Plot non-state variables in Decapodes

packages/algjulia-service/src/decapodes-service/initial_conditions.jl

@@ -31,20 +31,24 @@ This IC contains the domain and the initial conditions data.
 While these are currently tightly-interlinked with InitialConditionsData, they are formally separated to distinguish between the initial conditions schema and the data it might be parameterized over. 
 =#
 @data InitialConditions begin
+    Zeroes(r::Domain)
     # planar
     GaussianIC(r::Rectangle, ξ::GaussianData)
-    # spherical
+    # spheric
     TaylorVortexIC(d::Sphere, ξ::TaylorVortexData)
     SixVortexIC(m::Sphere, data::Any)
 end
 
 # DEFAULT METHOD
 GaussianIC(r::Rectangle) = GaussianIC(r, GaussianData(r))
+GaussianIC(s::Sphere) = GaussianIC(s, GaussianData(s)) # TODO this doesn't work
+
 TaylorVortexIC(d::Sphere) = TaylorVortexIC(d, TaylorVortexData())
 
+# since we need to plot non-state variables, we might need to pass in initial conditions for all variables.
 function initial_conditions(json_object::AbstractDict, geometry::Geometry, uuid2symb::Dict{String, Symbol})
-    ic_specs = json_object[:initialConditions] # this is "C" 
-    dict = Dict([uuid2symb[string(uuid)] => ic_specs[string(uuid)] for uuid ∈ keys(ic_specs)]...)
+    ic_specs = json_object[:initialConditions] # this is "C"
+    dict = Dict([uuid2symb[string(uuid)] => haskey(ic_specs, var) ? ic_specs[string(uuid)] : "Default" for uuid ∈ keys(uuid2symb)]...)
     initial_conditions(dict, geometry) # the resulting sim will only have (C,) as initial conditions
 end
 
@@ -59,6 +63,7 @@ function associate(str::String, geometry::Geometry)
    @match str begin
        "Gaussian" => GaussianIC(geometry.domain)
        "TaylorVortex" => TaylorVortexIC(geometry.domain)
+       "Default" => Zeroes(geometry.domain) # XXX create zeros?
        _ => error("$str is not implemented")
    end
 end
@@ -87,6 +92,10 @@ function initial_conditions(x::InitialConditions, args...)
     throw(ImplError("These initial conditions ($(x)) are"))
 end
 
+function initial_conditions(ics::Zeroes, geometry::Geometry)
+    zeros(nv(geometry.dualmesh))
+end
+
 function initial_conditions(ics::GaussianIC, geometry::Geometry)
     c_dist = MvNormal(ics.ξ)
     c = [pdf(c_dist, [p[1], p[2]]) for p ∈ geometry.dualmesh[:point]]

packages/algjulia-service/test/runtests.jl

@@ -107,27 +107,27 @@ end
 #= XXX ERRORING
 we are trying to index `soln.u[t]` by `Ċ `, but only `C` is present. I think this is because we generating initial conditions based on what was specified to the `initial_conditions` parameter, whereas in the past we were using `infer_state_names` to obtain that.
 =#
-# @testset "Simulation - Diffusion with Two Variables" begin
+@testset "Simulation - Diffusion with Two Variables" begin
 
-#     json_string = read(joinpath(@__DIR__, "test_jsons", "diffusion_data_twovars.json"), String);
-#     @test Set(keys(JSON3.read(json_string))) == KEYS
+    json_string = read(joinpath(@__DIR__, "test_jsons", "diffusion_data_twovars.json"), String);
+    @test Set(keys(JSON3.read(json_string))) == KEYS
 
-#     system = PodeSystem(json_string);
+    system = PodeSystem(json_string);
 
-#     simulator = evalsim(system.pode)
-#     f = simulator(system.geometry.dualmesh, system.generate, DiagonalHodge())
+    simulator = evalsim(system.pode)
+    f = simulator(system.geometry.dualmesh, system.generate, DiagonalHodge())
 
-#     soln = run_sim(f, system.init, 50.0, ComponentArray(k=0.5,)); 
+    soln = run_sim(f, system.init, 50.0, ComponentArray(k=0.5,));
 
-#     @test soln.retcode == ReturnCode.Success
+    @test soln.retcode == ReturnCode.Success
 
-#     result = SimResult(soln, system);
+    result = SimResult(soln, system);
 
-#     @test typeof(result.state) == Dict{String, Vector{AbstractArray{SVector{3, Float64}}}}
+    @test typeof(result.state) == Dict{String, Vector{AbstractArray{SVector{3, Float64}}}}
 
-#     jvs = JsonValue(result);
+    jvs = JsonValue(result);
 
-# end
+end
 
 @testset "Parsing the Model JSON Object - Diffusion Long Trip" begin
 

packages/algjulia-service/test/test_jsons/diffusion_data_twovars.json

@@ -68,11 +68,8 @@
       },
       "id": "01932404-10e5-7128-bb94-835e5d8d643f",
       "morType": {
-        "content": {
-          "content": "Object",
+          "content": "Nonscalar",
           "tag": "Basic"
-        },
-        "tag": "Hom"
       },
       "name": "",
       "over": {