Merge pull request #288 from FourierFlows/ncc/updates

Convert example to use Makie.jl instead of Plots.jl + add links to examples in Docs/Modules
FourierFlows · Aug 30, 2022 · 5caedde · 5caedde · navidcy · Aug 30, 2022
2 parents e15f1fb + e0a1975
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diff --git a/Project.toml b/Project.toml
@@ -21,7 +21,7 @@ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 CUDA = "^1, ^2.4.2, 3.0.0 - 3.6.4, ^3.7.1"
 DocStringExtensions = "^0.8, 0.9"
 FFTW = "^1"
-FourierFlows = "^0.9.2"
+FourierFlows = "^0.9.4"
 JLD2 = "^0.1, ^0.2, ^0.3, ^0.4"
 Reexport = "^0.2, ^1"
 SpecialFunctions = "^0.10, ^1, 2"

diff --git a/README.md b/README.md
@@ -62,14 +62,17 @@ Some animations created with GeophysicalFlows.jl are [online @ youtube].
 
 ## Modules
 
-* `TwoDNavierStokes`: the two-dimensional vorticity equation.
-* `SingleLayerQG`: the barotropic or equivalent-barotropic quasi-geostrophic equation, which 
-  generalizes `TwoDNavierStokes` to cases with topography, Coriolis parameters of the form 
-  `f = f₀ + βy`, and finite Rossby radius of deformation.
-* `MultiLayerQG`: a multi-layer quasi-geostrophic model over topography and with the ability 
-  to impose a zonal flow `U_n(y)` in each layer.
-* `SurfaceQG`: a surface quasi-geostrophic model.
-* `BarotropicQGQL`: the quasi-linear barotropic quasi-geostrophic equation.
+* [`TwoDNavierStokes`](https://fourierflows.github.io/GeophysicalFlowsDocumentation/stable/modules/twodnavierstokes/): the
+  two-dimensional vorticity equation.
+* [`SingleLayerQG`](https://fourierflows.github.io/GeophysicalFlowsDocumentation/stable/modules/singlelayerqg/): the barotropic
+  or equivalent-barotropic quasi-geostrophic equation, which generalizes `TwoDNavierStokes` to cases with topography, Coriolis
+  parameters of the form `f = f₀ + βy`, and finite Rossby radius of deformation.
+* [`MultiLayerQG`](https://fourierflows.github.io/GeophysicalFlowsDocumentation/stable/modules/multilayerqg/): a multi-layer
+  quasi-geostrophic model over topography allowing to impose a zonal flow `U_n(y)` in each layer.
+* [`SurfaceQG`](https://fourierflows.github.io/GeophysicalFlowsDocumentation/stable/modules/surfaceqg/): a surface
+  quasi-geostrophic model.
+* [`BarotropicQGQL`](https://fourierflows.github.io/GeophysicalFlowsDocumentation/stable/modules/barotropicqgql/): the
+  quasi-linear barotropic quasi-geostrophic equation.
 
 
 ## Scalability
@@ -143,7 +146,6 @@ than happy to help along the way.
 
 For more information, check out our [contributors' guide](https://github.com/FourierFlows/GeophysicalFlows.jl/blob/main/CONTRIBUTING.md).
 
-
 [FourierFlows.jl]: https://github.com/FourierFlows/FourierFlows.jl
 [documentation]: https://fourierflows.github.io/GeophysicalFlowsDocumentation/dev/
 [online @ youtube]: https://www.youtube.com/channel/UCO_0ugkNUwCsFUMtepwYTqw
diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,11 +1,11 @@
 [deps]
 CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
-Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 
 [compat]
 CUDA = "^1, ^2.4.2, 3.0.0 - 3.6.4, ^3.7.1"
 Literate = "≥2.9.0"
-Plots = "1.10.1 - 1.21.3"
diff --git a/docs/make.jl b/docs/make.jl
@@ -1,14 +1,9 @@
 using
   Documenter,
   Literate,
-  Plots,   # to not capture precompilation output
+  CairoMakie,   # to not capture precompilation output
   GeophysicalFlows
 
-# Gotta set this environment variable when using the GR run-time on CI machines.
-# This happens as examples will use Plots.jl to make plots and movies.
-# See: https://github.com/jheinen/GR.jl/issues/278
-ENV["GKSwstype"] = "100"
-
 #####
 ##### Generate literated examples
 #####

diff --git a/docs/src/modules/barotropicqgql.md b/docs/src/modules/barotropicqgql.md
@@ -115,4 +115,4 @@ Other diagnostic include: [`dissipation`](@ref GeophysicalFlows.BarotropicQGQL.d
 
 ## Examples
 
-- [`examples/barotropicqgql_betaforced.jl`](../../literated/barotropicqgql_betaforced/): A script that simulates forced-dissipative quasi-linear quasi-geostrophic flow on a beta plane demonstrating zonation. The forcing is temporally delta-correlated and its spatial structure is isotropic with power in a narrow annulus of total radius ``k_f`` in wavenumber space. This example demonstrates that the anisotropic inverse energy cascade is not required for zonation.
+- [`examples/barotropicqgql_betaforced.jl`](@ref barotropicqgql_betaforced_example): Simulate forced-dissipative quasi-linear quasi-geostrophic flow on a beta plane demonstrating zonation. The forcing is temporally delta-correlated and its spatial structure is isotropic with power in a narrow annulus of total radius ``k_f`` in wavenumber space. This example demonstrates that the anisotropic inverse energy cascade is not required for zonation.
diff --git a/docs/src/modules/multilayerqg.md b/docs/src/modules/multilayerqg.md
@@ -146,4 +146,4 @@ GeophysicalFlows.MultiLayerQG.fluxes
 
 ## Examples
 
- - [`examples/multilayerqg_2layer.jl`](../../literated/multilayerqg_2layer/): A script that simulates the growth and equilibration of baroclinic eddy turbulence in the Phillips 2-layer model.
+ - [`examples/multilayerqg_2layer.jl`](@ref multilayerqg_2layer_example): Simulate the growth and equilibration of baroclinic eddy turbulence in the Phillips 2-layer model.
diff --git a/docs/src/modules/singlelayerqg.md b/docs/src/modules/singlelayerqg.md
@@ -110,10 +110,10 @@ Other diagnostic include: [`energy_dissipation`](@ref GeophysicalFlows.SingleLay
 
 ## Examples
 
-- [`examples/singlelayerqg_betadecay.jl`](../../literated/singlelayerqg_betadecay/): A script that simulates decaying quasi-geostrophic flow on a beta plane demonstrating zonation.
+- [`examples/singlelayerqg_betadecay.jl`](@ref singlelayerqg_betadecay_example): Simulate decaying quasi-geostrophic flow on a beta plane demonstrating zonation.
 
-- [`examples/singlelayerqg_betaforced.jl`](../../literated/singlelayerqg_betaforced/): A script that simulates forced-dissipative quasi-geostrophic flow on a beta plane demonstrating zonation. The forcing is temporally delta-correlated with isotropic spatial structure with power in a narrow annulus in wavenumber space with total wavenumber ``k_f``.
+- [`examples/singlelayerqg_betaforced.jl`](@ref singlelayerqg_betaforced_example): Simulate forced-dissipative quasi-geostrophic flow on a beta plane demonstrating zonation. The forcing is temporally delta-correlated with isotropic spatial structure with power in a narrow annulus in wavenumber space with total wavenumber ``k_f``.
 
-- [`examples/singlelayerqg_decay_topography.jl`](../../literated/singlelayerqg_decay_topography/): A script that simulates two dimensional turbulence (barotropic quasi-geostrophic flow with ``\beta=0``) above topography.
+- [`examples/singlelayerqg_decay_topography.jl`](@ref singlelayerqg_decay_topography_example): Simulate two dimensional turbulence (barotropic quasi-geostrophic flow with ``\beta=0``) above topography.
 
-- [`examples/singlelayerqg_decaying_barotropic_equivalentbarotropic.jl`](../../literated singlelayerqg_decaying_barotropic_equivalentbarotropic/): A script that simulates two dimensional turbulence (``\beta=0``) with both infinite and finite Rossby radius of deformation and compares the evolution of the two.
+- [`examples/singlelayerqg_decaying_barotropic_equivalentbarotropic.jl`](@ref singlelayerqg_decaying_barotropic_equivalentbarotropic_example): Simulate two dimensional turbulence (``\beta=0``) with both infinite and finite Rossby radius of deformation and compares the evolution of the two.
diff --git a/docs/src/modules/surfaceqg.md b/docs/src/modules/surfaceqg.md
@@ -96,6 +96,6 @@ Other diagnostic include: [`buoyancy_dissipation`](@ref GeophysicalFlows.Surface
 
 ## Examples
 
-- [`examples/surfaceqg_decaying.jl`](../../literated/surfaceqg_decaying/): A script that simulates decaying surface quasi-geostrophic flow with a prescribed initial buoyancy field, producing an animation of the evolution of the surface buoyancy.
+- [`examples/surfaceqg_decaying.jl`](@ref surfaceqg_decaying_example): Simulate decaying surface quasi-geostrophic flow with a prescribed initial buoyancy field.
 
   > Capet, X. et al., (2008). Surface kinetic energy transfer in surface quasi-geostrophic flows. *J. Fluid Mech.*, **604**, 165-174.
diff --git a/docs/src/modules/twodnavierstokes.md b/docs/src/modules/twodnavierstokes.md
@@ -90,10 +90,10 @@ Other diagnostic include: [`energy_dissipation`](@ref GeophysicalFlows.TwoDNavie
 
 ## Examples
 
-- [`examples/twodnavierstokes_decaying.jl`](../../literated/twodnavierstokes_decaying/): A script that simulates decaying two-dimensional turbulence reproducing the results by
+- [`examples/twodnavierstokes_decaying.jl`](@ref twodnavierstokes_decaying_example): Simulates decaying two-dimensional turbulence reproducing the results by:
 
   > McWilliams, J. C. (1984). The emergence of isolated coherent vortices in turbulent flow. *J. Fluid Mech.*, **146**, 21-43.
 
-- [`examples/twodnavierstokes_stochasticforcing.jl`](../../literated/twodnavierstokes_stochasticforcing/): A script that simulates forced-dissipative two-dimensional turbulence with isotropic temporally delta-correlated stochastic forcing.
+- [`examples/twodnavierstokes_stochasticforcing.jl`](@ref twodnavierstokes_stochasticforcing_example): Simulate forced-dissipative two-dimensional turbulence with isotropic temporally delta-correlated stochastic forcing.
 
-- [`examples/twodnavierstokes_stochasticforcing_budgets.jl`](../../literated/twodnavierstokes_stochasticforcing_budgets/): A script that simulates forced-dissipative two-dimensional turbulence demonstrating how we can compute the energy and enstrophy budgets.
+- [`examples/twodnavierstokes_stochasticforcing_budgets.jl`](@ref twodnavierstokes_stochasticforcing_budgets_example): Simulate forced-dissipative two-dimensional turbulence demonstrating how we can compute the energy and enstrophy budgets.
diff --git a/examples/Project.toml b/examples/Project.toml
@@ -1,11 +1,8 @@
 [deps]
 CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 GeophysicalFlows = "44ee3b1c-bc02-53fa-8355-8e347616e15e"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
-Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
-
-[compat]
-Plots = "≥ 1.10.1"