Nuke Docs via GithubActions + add compat for CairoMakie v0.11, v0.12 (#…

…156) * disable docs previews * add compat for CairoMakie 0.11, 0.12 * Delete .github/workflows/Documenter.yml * Update make.jl * Update near_global_ocean_simulation.jl * import on_architecture * land mask is now handled by OceananicansMakie extension * enable previews previews from the ClimaOceanDocs repo are now deleted every week * simpler visualization of bathymetry + cleanup * add Oceananigans * Delete .github/workflows/DocPreviewCleanup.yml * Update Project.toml * Update Project.toml * define Nt * try shorter simulation * Allow latitude, longitude to be points * Improve single column simulation * Add various show methods and clean up type definitions * Move LatitudeDependentAlbedo to own file * Make latitdue dependent albedo default * Try to fix tabulated albedo but its still broken * Make fluxes SCM friendly * Allow ocean simulations that are already cleaned of calllbacks * Update make and examples * Update example * Run simulation longer * remove commented bit * tweak * tweak * tweak * tweak * fix bug in summary * add CFTime * drop package from its docs Project * Update make.jl * update Oceananigans compat * remove movie * update ECCOMetadata * fix show for OceanSeaIceModel * some tweaks * some tweaks * remove movie * fix hide * remove current figures * remove climaocean * remove T and e * remove debugging statement * use interior for surface fields * use interior for surface fields * fix * delete * add ECCO * minor fixes * remove stray line * fix name * fixes * cleanup * fix docstring0 * tweaks * fix name * fix name * fix makie * tweaks * fix * remove surface fluxes * cleaning --------- Co-authored-by: Gregory L. Wagner <[email protected]>
CliMA · Nov 2, 2024 · 985244e · 985244e
1 parent 8796b45
commit 985244e
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diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml
@@ -151,4 +151,3 @@ steps:
 
   - wait: ~
     continue_on_failure: true
-
diff --git a/.github/workflows/DocPreviewCleanup.yml b/.github/workflows/DocPreviewCleanup.yml
diff --git a/.github/workflows/Documenter.yml b/.github/workflows/Documenter.yml
diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,11 +1,14 @@
 [deps]
+CFTime = "179af706-886a-5703-950a-314cd64e0468"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 DataDeps = "124859b0-ceae-595e-8997-d05f6a7a8dfe"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
+Oceananigans = "9e8cae18-63c1-5223-a75c-80ca9d6e9a09"
 OrthogonalSphericalShellGrids = "c2be9673-fb75-4747-82dc-aa2bb9f4aed0"
 
 [compat]
-CairoMakie = "0.10.12"
+CairoMakie = "0.10.12, 0.11, 0.12"
 DataDeps = "0.7"
 Documenter = "1"
+Oceananigans = "0.93.1"
diff --git a/docs/make.jl b/docs/make.jl
@@ -1,9 +1,7 @@
-pushfirst!(LOAD_PATH, joinpath(@__DIR__, "..")) # add ClimaOcean to environment stack
-
 using
+  ClimaOcean,
   Documenter,
-  Literate,
-  ClimaOcean
+  Literate
 
 ENV["DATADEPS_ALWAYS_ACCEPT"] = "true"
 
@@ -15,11 +13,11 @@ const EXAMPLES_DIR = joinpath(@__DIR__, "..", "examples")
 const OUTPUT_DIR   = joinpath(@__DIR__, "src/literated")
 
 to_be_literated = [
-    # "inspect_ECCO_data.jl",
+    "inspect_ecco_data.jl",
     "generate_bathymetry.jl",
-    "generate_surface_fluxes.jl",
-    # "single_column_simulation.jl",
-    # "mediterranean_simulation_with_ECCO_restoring.jl",
+    # "generate_surface_fluxes.jl",
+    "single_column_os_papa_simulation.jl",
+    # "mediterranean_simulation_with_ecco_restoring.jl",
     "near_global_ocean_simulation.jl"
 ]
 
@@ -34,12 +32,10 @@ end
 ##### Build and deploy docs
 #####
 
-format = Documenter.HTML(
-   collapselevel = 2,
-  size_threshold = nothing,
-      prettyurls = get(ENV, "CI", nothing) == "true",
-       canonical = "https://clima.github.io/ClimaOceanDocumentation/dev/",
-)
+format = Documenter.HTML(collapselevel = 2,
+                         size_threshold = nothing,
+                         prettyurls = get(ENV, "CI", nothing) == "true",
+                         canonical = "https://clima.github.io/ClimaOceanDocumentation/dev/")
 
 pages = [
     "Home" => "index.md",
@@ -52,25 +48,21 @@ pages = [
         ],
 
     "Examples" => [
-        # "Inspect ECCO2 data" => "literated/inspect_ECCO_data.md",
+        "Inspect ECCO2 data" => "literated/inspect_ecco_data.md",
         "Generate bathymetry" => "literated/generate_bathymetry.md",
-        "Surface fluxes" => "literated/generate_surface_fluxes.md",
-        # "Single column simulation" => "literated/single_column_simulation.md",
-        # "Mediterranean simulation with ECCO restoring" => "literated/mediterranean_simulation_with_ECCO_restoring.md",
+        # "Surface fluxes" => "literated/generate_surface_fluxes.md",
+        "Single column simulation" => "literated/single_column_os_papa_simulation.md",
+        # "Mediterranean simulation with ECCO restoring" => "literated/mediterranean_simulation_with_ecco_restoring.md",
         "Near-global Ocean simulation" => "literated/near_global_ocean_simulation.md",
         ]
 ]
 
-makedocs(
-     sitename = "ClimaOcean.jl",
-      modules = [ClimaOcean],
-       format = format,
-        pages = pages,
-      doctest = true,
-        clean = true,
-     warnonly = [:cross_references, :missing_docs],
-    checkdocs = :exports
-)
+makedocs(sitename = "ClimaOcean.jl"; format, pages, 
+         modules = [ClimaOcean],
+         doctest = true,
+         clean = true,
+         warnonly = [:cross_references, :missing_docs],
+         checkdocs = :exports)
 
 @info "Clean up temporary .jld2 and .nc output created by doctests or literated examples..."
 
@@ -95,8 +87,8 @@ end
 
 withenv("GITHUB_REPOSITORY" => "github.com/CliMA/ClimaOceanDocumentation.git") do
     deploydocs(repo = "github.com/CliMA/ClimaOceanDocumentation.git",
-           versions = ["stable" => "v^", "v#.#.#", "dev" => "dev"],
-          forcepush = true,
-          devbranch = "main",
-       push_preview = true)
+               versions = ["stable" => "v^", "dev" => "dev", "v#.#.#"],
+               forcepush = true,
+               devbranch = "main",
+               push_preview = true)
 end
diff --git a/docs/make_without_examples.jl b/docs/make_without_examples.jl
diff --git a/examples/generate_atmos_dataset.jl b/examples/generate_atmos_dataset.jl
@@ -15,4 +15,3 @@ T = Array(interior(Tt[1], 1:4:Nx, 1:4:Ny, 1))
 p = Array(interior(pt[1], 1:4:Nx, 1:4:Ny, 1))
 
 @save "atmospheric_state.jld2" q T p
-
diff --git a/examples/generate_bathymetry.jl b/examples/generate_bathymetry.jl
@@ -1,7 +1,7 @@
 # # Generate bathymetry data for the Mediterranean Sea
 #
-# This script shows how to configure an Immersed boundary grid with realistic bathymetry using ClimaOcean.jl
-# by generating the bathymetry data for the Mediterranean Sea.
+# This example shows how to configure an Immersed boundary grid with realistic bathymetry
+# using ClimaOcean.jl by generating the bathymetry data for the Mediterranean Sea.
 #
 # For this example, we need Oceananigans for the LatitudeLongitudeGrid and Field utilities, 
 # ClimaOcean to donwload and regrid the bathymetry, and CairoMakie to visualize the grid.
@@ -25,15 +25,16 @@ Nλ = 25 * (longitude_range[2] - longitude_range[1])
 grid = LatitudeLongitudeGrid(size = (Nλ, Nφ, 1),
                              latitude = latitude_range,
                              longitude = longitude_range,
-                             z = (0, 1))
+                             z = (0, 1),
+                             halo = (7, 7, 1))
 
 # Next, we generate the bathymetry data for the Mediterranean Sea using the
 # `regrid_bathymetry` function from ClimaOcean. The function downloads the bathymetry
 # data from the ETOPO1 dataset, regrids it to the provided grid, and returns the
 # bathymetry field. The three different regidding procedures below demonstrate the effect
 # of different parameters on the generated bathymetry:
 #
-# - `h_rough`  shows the output of the function with default parameters, which means only
+# - `h_rough` shows the output of the function with default parameters, which means only
 #   one interpolation passes and no restrictions on connected regions.
 # - `h_smooth` shows the output of the function with 40 interpolation passes, which results
 #    in a smoother bathymetry.
@@ -44,7 +45,7 @@ grid = LatitudeLongitudeGrid(size = (Nλ, Nφ, 1),
 h_rough = regrid_bathymetry(grid)
 h_smooth = regrid_bathymetry(grid; interpolation_passes = 40)
 h_one_basin = regrid_bathymetry(grid; major_basins = 1)
-nothing # hide
+nothing #hide
 
 # Finally, we visualize the generated bathymetry data for the Mediterranean Sea using CairoMakie.
 
@@ -59,7 +60,7 @@ interior(h_rough)[land_rough] .= NaN
 land_one_basin = interior(h_one_basin) .>= 0
 interior(h_one_basin)[land_one_basin] .= NaN
 
-fig = Figure(resolution=(850, 1150))
+fig = Figure(size=(850, 1150))
 
 ax = Axis(fig[1, 1], title = "Rough bathymetry", xlabel = "Longitude", ylabel = "Latitude")
 hm = heatmap!(ax, λ, φ, - interior(h_rough, :, :, 1), nan_color=:white, colormap = Reverse(:deep))

diff --git a/examples/generate_surface_fluxes.jl b/examples/generate_surface_fluxes.jl
@@ -3,7 +3,7 @@
 # ClimaOcean uses bulk formulae to estimate the surface exchange of momentum,
 # heat, and water vapor between the atmosphere and the ocean.
 #
-# This script demonstrates an example of the turbulent surface flux calculations performed in ClimaOcean
+# This example demonstrates an example of the turbulent surface flux calculations performed in ClimaOcean
 # using ECCO2 data for the ocean and JRA55 data for the atmosphere.
 #
 # For this example, we need ClimaOcean with its DataWrangling modules: ECCO2 and JRA55.
@@ -28,7 +28,7 @@ grid = ImmersedBoundaryGrid(grid, GridFittedBoundary(mask))
 fig = Figure()
 ax  = Axis(fig[1, 1])
 heatmap!(ax, interior(grid.immersed_boundary.mask, :, :, grid.Nz))
-save("ECCO_continents.png", fig) # hide
+save("ECCO_continents.png", fig) #hide
 
 # ![](ECCO_continents.png)
 
@@ -47,7 +47,7 @@ save("ECCO_continents.png", fig) # hide
 # We invoke the constructor with only the first two time indices, corresponding to 
 # January 1st (at 00:00 AM and 03:00 AM).
 
-atmosphere  = JRA55_prescribed_atmosphere(1:2; backend = InMemory())
+atmosphere = JRA55_prescribed_atmosphere(1:2; backend = InMemory())
 ocean = ocean_simulation(grid)
 
 # Now that we have an atmosphere and ocean, we `set!` the ocean temperature and salinity
@@ -92,4 +92,3 @@ heatmap!(ax, Mv; colormap = :bwr)
 
 save("fluxes.png", fig)
 # ![](fluxes.png)
-
diff --git a/examples/inspect_ecco_data.jl b/examples/inspect_ecco_data.jl
@@ -3,10 +3,10 @@
 # ClimaOcean can download and utilize data from the "ECCO" state estimate,
 # which stands for "Estimating the Circulation and Climate of the Ocean" --- two!
 #
-# This script shows how to download three-dimensional temperature and salinity fields
+# This example shows how to download three-dimensional temperature and salinity fields
 # from ECCO, and makes a short animation to showcase the fields' content.
 #
-# For this example we need Oceananigans for Field utilities, CairoMakie for plotting
+# For this example we need Oceananigans for Field utilities, CairoMakie for plotting,
 # Printf for nice labeling, and of course ClimaOcean to actually download and construct
 # the ECCO fields.
 
@@ -16,8 +16,8 @@ using Printf
 
 using ClimaOcean.DataWrangling.ECCO: ECCO_field
 
-# The function `ECCO_field` provided by `ClimaOcean.DataWrangling.ECCO` will automatically
-# download ECCO data if it doesn't already exist at the default location.
+# The function `ECCO_field` provided by `ClimaOcean.DataWrangling.ECCO` automatically
+# downloads ECCO data if that doesn't already exist at the default location.
 
 T = ECCO_field(:temperature)
 S = ECCO_field(:salinity)
@@ -40,8 +40,6 @@ fig = Figure(size=(1200, 1400))
 axT = Axis(fig[1, 1])
 axS = Axis(fig[2, 1])
 
-λ, φ, z = nodes(T)
-
 # To make an animation that scrolls through the 3D temperature
 # and salinity fields, we make an Observable for the vertical index,
 # and then construct slices of T, S using the Observable, `k`.
Original file line number	Diff line number	Diff line change
Expand Up		@@ -151,4 +151,3 @@ steps:

		- wait: ~
		continue_on_failure: true
Original file line number	Diff line number	Diff line change
Expand Up		@@ -15,4 +15,3 @@ T = Array(interior(Tt[1], 1:4:Nx, 1:4:Ny, 1))
		p = Array(interior(pt[1], 1:4:Nx, 1:4:Ny, 1))

		@save "atmospheric_state.jld2" q T p