resolved merge conflicts

.github/workflows/TagBot.yml

@@ -27,7 +27,4 @@ jobs:
     steps:
       - uses: JuliaRegistries/TagBot@v1
         with:
-          token: ${{ secrets.GITHUB_TOKEN }}
-          # Edit the following line to reflect the actual name of the GitHub Secret containing your private key
-          ssh: ${{ secrets.DOCUMENTER_KEY }}
-          # ssh: ${{ secrets.NAME_OF_MY_SSH_PRIVATE_KEY_SECRET }}
+          token: ${{ secrets.SERVICE_TOKEN }}

Project.toml

@@ -1,24 +1,23 @@
 name = "Decapodes"
 uuid = "679ab3ea-c928-4fe6-8d59-fd451142d391"
 authors = ["James Fairbanks", "Andrew Baas", "Evan Patterson", "Luke Morris", "George Rauta"]
-version = "0.4.0"
+version = "0.5.0"
 
 [deps]
 ACSets = "227ef7b5-1206-438b-ac65-934d6da304b8"
 Artifacts = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
 Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
 CombinatorialSpaces = "b1c52339-7909-45ad-8b6a-6e388f7c67f2"
+ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 DiagrammaticEquations = "6f00c28b-6bed-4403-80fa-30e0dc12f317"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
-GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
 GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078"
-MultiScaleArrays = "f9640e96-87f6-5992-9c3b-0743c6a49ffa"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 PreallocationTools = "d236fae5-4411-538c-8e31-a6e3d9e00b46"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
@@ -27,25 +26,30 @@ Unicode = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
 [compat]
 ACSets = "0.2"
 CombinatorialSpaces = "0.5, 0.6"
+Artifacts = "1"
+Catlab = "0.15, 0.16"
+CombinatorialSpaces = "0.5, 0.6"
+ComponentArrays = "0.15"
 DataStructures = "0.18.13"
 Distributions = "0.25"
 FileIO = "1.16"
-GLMakie = "0.8"
 GeometryBasics = "0.4.2"
 JLD2 = "0.4"
 JSON = "0.21"
+LinearAlgebra = "1.9"
 MLStyle = "0.4.17"
-MultiScaleArrays = "1.10"
 OrdinaryDiffEq = "6.47"
 PreallocationTools = "0.4"
 Requires = "1.3"
+Unicode = "1.9"
 julia = "1.9"
 
 [extras]
 AlgebraicPetri = "4f99eebe-17bf-4e98-b6a1-2c4f205a959b"
+Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["AlgebraicPetri", "Test", "Random", "GeometryBasics"]
+test = ["AlgebraicPetri", "Distributions", "Test", "Random", "GeometryBasics"]

docs/Project.toml

@@ -1,19 +1,21 @@
 [deps]
 AlgebraicPetri = "4f99eebe-17bf-4e98-b6a1-2c4f205a959b"
-AlgebraicRewriting = "725a01d3-f174-5bbd-84e1-b9417bad95d9"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
 CombinatorialSpaces = "b1c52339-7909-45ad-8b6a-6e388f7c67f2"
+ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66"
 Decapodes = "679ab3ea-c928-4fe6-8d59-fd451142d391"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DynamicalSystems = "61744808-ddfa-5f27-97ff-6e42cc95d634"
+FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
 GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
 HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
+Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
-MultiScaleArrays = "f9640e96-87f6-5992-9c3b-0743c6a49ffa"
 MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
+StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"

docs/make.jl

@@ -48,6 +48,7 @@ makedocs(
     "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"

docs/src/bc_debug.md

@@ -126,7 +126,7 @@ modified initial condition is shown below:
 
 ```@example Debug
 using LinearAlgebra
-using MultiScaleArrays
+using ComponentArrays
 using MLStyle
 using CombinatorialSpaces.DiscreteExteriorCalculus: ∧
 include("../../examples/boundary_helpers.jl")
@@ -167,16 +167,16 @@ fₘ = sim(plot_mesh_dual, generate)
 velocity(p) = [-0.5, 0.0, 0.0]
 v = ♭(plot_mesh_dual, DualVectorField(velocity.(plot_mesh_dual[triangle_center(plot_mesh_dual),:dual_point]))).data
 
-u₀ = construct(PhysicsState, [VectorForm(c)], Float64[], [:C])
+u₀ = ComponentArray(C=c)
 params = (V = v,)
 
 prob = ODEProblem(fₘ, u₀, (0.0, 100.0), params)
 sol = solve(prob, Tsit5());
 
 # Plot the result
 times = range(0.0, 100.0, length=150)
-colors = [findnode(sol(t), :C) for t in times]
-
+colors = [sol(t).C for t in times]
+extrema
 # Initial frame
 fig, ax, ob = mesh(plot_mesh, color=colors[1], colorrange = extrema(vcat(colors...)))
 ax.aspect = AxisAspect(3.0)
@@ -185,7 +185,7 @@ framerate = 30
 
 # Animation
 record(fig, "diff_adv_right.gif", range(0.0, 100.0; length=150); framerate = 30) do t
-  ob.color = findnode(sol(t), :C)
+  ob.color = sol(t).C
 end
 ```
 

docs/src/budyko_sellers_halfar.md

@@ -11,7 +11,7 @@ using Decapodes
 
 # External Dependencies
 using MLStyle
-using MultiScaleArrays
+using ComponentArrays
 using LinearAlgebra
 using OrdinaryDiffEq
 using JLD2
@@ -167,12 +167,8 @@ lines(map(x -> x[1], point(s′)), h₀)
 
 ``` @example DEC
 # Store these values to be passed to the solver.
-u₀ = construct(PhysicsState, [
-  VectorForm(Tₛ₀),
-  VectorForm(h₀),
-  ], Float64[], [
-  :Tₛ,
-  :halfar_h])
+u₀ = ComponentArray(Tₛ=Tₛ₀,halfar_h=h₀)
+
 constants_and_parameters = (
   budyko_sellers_absorbed_radiation_α = α,
   budyko_sellers_outgoing_radiation_A = A,
@@ -277,12 +273,12 @@ We can save the solution file to examine later.
 
 Quickly examine the final conditions for temperature.
 ``` @example DEC
-lines(map(x -> x[1], point(s′)), findnode(soln(tₑ), :Tₛ))
+lines(map(x -> x[1], point(s′)), soln(tₑ).Tₛ)
 ```
 
 Quickly examine the final conditions for ice height.
 ``` @example DEC
-lines(map(x -> x[1], point(s′)), findnode(soln(tₑ), :halfar_h))
+lines(map(x -> x[1], point(s′)), soln(tₑ).halfar_h)
 ```
 
 Create animated GIFs of the temperature and ice height dynamics.
@@ -291,31 +287,31 @@ begin
 # Initial frame
 frames = 100
 fig = Figure(resolution = (800, 800))
-ax1 = Axis(fig[1,1])
+ax1 = CairoMakie.Axis(fig[1,1])
 xlims!(ax1, extrema(map(x -> x[1], point(s′))))
-ylims!(ax1, extrema(findnode(soln(tₑ), :Tₛ)))
+ylims!(ax1, extrema(soln(tₑ).Tₛ))
 Label(fig[1,1,Top()], "Surface temperature, Tₛ, [C°]")
 Label(fig[2,1,Top()], "Line plot of temperature from North to South pole, every $(tₑ/frames) time units")
 
 # Animation
 record(fig, "budyko_sellers_halfar_T.gif", range(0.0, tₑ; length=frames); framerate = 15) do t
-  lines!(fig[1,1], map(x -> x[1], point(s′)), findnode(soln(t), :Tₛ))
+  lines!(fig[1,1], map(x -> x[1], point(s′)), soln(t).Tₛ)
 end
 end
 
 begin
 # Initial frame
 frames = 100
 fig = Figure(resolution = (800, 800))
-ax1 = Axis(fig[1,1])
+ax1 = CairoMakie.Axis(fig[1,1])
 xlims!(ax1, extrema(map(x -> x[1], point(s′))))
-ylims!(ax1, extrema(findnode(soln(tₑ), :halfar_h)))
+ylims!(ax1, extrema(soln(tₑ).halfar_h))
 Label(fig[1,1,Top()], "Ice height, h")
 Label(fig[2,1,Top()], "Line plot of ice height from North to South pole, every $(tₑ/frames) time units")
 
 # Animation
 record(fig, "budyko_sellers_halfar_h.gif", range(0.0, tₑ; length=frames); framerate = 15) do t
-  lines!(fig[1,1], map(x -> x[1], point(s′)), findnode(soln(t), :halfar_h))
+  lines!(fig[1,1], map(x -> x[1], point(s′)), soln(t).halfar_h)
 end
 end
 ```