Cm/docs pmap

.buildkite/pipeline.yml

@@ -12,7 +12,7 @@ steps:
 
   - label: ":scroll: Build docs and run tests"
     command:
-      - "srun --cpus-per-task=16 --mem=8G --time=1:00:00 --output=.buildkite/build_%j.log --unbuffered .buildkite/jobscript.sh"
+      - "srun --cpus-per-task=16 --mem=64G --time=3:00:00 --output=.buildkite/build_%j.log --unbuffered .buildkite/jobscript.sh"
     env:
       JULIA_PROJECT: "docs/"
 

docs/make.jl

@@ -16,54 +16,62 @@ if !(haskey(ENV, "GITHUB_ACTIONS") || haskey(ENV, "GITLAB_CI"))
   config["repo_root_url"] = "https://github.com/AlgebraicJulia/Decapodes.jl/blob/main/docs"
 end
 
-# const literate_dir = joinpath(@__DIR__, "..", "examples")
-# const generated_dir = joinpath(@__DIR__, "src", "examples")
+const literate_dir = joinpath(@__DIR__, "..", "examples")
+const generated_dir = joinpath(@__DIR__, "src", "examples")
 
-# @info "Building literate files"
-# for (root, dirs, files) in walkdir(literate_dir)
-#   out_dir = joinpath(generated_dir, relpath(root, literate_dir))
-#   # @showprogress pmap(files) do file
-#   for file in files
-#     f,l = splitext(file)
-#     if l == ".jl" && !startswith(f, "_")
-#       Literate.markdown(joinpath(root, file), out_dir;
-#         config=config, documenter=true, credit=false)
-#       Literate.notebook(joinpath(root, file), out_dir;
-#         execute=true, documenter=true, credit=false)
-#     end
-#   end
-# end
+@info "Building literate files"
+for (root, dirs, files) in walkdir(literate_dir)
+  out_dir = joinpath(generated_dir, relpath(root, literate_dir))
+  pmap(files) do file
+    f,l = splitext(file)
+    if l == ".jl" && !startswith(f, "_")
+      Literate.markdown(joinpath(root, file), out_dir;
+        config=config, documenter=true, credit=false)
+      Literate.notebook(joinpath(root, file), out_dir;
+        execute=true, documenter=true, credit=false)
+    end
+  end
+end
+@info "Completed literate"
+
+pages = Any[]
+push!(pages, "Decapodes.jl"      => "index.md")
+push!(pages, "Overview"          => "overview.md")
+push!(pages, "Equations"         => "equations.md")
+push!(pages, "BC Debug"          => "bc_debug.md")
+push!(pages, "ASCII Operators"   => "ascii.md")
+dirs = Dict("physics"  => "Physics"
+	   ,"biology"  => "Biology"
+	   ,"climate"  => "Climate")
+for d in keys(dirs)
+  dir   = joinpath(@__DIR__, "src", d)
+  files = readdir(dir)
+  push!(pages, dirs[d] => joinpath.(d, files))
+end
+
+push!(pages, "Examples" => [
+	"Brusselator"        => "examples/chemistry/brusselator.md",
+	"Brusselator Teapot" => "examples/chemistry/brusselator_teapot.md",
+	"Gray-Scott"         => "examples/chemistry/gray_scott.md",
+	"Budyko-Sellers"     => "examples/climate/budyko_sellers.md",
+	"Budyko-Sellers-Halfar" => "examples/climate/budyko_sellers_halfar.md",
+	"Burger" => "examples/diff_adv/burger.md",
+])
+push!(pages, "Canonical Models"  => "canon.md")
+push!(pages, "Library Reference" => "api.md")
 
 @info "Building Documenter.jl docs"
 makedocs(
   modules   = [Decapodes],
   format    = Documenter.HTML(
     assets = ["assets/analytics.js"],
   ),
+  remotes   = nothing,
   sitename  = "Decapodes.jl",
   doctest   = false,
   checkdocs = :none,
-  pages     = Any[
-    "Decapodes.jl" => "index.md",
-    "Halfar-NS" => "halmo.md",
-    "Overview" => "overview.md",
-    "Klausmeier" => "klausmeier.md",
-    "Glacial Flow" => "ice_dynamics.md",
-    "Grigoriev Ice Cap" => "grigoriev.md",
-    "Budyko-Sellers-Halfar" => "budyko_sellers_halfar.md",
-    "CISM v2.1" => "cism.md",
-    "NHS" => "nhs.md",
-    "Equations" => "equations.md",
-    "ASCII Operators" => "ascii.md",
-    "Misc Features" => "bc_debug.md",
-    "Pipe Flow" => "poiseuille.md",
-    # "Examples" => Any[
-    #   "examples/cfd_example.md"
-    # ],
-    "Canonical Models" => "canon.md",
-    "Library Reference" => "api.md"
-  ]
-)
+  pages     = pages)
+
 
 @info "Deploying docs"
 deploydocs(

docs/src/grigoriev.md → docs/src/climate/grigoriev.md

@@ -34,7 +34,7 @@ Point3D = Point3{Float64}; # hide
 The ice thickness data is [stored in a TIF](https://zenodo.org/api/records/7735970/files-archive). We have downloaded it locally, and load it using basic `FileIO`.
 
 ``` @example DEC
-file_name = "Icethickness_Grigoriev_ice_cap_2021.tif"
+file_name = "../../assets/Icethickness_Grigoriev_ice_cap_2021.tif"
 ice_thickness_tif = load(file_name)
 ```
 
@@ -112,7 +112,7 @@ halfar_eq2 = @decapode begin
   n::Constant
 
   ḣ == ∂ₜ(h)
-  ḣ == ∘(⋆, d, ⋆)(Γ * d(h) * avg₀₁(mag(♯(d(h)))^(n-1)) * avg₀₁(h^(n+2)))
+  ḣ == ∘(⋆, d, ⋆)(Γ * d(h) ∧ (mag(♯(d(h)))^(n-1)) ∧ (h^(n+2)))
 end
 
 glens_law = @decapode begin
@@ -138,36 +138,15 @@ to_graphviz(ice_dynamics)
 # Define our functions
 
 ``` @example DEC
-include("sharp_op.jl")
 function generate(sd, my_symbol; hodge=GeometricHodge())
-  ♯_m = ♯_mat(sd)
-  I = Vector{Int64}()
-  J = Vector{Int64}()
-  V = Vector{Float64}()
-  for e in 1:ne(s)
-      append!(J, [s[e,:∂v0],s[e,:∂v1]])
-      append!(I, [e,e])
-      append!(V, [0.5, 0.5])
-  end
-  avg_mat = sparse(I,J,V)
   op = @match my_symbol begin
-    :♯ => x -> begin
-      ♯(sd, EForm(x))
-    end
     :mag => x -> begin
       norm.(x)
     end
-    :avg₀₁ => x -> begin
-      avg_mat * x
-    end
-    :^ => (x,y) -> x .^ y
-    :* => (x,y) -> x .* y
-    :abs => x -> abs.(x)
-    :show => x -> begin
-      println(x)
-      x
+    :^ => (x,y) -> begin
+      x .^ y
     end
-    x => error("Unmatched operator $my_symbol")
+    _ => default_dec_matrix_generate(sd, my_symbol, hodge)
   end
   return (args...) -> op(args...)
 end

docs/src/poiseuille.md → docs/src/physics/poiseuille.md

@@ -55,7 +55,7 @@ In order to solve our equations, we will need numerical linear operators that gi
 
 ```@example Poiseuille
 using MLStyle
-include("../../examples/boundary_helpers.jl")
+include("../../../examples/boundary_helpers.jl")
 
 function generate(sd, my_symbol; hodge=GeometricHodge())
   op = @match my_symbol begin