Merge pull request #293 from FourierFlows/ncc/views

Bit of cleanup and using `views` in `MultiLayerQG` module

.github/workflows/Documenter.yml

@@ -12,13 +12,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.8.0
+        uses: styfle/cancel-workflow-action@0.11.0
         with:
           access_token: ${{ github.token }}
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - uses: julia-actions/setup-julia@latest
         with:
-          version: '1.6'
+          version: '1.8'
       - name: Install dependencies
         run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
       - name: Build and deploy

docs/Project.toml

@@ -2,11 +2,11 @@
 CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-Glob = "c27321d9-0574-5035-807b-f59d2c89b15c"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 
 [compat]
-CUDA = "^1, ^2.4.2, 3.0.0 - 3.6.4, ^3.7.1"
+CairoMakie = "< 0.10.5"
+CUDA = "1, 2.4.2, 3.0.0 - 3.6.4, 3.7.1, 4"
 Literate = "≥2.9.0"

docs/make.jl

@@ -1,9 +1,9 @@
-using
-  Documenter,
-  Literate,
-  CairoMakie,   # to not capture precompilation output
-  GeophysicalFlows,
-  Glob
+using Documenter, Literate
+
+using CairoMakie
+# CairoMakie.activate!(type = "svg")
+
+using GeophysicalFlows
 
 #####
 ##### Generate literated examples
@@ -25,23 +25,22 @@ examples = [
   "surfaceqg_decaying.jl",
 ]
 
+
 for example in examples
   withenv("GITHUB_REPOSITORY" => "FourierFlows/GeophysicalFlowsDocumentation") do
     example_filepath = joinpath(EXAMPLES_DIR, example)
-    Literate.markdown(example_filepath, OUTPUT_DIR; flavor = Literate.DocumenterFlavor())
-    Literate.notebook(example_filepath, OUTPUT_DIR)
-    Literate.script(example_filepath, OUTPUT_DIR)
+    withenv("JULIA_DEBUG" => "Literate") do
+      Literate.markdown(example_filepath, OUTPUT_DIR;
+                        flavor = Literate.DocumenterFlavor(), execute = true)
+    end
   end
 end
 
+
 #####
 ##### Build and deploy docs
 #####
 
-# Set up a timer to print a space ' ' every 240 seconds. This is to avoid CI machines
-# timing out when building demanding Literate.jl examples.
-Timer(t -> println(" "), 0, interval=240)
-
 format = Documenter.HTML(
   collapselevel = 2,
      prettyurls = get(ENV, "CI", nothing) == "true",
@@ -50,14 +49,14 @@ format = Documenter.HTML(
 
 makedocs(
  modules = [GeophysicalFlows],
- doctest = false,
+ doctest = true,
    clean = true,
 checkdocs = :all,
   format = format,
- authors = "Navid C. Constantinou and Gregory L. Wagner",
+ authors = "Navid C. Constantinou, Gregory L. Wagner, and contributors",
 sitename = "GeophysicalFlows.jl",
    pages = Any[
-            "Home"    => "index.md",
+            "Home" => "index.md",
             "Installation instructions" => "installation_instructions.md",
             "Aliasing" => "aliasing.md",
             "GPU" => "gpu.md",
@@ -100,9 +99,24 @@ sitename = "GeophysicalFlows.jl",
            ]
 )
 
-@info "Cleaning up temporary .jld2 and .nc files created by doctests..."
+@info "Clean up temporary .jld2 and .nc output created by doctests or literated examples..."
+
+"""
+    recursive_find(directory, pattern)
+
+Return list of filepaths within `directory` that contains the `pattern::Regex`.
+"""
+recursive_find(directory, pattern) =
+    mapreduce(vcat, walkdir(directory)) do (root, dirs, files)
+        joinpath.(root, filter(contains(pattern), files))
+    end
+
+files = []
+for pattern in [r"\.jld2", r"\.nc"]
+    global files = vcat(files, recursive_find(@__DIR__, pattern))
+end
 
-for file in vcat(glob("docs/*.jld2"), glob("docs/*.nc"))
+for file in files
     rm(file)
 end
 

docs/src/stochastic_forcing.md

@@ -321,7 +321,7 @@ hl3 = lines!(ax, μ * t, E_str[:, 1];
 
 Legend(fig[1, 2], [hl1, hl2, hl3], ["½ xₜ²", "Eₜ (Ito)", "Eₜ (Stratonovich)"])
 
-save("assets/energy_comparison.svg", fig); nothing # hide
+save("assets/energy_comparison.svg", fig); nothing #hide
 ```
 
 ![energy_comparison](assets/energy_comparison.svg)
@@ -378,7 +378,7 @@ hl3 = lines!(ax2, μ * t[1:nsteps-1], dEdt_theory[1:nsteps-1];
 Legend(fig[2, 2], [hl1, hl2, hl3],
                   ["numerical 𝖽⟨E⟩/𝖽t", "⟨work - dissipation⟩", "theoretical 𝖽⟨E⟩/𝖽t"])
 
-save("assets/energy_budgets_Ito.svg", fig); nothing # hide
+save("assets/energy_budgets_Ito.svg", fig); nothing #hide
 ```
 
 ![energy_budgets_Ito](assets/energy_budgets_Ito.svg)
@@ -423,7 +423,7 @@ hl3 = lines!(ax2, μ * t[1:nsteps-1], dEdt_theory[1:nsteps-1];
 Legend(fig[2, 2], [hl1, hl2, hl3],
                   ["numerical 𝖽⟨E⟩/𝖽t", "⟨work - dissipation⟩", "theoretical 𝖽⟨E⟩/𝖽t"])
 
-save("assets/energy_budgets_Stratonovich.svg", fig); nothing # hide
+save("assets/energy_budgets_Stratonovich.svg", fig); nothing #hide
 ```
 
 ![energy_budgets_Stratonovich](assets/energy_budgets_Stratonovich.svg)

examples/barotropicqgql_betaforced.jl

@@ -1,7 +1,5 @@
 # # [Quasi-Linear forced-dissipative barotropic QG beta-plane turbulence](@id barotropicqgql_betaforced_example)
 #
-#md # This example can be viewed as a Jupyter notebook via [![](https://img.shields.io/badge/show-nbviewer-579ACA.svg)](@__NBVIEWER_ROOT_URL__/literated/barotropicqgql_betaforced.ipynb).
-#
 # A simulation of forced-dissipative barotropic quasi-geostrophic turbulence on 
 # a beta plane under the *quasi-linear approximation*. The dynamics include 
 # linear drag and stochastic excitation.
@@ -24,12 +22,12 @@ using Statistics: mean
 
 parsevalsum = FourierFlows.parsevalsum
 record = CairoMakie.record                # disambiguate between CairoMakie.record and CUDA.record
-nothing # hide
+nothing #hide
 
 # ## Choosing a device: CPU or GPU
 
 dev = CPU()     # Device (CPU/GPU)
-nothing # hide
+nothing #hide
 
 
 # ## Numerical parameters and time-stepping parameters
@@ -39,15 +37,15 @@ stepper = "FilteredRK4"  # timestepper
      dt = 0.05           # timestep
  nsteps = 8000           # total number of time-steps
  nsubs  = 10             # number of time-steps for intermediate logging/plotting (nsteps must be multiple of nsubs)
-nothing # hide
+nothing #hide
 
 
 # ## Physical parameters
 
 L = 2π        # domain size
 β = 10.0      # planetary PV gradient
 μ = 0.01      # bottom drag
-nothing # hide
+nothing #hide
 
 
 # ## Forcing
@@ -72,12 +70,12 @@ forcing_spectrum = @. exp(-(K - forcing_wavenumber)^2 / (2 * forcing_bandwidth^2
 
 ε0 = parsevalsum(forcing_spectrum .* grid.invKrsq / 2, grid) / (grid.Lx * grid.Ly)
 @. forcing_spectrum *= ε/ε0       # normalize forcing to inject energy at rate ε
-nothing # hide
+nothing #hide
 
 
 # We reset of the random number generator for reproducibility
 if dev==CPU(); Random.seed!(1234); else; CUDA.seed!(1234); end
-nothing # hide
+nothing #hide
 
 
 # Next we construct function `calcF!` that computes a forcing realization every timestep.
@@ -91,7 +89,7 @@ function calcF!(Fh, sol, t, clock, vars, params, grid)
 
   return nothing
 end
-nothing # hide
+nothing #hide
 
 
 # ## Problem setup
@@ -102,13 +100,13 @@ nothing # hide
 # Thus, we choose not to do any dealiasing by providing `aliased_fraction=0`.
 prob = BarotropicQGQL.Problem(dev; nx=n, Lx=L, β, μ, dt, stepper, 
                               calcF=calcF!, stochastic=true, aliased_fraction=0)
-nothing # hide
+nothing #hide
 
 # and define some shortcuts.
 sol, clock, vars, params, grid = prob.sol, prob.clock, prob.vars, prob.params, prob.grid
 x,  y  = grid.x, grid.y
 Lx, Ly = grid.Lx, grid.Ly
-nothing # hide
+nothing #hide
 
 
 # First let's see how a forcing realization looks like. Note that when plotting, we decorate 
@@ -136,24 +134,24 @@ fig
 
 # Our initial condition is simply fluid at rest.
 BarotropicQGQL.set_zeta!(prob, device_array(dev)(zeros(grid.nx, grid.ny)))
-nothing # hide
+nothing #hide
 
 # ## Diagnostics
 
 # Create Diagnostics -- `energy` and `enstrophy` are functions imported at the top.
 E = Diagnostic(BarotropicQGQL.energy, prob; nsteps)
 Z = Diagnostic(BarotropicQGQL.enstrophy, prob; nsteps)
-nothing # hide
+nothing #hide
 
 # We can also define our custom diagnostics via functions.
 zetaMean(prob) = prob.sol[1, :]
 
 zMean = Diagnostic(zetaMean, prob; nsteps, freq=10)  # the zonal-mean vorticity
-nothing # hide
+nothing #hide
 
 # We combile all diags in a list.
 diags = [E, Z, zMean] # A list of Diagnostics types passed to "stepforward!" will  be updated every timestep.
-nothing # hide
+nothing #hide
 
 
 # ## Output
@@ -163,12 +161,12 @@ filepath = "."
 plotpath = "./plots_forcedbetaQLturb"
 plotname = "snapshots"
 filename = joinpath(filepath, "forcedbetaQLturb.jld2")
-nothing # hide
+nothing #hide
 
 # Do some basic file management,
 if isfile(filename); rm(filename); end
 if !isdir(plotpath); mkdir(plotpath); end
-nothing # hide
+nothing #hide
 
 # and then create Output.
 get_sol(prob) = prob.sol # extracts the Fourier-transformed solution
@@ -255,7 +253,7 @@ lines!(axū, 0y, y; linewidth = 1, linestyle=:dash)
 lines!(axE, μt, energy; linewidth = 3)
 lines!(axZ, μt, enstrophy; linewidth = 3, color = :red)
 
-nothing # hide
+nothing #hide
 
 
 # ## Time-stepping the `Problem` forward
@@ -291,7 +289,7 @@ record(fig, "barotropicqgql_betaforced.mp4", frames, framerate = 18) do j
   stepforward!(prob, diags, nsubs)
   BarotropicQGQL.updatevars!(prob)
 end
-nothing # hide
+nothing #hide
 
 # ![](barotropicqgql_betaforced.mp4)
 

examples/multilayerqg_2layer.jl

@@ -1,7 +1,5 @@
 # # [Phillips model of Baroclinic Instability](@id multilayerqg_2layer_example)
 #
-#md # This example can be viewed as a Jupyter notebook via [![](https://img.shields.io/badge/show-nbviewer-579ACA.svg)](@__NBVIEWER_ROOT_URL__/literated/multilayerqg_2layer.ipynb).
-#
 # A simulation of the growth of barolinic instability in the Phillips 2-layer model
 # when we impose a vertical mean flow shear as a difference ``\Delta U`` in the
 # imposed, domain-averaged, zonal flow at each layer.
@@ -26,7 +24,7 @@ using Random: seed!
 # ## Choosing a device: CPU or GPU
 
 dev = CPU()     # Device (CPU/GPU)
-nothing # hide
+nothing #hide
 
 
 # ## Numerical parameters and time-stepping parameters
@@ -36,7 +34,7 @@ stepper = "FilteredRK4"  # timestepper
      dt = 2.5e-3         # timestep
  nsteps = 20000          # total number of time-steps
  nsubs  = 50             # number of time-steps for plotting (nsteps must be multiple of nsubs)
-nothing # hide
+nothing #hide
 
 
 # ## Physical parameters
@@ -52,7 +50,7 @@ H = [0.2, 0.8]           # the rest depths of each layer
 U = zeros(nlayers)       # the imposed mean zonal flow in each layer
 U[1] = 1.0
 U[2] = 0.0
-nothing # hide
+nothing #hide
 
 
 # ## Problem setup
@@ -63,12 +61,12 @@ nothing # hide
 
 prob = MultiLayerQG.Problem(nlayers, dev; nx=n, Lx=L, f₀, g, H, ρ, U, μ, β,
                             dt, stepper, aliased_fraction=0)
-nothing # hide
+nothing #hide
 
 # and define some shortcuts.
 sol, clock, params, vars, grid = prob.sol, prob.clock, prob.params, prob.vars, prob.grid
 x, y = grid.x, grid.y
-nothing # hide
+nothing #hide
 
 
 # ## Setting initial conditions
@@ -85,15 +83,15 @@ q₀h = prob.timestepper.filter .* rfft(q₀, (1, 2)) # apply rfft  only in dims
 q₀  = irfft(q₀h, grid.nx, (1, 2))                 # apply irfft only in dims=1, 2
 
 MultiLayerQG.set_q!(prob, q₀)
-nothing # hide
+nothing #hide
 
 
 # ## Diagnostics
 
 # Create Diagnostics -- `energies` function is imported at the top.
 E = Diagnostic(MultiLayerQG.energies, prob; nsteps)
 diags = [E] # A list of Diagnostics types passed to "stepforward!" will  be updated every timestep.
-nothing # hide
+nothing #hide
 
 
 # ## Output
@@ -103,12 +101,12 @@ filepath = "."
 plotpath = "./plots_2layer"
 plotname = "snapshots"
 filename = joinpath(filepath, "2layer.jld2")
-nothing # hide
+nothing #hide
 
 # Do some basic file management
 if isfile(filename); rm(filename); end
 if !isdir(plotpath); mkdir(plotpath); end
-nothing # hide
+nothing #hide
 
 # And then create Output
 
@@ -126,7 +124,7 @@ function get_u(prob)
 end
 
 out = Output(prob, filename, (:sol, get_sol), (:u, get_u))
-nothing # hide
+nothing #hide
 
 
 # ## Visualizing the simulation
@@ -258,7 +256,7 @@ record(fig, "multilayerqg_2layer.mp4", frames, framerate = 18) do j
   stepforward!(prob, diags, nsubs)
   MultiLayerQG.updatevars!(prob)
 end
-nothing # hide
+nothing #hide
 
 # ![](multilayerqg_2layer.mp4)