Use CairoMakie v0.11 for example/docs (#3443)

* use CairoMakie v0.11 * fix doctest * resolve dependencies * fix journal name
CliMA · Jan 25, 2024 · 34e9fab · 34e9fab
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diff --git a/docs/Manifest.toml b/docs/Manifest.toml
diff --git a/docs/Project.toml b/docs/Project.toml
@@ -11,7 +11,7 @@ Polynomials = "f27b6e38-b328-58d1-80ce-0feddd5e7a45"
 TimesDates = "bdfc003b-8df8-5c39-adcd-3a9087f5df4a"
 
 [compat]
-CairoMakie = "0.10.11"
+CairoMakie = "0.11"
 Documenter = "1"
 DocumenterCitations = "1"
 Literate = "≥2.9.0"

diff --git a/docs/oceananigans.bib b/docs/oceananigans.bib
@@ -644,7 +644,7 @@ @article{Verstappen18
 	title = {How much eddy dissipation is needed to counterbalance the nonlinear production of small, unresolved scales in a large-eddy simulation of turbulence?},
 	volume = {176},
 	doi = {10.1016/j.compfluid.2016.12.016},
-	journal = {Computers & Fluids},
+	journal = {Computers \& Fluids},
 	author = {Verstappen, Roel},
 	year = {2018},
 	pages = {276--284}
@@ -665,7 +665,7 @@ @article{Bruneau06
 	volume = {35},
 	doi = {10/fvshbk},
 	number = {3},
-	journal = {Computers & Fluids},
+	journal = {Computers \& Fluids},
 	author = {Bruneau, Charles-Henri and Saad, Mazen},
 	year = {2006},
 	pages = {326--348}
@@ -676,7 +676,7 @@ @article{Botella98
 	volume = {27},
 	doi = {10/chbd5b},
 	number = {4},
-	journal = {Computers & Fluids},
+	journal = {Computers \& Fluids},
 	author = {Botella, O. and Peyret, R.},
 	year = {1998},
 	pages = {421--433}

diff --git a/docs/src/model_setup/grids.md b/docs/src/model_setup/grids.md
@@ -144,7 +144,7 @@ We can easily visualize the spacing of ``y`` and ``z`` directions.
 ```@example 1
 using CairoMakie
 
-fig = Figure(resolution=(800, 900))
+fig = Figure(size=(800, 900))
 
 ax1 = Axis(fig[1, 1]; xlabel = "y (m)", ylabel = "y-spacing (m)", limits = (nothing, (0, 250)))
 lines!(ax1, grid.yᵃᶜᵃ[1:Ny], grid.Δyᵃᶜᵃ[1:Ny])

diff --git a/examples/baroclinic_adjustment.jl b/examples/baroclinic_adjustment.jl
@@ -221,7 +221,7 @@ nothing #hide
 # Then we create a 3D axis. We use `zonal_slice_displacement` to control where the plot of the instantaneous
 # zonal average flow is located.
 
-fig = Figure(resolution = (1600, 800))
+fig = Figure(size = (1600, 800))
 
 zonal_slice_displacement = 1.2
 
@@ -309,7 +309,7 @@ yv = yv ./ 1e3 # convert m -> km
 
 set_theme!(Theme(fontsize=24))
 
-fig = Figure(resolution=(1800, 1000))
+fig = Figure(size=(1800, 1000))
 
 axb = Axis(fig[1, 2], xlabel="x (km)", ylabel="y (km)", aspect=1)
 axζ = Axis(fig[1, 3], xlabel="x (km)", ylabel="y (km)", aspect=1, yaxisposition=:right)

diff --git a/examples/convecting_plankton.jl b/examples/convecting_plankton.jl
@@ -70,7 +70,7 @@ set_theme!(Theme(fontsize = 24, linewidth=2))
 
 times = range(0, 12hours, length=100)
 
-fig = Figure(resolution = (800, 300))
+fig = Figure(size = (800, 300))
 ax = Axis(fig[1, 1]; xlabel = "Time (hours)", ylabel = "Surface buoyancy flux (m² s⁻³)")
 
 flux_time_series = [buoyancy_flux(0, t, buoyancy_flux_parameters) for t in times]
@@ -239,7 +239,7 @@ w_lims = (-w_lim, w_lim)
 
 P_lims = (0.95, 1.1)
 
-fig = Figure(resolution = (1200, 1000))
+fig = Figure(size = (1200, 1000))
 
 ax_w = Axis(fig[2, 2]; xlabel = "x (m)", ylabel = "z (m)", aspect = 1)
 ax_P = Axis(fig[3, 2]; xlabel = "x (m)", ylabel = "z (m)", aspect = 1)

diff --git a/examples/horizontal_convection.jl b/examples/horizontal_convection.jl
@@ -222,7 +222,7 @@ axis_kwargs = (xlabel = L"x / H",
                aspect = Lx / H,
                titlesize = 20)
 
-fig = Figure(resolution = (600, 1100))
+fig = Figure(size = (600, 1100))
 
 ax_s = Axis(fig[2, 1];
             title = L"speed, $(u^2+w^2)^{1/2} / (L_x b_*) ^{1/2}", axis_kwargs...)
@@ -336,7 +336,7 @@ for i = 1:length(t)
     Nu[i] = χ[1, 1, 1] / χ_diff
 end
 
-fig = Figure(resolution = (850, 450))
+fig = Figure(size = (850, 450))
 
 ax_KE = Axis(fig[1, 1], xlabel = L"t \, (b_* / L_x)^{1/2}", ylabel = L"KE $ / (L_x b_*)$")
 lines!(ax_KE, t, kinetic_energy; linewidth = 3)

diff --git a/examples/internal_wave.jl b/examples/internal_wave.jl
@@ -138,7 +138,7 @@ run!(simulation)
 using CairoMakie
 set_theme!(Theme(fontsize = 24))
 
-fig = Figure(resolution = (600, 600))
+fig = Figure(size = (600, 600))
 
 ax = Axis(fig[2, 1]; xlabel = "x", ylabel = "z",
           limits = ((-π, π), (-π, π)), aspect = AxisAspect(1))

diff --git a/examples/kelvin_helmholtz_instability.jl b/examples/kelvin_helmholtz_instability.jl
@@ -48,7 +48,7 @@ zC = znodes(grid, Center())
 
 Ri, h = B.parameters
 
-fig = Figure(resolution = (850, 450))
+fig = Figure(size = (850, 450))
 
 ax = Axis(fig[1, 1], xlabel = "U(z)", ylabel = "z")
 lines!(ax, shear_flow.(0, zC, 0), zC; linewidth = 3)
@@ -307,7 +307,7 @@ growth_rates, power_method_data = estimate_growth_rate(simulation, mean_perturba
 
 n = Observable(1)
 
-fig = Figure(resolution=(800, 600))
+fig = Figure(size=(800, 600))
 
 kwargs = (xlabel="x", ylabel="z", limits = ((xω[1], xω[end]), (zω[1], zω[end])), aspect=1,)
 
@@ -415,7 +415,7 @@ n = Observable(1)
 ωₙ = @lift interior(ω_timeseries, :, 1, :, $n)
 bₙ = @lift interior(b_timeseries, :, 1, :, $n)
 
-fig = Figure(resolution=(800, 600))
+fig = Figure(size=(800, 600))
 
 kwargs = (xlabel="x", ylabel="z", limits = ((xω[1], xω[end]), (zω[1], zω[end])), aspect=1,)
 
@@ -474,7 +474,7 @@ n = Observable(1)
 Ωₙ = @lift interior(Ω_timeseries, :, 1, :, $n)
 Bₙ = @lift interior(B_timeseries, :, 1, :, $n)
 
-fig = Figure(resolution=(800, 600))
+fig = Figure(size=(800, 600))
 
 kwargs = (xlabel="x", ylabel="z", limits = ((xω[1], xω[end]), (zω[1], zω[end])), aspect=1,)
 

diff --git a/examples/langmuir_turbulence.jl b/examples/langmuir_turbulence.jl
@@ -269,7 +269,7 @@ wxy_title = @lift string("w(x, y, t) at z=-8 m and t = ", prettytime(times[$n]))
 wxz_title = @lift string("w(x, z, t) at y=0 m and t = ", prettytime(times[$n]))
 uxz_title = @lift string("u(x, z, t) at y=0 m and t = ", prettytime(times[$n]))
 
-fig = Figure(resolution = (850, 850))
+fig = Figure(size = (850, 850))
 
 ax_B = Axis(fig[1, 4];
             xlabel = "Buoyancy (m s⁻²)",

diff --git a/examples/ocean_wind_mixing_and_convection.jl b/examples/ocean_wind_mixing_and_convection.jl
@@ -63,7 +63,7 @@ grid = RectilinearGrid(size = (Nx, Nx, Nz),
 
 # We plot vertical spacing versus depth to inspect the prescribed grid stretching:
 
-fig = Figure(resolution=(1200, 800))
+fig = Figure(size=(1200, 800))
 ax = Axis(fig[1, 1], ylabel = "Depth (m)", xlabel = "Vertical spacing (m)")
 
 lines!(ax, zspacings(grid, Center()), znodes(grid, Center()))
@@ -258,7 +258,7 @@ n = Observable(intro)
  Sₙ = @lift interior(time_series.S[$n],  :, 1, :)
 νₑₙ = @lift interior(time_series.νₑ[$n], :, 1, :)
 
-fig = Figure(resolution = (1000, 500))
+fig = Figure(size = (1000, 500))
 
 axis_kwargs = (xlabel="x (m)",
                ylabel="z (m)",

diff --git a/examples/shallow_water_Bickley_jet.jl b/examples/shallow_water_Bickley_jet.jl
@@ -166,7 +166,7 @@ nothing #hide
 # Read in the `output_writer` for the two-dimensional fields and then create an animation 
 # showing both the total and perturbation vorticities.
 
-fig = Figure(resolution = (1200, 660))
+fig = Figure(size = (1200, 660))
 
 axis_kwargs = (xlabel = "x", ylabel = "y")
 ax_ω  = Axis(fig[2, 1]; title = "Total vorticity, ω", axis_kwargs...)

diff --git a/examples/tilted_bottom_boundary_layer.jl b/examples/tilted_bottom_boundary_layer.jl
@@ -207,7 +207,7 @@ xv, yv, zv = nodes(V)
 
 ds = NCDataset(simulation.output_writers[:fields].filepath, "r")
 
-fig = Figure(resolution = (800, 600))
+fig = Figure(size = (800, 600))
 
 axis_kwargs = (xlabel = "Across-slope distance (m)",
                ylabel = "Slope-normal\ndistance (m)",

diff --git a/examples/two_dimensional_turbulence.jl b/examples/two_dimensional_turbulence.jl
@@ -120,7 +120,7 @@ set_theme!(Theme(fontsize = 24))
 
 @info "Making a neat movie of vorticity and speed..."
 
-fig = Figure(resolution = (800, 500))
+fig = Figure(size = (800, 500))
 
 axis_kwargs = (xlabel = "x",
                ylabel = "y",

diff --git a/src/AbstractOperations/conditional_operations.jl b/src/AbstractOperations/conditional_operations.jl
@@ -61,7 +61,7 @@ julia> f(i, j, k, grid, c) = i < 2; d = condition_operand(cos, c, f, 10)
 ConditionalOperation at (Center, Center, Center)
 ├── operand: 2×1×1 Field{Center, Center, Center} on RectilinearGrid on CPU
 ├── grid: 2×1×1 RectilinearGrid{Float64, Periodic, Periodic, Bounded} on CPU with 3×3×3 halo
-├── func: cos (generic function with 40 methods)
+├── func: cos (generic function with 31 methods)
 ├── condition: f (generic function with 1 method)
 └── mask: 10