Implement DiffEqBase.anyeltypedual for GraphDynamics types

The PR #32 somehow broke a
couple things in the Neuroblox.jl docs building pipeline due to how it
interacted with the GraphDynamics tutorial. This change (which is good
to do anyways) should fix that breakage. It basically just helps the
differential equation solvers tell if anything in the problem is a
dual number.

I also did a little cleanup of unwanted stuff, and implemented a
couple SymbolicIndexingInterface methods for `Num`s with observed variables.

Author: MasonProtter

Project.toml

@@ -5,6 +5,7 @@ version = "0.4.4"
 [deps]
 Accessors = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697"
 ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
+DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
 OhMyThreads = "67456a42-1dca-4109-a031-0a68de7e3ad5"
 OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
@@ -22,6 +23,7 @@ MTKExt = ["Symbolics", "ModelingToolkit"]
 [compat]
 Accessors = "0.1"
 ConstructionBase = "1.5"
+DiffEqBase = "6"
 ModelingToolkit = "9"
 OhMyThreads = "0.6, 0.7, 0.8"
 OrderedCollections = "1.6.3"

ext/MTKExt.jl

@@ -25,4 +25,12 @@ function SymbolicIndexingInterface.is_independent_variable(sys::PartitionedGraph
     SymbolicIndexingInterface.is_independent_variable(sys, tosymbol(var; escape=false))
 end
 
+function SymbolicIndexingInterface.is_observed(sys::PartitionedGraphSystem, var::Num)
+    SymbolicIndexingInterface.is_observed(sys, tosymbol(var; escape=false))
+end
+
+function SymbolicIndexingInterface.observed(sys::PartitionedGraphSystem, var::Num)
+    SymbolicIndexingInterface.observed(sys, tosymbol(var; escape=false))
+end
+
 end

src/GraphDynamics.jl

@@ -125,6 +125,9 @@ using OrderedCollections:
     OrderedCollections,
     OrderedDict
 
+using DiffEqBase:
+    DiffEqBase,
+    anyeltypedual
 
 #----------------------------------------------------------
 # Random utils

src/problems.jl

@@ -44,9 +44,8 @@ function SciMLBase.SDEProblem(g::PartitionedGraphSystem, u0map, tspan, param_map
     end
     noise_rate_prototype = nothing # this'll need to change once we support correlated noise
     prob = SDEProblem(f, graph_noise!, u, tspan, p; callback, noise_rate_prototype, tstops = vcat(tstops, nt.tstops), kwargs...)
-    let ukeys = map(first, u0map),
-        uvals = map(last, u0map)
-        setu(prob, ukeys)(prob, uvals)
+    for (k, v) ∈ u0map
+        setu(prob, k)(prob, v)
     end
     @reset prob.p = set_params!!(prob.p, param_map)
     prob
@@ -67,17 +66,6 @@ Base.@kwdef struct GraphSystemParameters{PP, CM, S, PAP, DEC, NP, CONM, SNM, PNM
 end
 
 function Base.copy(p::GraphSystemParameters)
-    copy.(p.params_partitioned)
-    copy(p.connection_matrices)
-    p.scheduler
-    p.partition_plan
-    copy.(p.discrete_event_cache)
-    copy.(p.names_partitioned)
-    copy(p.connection_namemap)
-    copy(p.state_namemap)
-    copy(p.param_namemap)
-    copy(p.compu_namemap)
-    map(copy, p.extra_params)
     GraphSystemParameters(
         copy.(p.params_partitioned),
         copy(p.connection_matrices),
@@ -93,6 +81,16 @@ function Base.copy(p::GraphSystemParameters)
     )
 end
 
+function DiffEqBase.anyeltypedual(p::GraphSystemParameters, ::Type{Val{counter}}) where {counter}
+    anyeltypedual((p.params_partitioned, p.connection_matrices))
+end
+function DiffEqBase.anyeltypedual(p::ConnectionMatrices, ::Type{Val{counter}}) where {counter}
+    anyeltypedual(p.matrices)
+end
+function DiffEqBase.anyeltypedual(p::ConnectionMatrix, ::Type{Val{counter}}) where {counter}
+    anyeltypedual(p.data)
+end
+
 function _problem(g::PartitionedGraphSystem, tspan; scheduler, allow_nonconcrete, u0map, param_map, global_events)
     (; states_partitioned,
      params_partitioned,

src/symbolic_indexing.jl

@@ -249,8 +249,7 @@ function set_params!!(buffer::GraphSystemParameters, param_map)
         elseif haskey(connection_namemap, key)
             buffer = set_param!!(buffer, key, connection_namemap[key], val)
         else
-            @info "" keys(connection_namemap)
-            error("Key $key does not correspond to a known parameter")
+            error("Key $key does not correspond to a known parameter. ")
         end
     end
     buffer