fourier); let fig = Figure(resolution = (700, 600)) ax = Axis3(fig[1, 1]; aspect = :data, xlabel = "x", ylabel = "y", zlabel = "z") - ω_norm = vecnorm(ωs) + ω_norm = parent(vecnorm(ωs)) ct = contour!( ax, grid.x, grid.y, grid.z, ω_norm; alpha = 0.1, levels = 0.8:0.2:2.0, colormap = :viridis, colorrange = (0.8, 2.0), + highclip = (:red, 0.2), lowclip = (:green, 0.2), ) cb = Colorbar(fig[1, 2], ct; label = "Vorticity magnitude") fig @@ -436,7 +439,7 @@ params = (; ) tspan = (0.0, 10.0) -prob = ODEProblem(ns_rhs!, vs_init_ode, tspan, params) +prob = ODEProblem{true}(ns_rhs!, vs_init_ode, tspan, params) integrator = init(prob, RK4(); dt = 1e-3, save_everystep = false); # We finally solve the problem over time and plot the vorticity associated to @@ -484,12 +487,13 @@ fig = let fig[1, 1][1, 1]; title = @lift("t = $(round($t_plot, digits = 3))"), aspect = :data, xlabel = "x", ylabel = "y", zlabel = "z", ) - ω_mag = @lift vecnorm($ω⃗_plot) + ω_mag = @lift parent(vecnorm($ω⃗_plot)) ω_mag_norm = @lift $ω_mag ./ maximum($ω_mag) ct = contour!( ax, grid.x, grid.y, grid.z, ω_mag_norm; alpha = 0.3, levels = 3, colormap = :viridis, colorrange = (0.0, 1.0), + highclip = (:red, 0.2), lowclip = (:green, 0.2), ) cb = Colorbar(fig[1, 1][1, 2], ct; label = "Normalised vorticity magnitude") ax_sp = Axis( diff --git a/docs/make.jl b/docs/make.jl index c0d8c2fa..fc6d6752 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -43,7 +43,7 @@ examples = MPI.bcast(examples, 0, comm) :: Vector{String} @time makedocs( modules = [PencilFFTs], authors = "Juan Ignacio Polanco and contributors", - repo = "https://github.com/jipolanco/PencilFFTs.jl/blob/{commit}{path}#L{line}", + repo = Remotes.GitHub("jipolanco", "PencilFFTs.jl"), sitename = "PencilFFTs.jl", format = Documenter.HTML( prettyurls = true, # needed for correct path to movies (Navier-Stokes example) @@ -69,12 +69,6 @@ examples = MPI.bcast(examples, 0, comm) :: Vector{String} "benchmarks.md", ], doctest = true, - # linkcheck = true, - linkcheck_ignore = [ - # This URL is correct, but gets incorrectly flagged by linkcheck. - "https://jipolanco.github.io/PencilArrays.jl/dev/PencilArrays/#PencilArrays.Pencils.range_local-Tuple{Union{PencilArray,%20Union{Tuple{Vararg{A,N}%20where%20N},%20AbstractArray{A,N}%20where%20N}%20where%20A%3C:PencilArray}}", - ], - # checkdocs = :all, ) if rank == 0