Update to Documenter.jl 1.0 (#68)

* Update NS example to latest Makie

* Use Documenter 1.0

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"

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(

docs/make.jl

@@ -43,7 +43,7 @@ examples = MPI.bcast(examples, 0, comm) :: Vector{String}
 @time makedocs(
     modules = [PencilFFTs],
     authors = "Juan Ignacio Polanco <[email protected]> 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