addressed feedback from PR

.buildkite/jobscript.sh

@@ -8,4 +8,4 @@ echo "Running Tests..."
 julia --project -e 'using Pkg; Pkg.status(); Pkg.test()'
 
 echo "Building Documentation..."
-julia -t 32 --project=docs -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.status(); Pkg.instantiate(); include("docs/make.jl")'
+julia -t 16 --project=docs -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.status(); Pkg.instantiate(); include("docs/make.jl")'

.buildkite/pipeline.yml

@@ -12,7 +12,7 @@ steps:
 
   - label: ":scroll: Build docs and run tests"
     command:
-      - "srun --cpus-per-task=32 --mem=8G --time=1:00:00 --output=.buildkite/build_%j.log --unbuffered .buildkite/jobscript.sh"
+      - "srun --cpus-per-task=16 --mem=8G --time=1:00:00 --output=.buildkite/build_%j.log --unbuffered .buildkite/jobscript.sh"
     env:
       JULIA_PROJECT: "docs/"
 

.buildkite/toolbox/dryrun.sh

@@ -10,7 +10,7 @@ fi
 # check if we are in a valid git repository 
 REPO=`git rev-parse --show-toplevel`
 if [[ ! $REPO ]]; then 
-  echo "badness"  
+  echo "We are not in a valid git repo $(pwd)"  
   exit 1
 fi
 

.buildkite/toolbox/srun.sh

@@ -1,6 +1,6 @@
-srun --cpus-per-task=32 \
+srun --cpus-per-task=16 \
   --mem=8G \
   --time=1:00:00 \
-  --output=.buildkite/log_%jl.log \
+  --output=.buildkite/build_%j.log \
   --unbuffered \
   .buildkite/jobscript.sh

Project.toml

@@ -33,7 +33,6 @@ Catlab = "0.15, 0.16"
 CombinatorialSpaces = "0.5, 0.6"
 ComponentArrays = "0.15"
 DataStructures = "0.18.13"
-DiagrammaticEquations = "0.1.2"
 Distributions = "0.25"
 FileIO = "1.16"
 GeometryBasics = "0.4.2"

docs/make.jl

@@ -0,0 +1,70 @@
+using Documenter
+using Literate
+using Distributed
+
+@info "Loading Decapodes"
+using Decapodes
+using Catlab
+using Catlab.WiringDiagrams
+using AlgebraicPetri
+using CairoMakie
+
+# Set Literate.jl config if not being compiled on recognized service.
+config = Dict{String,String}()
+if !(haskey(ENV, "GITHUB_ACTIONS") || haskey(ENV, "GITLAB_CI"))
+  config["nbviewer_root_url"] = "https://nbviewer.jupyter.org/github/AlgebraicJulia/Decapodes.jl/blob/gh-pages/dev"
+  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")
+
+# 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 "Building Documenter.jl docs"
+makedocs(
+  modules   = [Decapodes],
+  format    = Documenter.HTML(
+    assets = ["assets/analytics.js"],
+  ),
+  sitename  = "Decapodes.jl",
+  doctest   = false,
+  checkdocs = :none,
+  pages     = Any[
+    "Decapodes.jl" => "index.md",
+    "Overview" => "overview.md",
+    "CISM v2.1" => "cism.md",
+    "Klausmeier" => "klausmeier.md",
+    "Equations" => "equations.md",
+    "ASCII Operators" => "ascii.md",
+    "Misc Features" => "bc_debug.md",
+    "Pipe Flow" => "poiseuille.md",
+    "Glacial Flow" => "ice_dynamics.md",
+    "Grigoriev Ice Cap" => "grigoriev.md",
+    "Budyko-Sellers-Halfar" => "budyko_sellers_halfar.md",
+#    "Examples" => Any[
+#      "examples/cfd_example.md"
+#    ],
+    "Canonical Models" => "canon.md",
+    "Library Reference" => "api.md"
+  ]
+)
+
+@info "Deploying docs"
+deploydocs(
+  target = "build",
+  repo   = "github.com/AlgebraicJulia/Decapodes.jl.git",
+  branch = "gh-pages",
+  devbranch = "main"
+)

examples/chemistry/brusselator.jl

@@ -8,12 +8,14 @@ using Decapodes
 using MLStyle
 using OrdinaryDiffEq
 using LinearAlgebra
-using CairoMakie
 using Logging
 using JLD2
 using Printf
+using CairoMakie
+import CairoMakie: wireframe, mesh, Figure, Axis
 using ComponentArrays
 
+
 using GeometryBasics: Point2, Point3
 Point2D = Point2{Float64}
 Point3D = Point3{Float64}
@@ -59,7 +61,7 @@ s[:point] = map(x -> scaling_mat*x, s[:point])
 s[:edge_orientation] = false
 orient!(s)
 # Visualize the mesh.
-CairoMakie.wireframe(s)
+wireframe(s)
 sd = EmbeddedDeltaDualComplex2D{Bool,Float64,Point2D}(s)
 subdivide_duals!(sd, Circumcenter())
 
@@ -93,7 +95,7 @@ end
 F₁ = map(sd[:point]) do (x,y)
  (x-0.3)^2 + (y-0.6)^2 ≤ (0.1)^2 ? 5.0 : 0.0
 end
-CairoMakie.mesh(s, color=F₁, colormap=:jet)
+mesh(s, color=F₁, colormap=:jet)
 
 # TODO: Try making this sparse.
 F₂ = zeros(nv(sd))
@@ -113,14 +115,14 @@ fₘ = sim(sd, generate)
 
 # Create problem and run sim for t ∈ [0,tₑ).
 # Map symbols to data.
-u₀ = ComponentArrays(U=U, V=V, One=One)
+u₀ = ComponentArray(U=U, V=V, One=One)
 
 # Visualize the initial conditions.
 # If GLMakie throws errors, then update your graphics drivers,
-# or use an alternative Makie backend like CairoMakie.
-fig_ic = CairoMakie.Figure()
-p1 = CairoMakie.mesh(fig_ic[1,2], s, color=u₀.U, colormap=:jet)
-p2 = CairoMakie.mesh(fig_ic[1,3], s, color=u₀.V, colormap=:jet)
+# or use an alternative Makie backend like 
+fig_ic = Figure()
+p1 = mesh(fig_ic[1,2], s, color=u₀.U, colormap=:jet)
+p2 = mesh(fig_ic[1,3], s, color=u₀.V, colormap=:jet)
 
 tₑ = 11.5
 
@@ -136,14 +138,14 @@ soln = solve(prob, Tsit5())
 @save "brusselator.jld2" soln
 
 # Visualize the final conditions.
-CairoMakie.mesh(s, color=soln(tₑ).U, colormap=:jet)
+mesh(s, color=soln(tₑ).U, colormap=:jet)
 
 # BEGIN Gif creation
 begin 
 frames = 100
-fig = CairoMakie.Figure(resolution = (1200, 800))
-p1 = CairoMakie.mesh(fig[1,2], s, color=soln(0).U, colormap=:jet, colorrange=extrema(soln(0).U))
-p2 = CairoMakie.mesh(fig[1,4], s, color=soln(0).V, colormap=:jet, colorrange=extrema(soln(0).V))
+fig = Figure(resolution = (1200, 800))
+p1 = mesh(fig[1,2], s, color=soln(0).U, colormap=:jet, colorrange=extrema(soln(0).U))
+p2 = mesh(fig[1,4], s, color=soln(0).V, colormap=:jet, colorrange=extrema(soln(0).V))
 ax1 = Axis(fig[1,2], width = 400, height = 400)
 ax2 = Axis(fig[1,4], width = 400, height = 400)
 hidedecorations!(ax1)
@@ -172,7 +174,7 @@ s = loadmesh(Icosphere(5))
 s[:edge_orientation] = false
 orient!(s)
 # Visualize the mesh.
-CairoMakie.wireframe(s)
+wireframe(s)
 sd = EmbeddedDeltaDualComplex2D{Bool,Float64,Point3D}(s)
 subdivide_duals!(sd, Circumcenter())
 
@@ -201,7 +203,7 @@ end
 F₁ = map(sd[:point]) do (_,_,z)
   z ≥ 0.8 ? 5.0 : 0.0
 end
-CairoMakie.mesh(s, color=F₁, colormap=:jet)
+mesh(s, color=F₁, colormap=:jet)
 
 # TODO: Try making this sparse.
 F₂ = zeros(nv(sd))
@@ -220,14 +222,14 @@ fₘ = sim(sd, generate)
 
 # Create problem and run sim for t ∈ [0,tₑ).
 # Map symbols to data.
-u₀ = ComponentArrays(U=U, V=V, One=One)
+u₀ = ComponentArray(U=U, V=V, One=One)
 
 # Visualize the initial conditions.
 # If GLMakie throws errors, then update your graphics drivers,
 # or use an alternative Makie backend like CairoMakie.
-fig_ic = CairoMakie.Figure()
-p1 = CairoMakie.mesh(fig_ic[1,2], s, color=u₀.U, colormap=:jet)
-p2 = CairoMakie.mesh(fig_ic[1,3], s, color=u₀.V, colormap=:jet)
+fig_ic = Figure()
+p1 = mesh(fig_ic[1,2], s, color=u₀.U, colormap=:jet)
+p2 = mesh(fig_ic[1,3], s, color=u₀.V, colormap=:jet)
 display(fig_ic)
 
 tₑ = 11.5
@@ -244,14 +246,14 @@ soln = solve(prob, Tsit5())
 @save "brusselator_sphere.jld2" soln
 
 # Visualize the final conditions.
-CairoMakie.mesh(s, color=soln(tₑ).U, colormap=:jet)
+mesh(s, color=soln(tₑ).U, colormap=:jet)
 
 # BEGIN Gif creation
 begin 
 frames = 800
-fig = CairoMakie.Figure(resolution = (1200, 1200))
-p1 = CairoMakie.mesh(fig[1,1], s, color=soln(0).U, colormap=:jet, colorrange=extrema(soln(0).U))
-p2 = CairoMakie.mesh(fig[2,1], s, color=soln(0).V, colormap=:jet, colorrange=extrema(soln(0).V))
+fig = Figure(resolution = (1200, 1200))
+p1 = mesh(fig[1,1], s, color=soln(0).U, colormap=:jet, colorrange=extrema(soln(0).U))
+p2 = mesh(fig[2,1], s, color=soln(0).V, colormap=:jet, colorrange=extrema(soln(0).V))
 Colorbar(fig[1,2])
 Colorbar(fig[2,2])
 

src/canon/Physics.jl

@@ -78,29 +78,30 @@ end)
   end
  )
 
-# @docapode(:OutgoingLongwaveRadiation
-#   ,"https://www.google.com"
-#   ,"desc"
-#   ,:outgoing_longwave_radiation
-#   ,begin
-#     (Tₛ, OLR)::Form0
-#     (A,B)::Constant
-
-#     OLR == A .+ (B .* Tₛ)
-#   end
-# )
-
-# @docapode("Heat Transfer"
-#   ,"https://www.google.com"
-#   ,"desc"
-#   ,"heat_transfer"
-#   ,begin
-#     (HT, Tₛ)::Form0
-#     (D,cosϕᵖ,cosϕᵈ)::Constant
-
-#     HT == (D ./ cosϕᵖ) .* ⋆(d(cosϕᵈ .* ⋆(d(Tₛ))))
-#   end
-# )
+## TODO
+@docapode("Outgoing Longwave Radiation"
+  ,"https://www.google.com"
+  ,""
+  ,:outgoing_longwave_radiation
+  ,begin
+    (Tₛ, OLR)::Form0
+    (A,B)::Constant
+
+    OLR == A .+ (B .* Tₛ)
+  end
+)
+
+@docapode("Heat Transfer"
+  ,"https://www.google.com"
+  ,""
+  ,:heat_transfer
+  ,begin
+    (HT, Tₛ)::Form0
+    (D,cosϕᵖ,cosϕᵈ)::Constant
+
+    HT == (D ./ cosϕᵖ) .* ⋆(d(cosϕᵈ .* ⋆(d(Tₛ))))
+  end
+)
 
 @docapode(Schoedinger
   ,"https://en.wikipedia.org/wiki/Schrodinger_equation"