Merge branch 'master' into connection_index

.github/workflows/tagbot.yml

@@ -0,0 +1,33 @@
+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+    inputs:
+      lookback:
+        default: "3"
+permissions:
+  actions: read
+  checks: read
+  contents: write
+  deployments: read
+  issues: read
+  discussions: read
+  packages: read
+  pages: read
+  pull-requests: read
+  repository-projects: read
+  security-events: read
+  statuses: read
+jobs:
+  TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+    runs-on: ubuntu-latest
+    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 }}

src/GraphDynamics.jl

@@ -2,7 +2,8 @@ module GraphDynamics
 
 macro public(ex)
     if VERSION >= v"1.11.0-DEV.469"
-        args = ex isa Symbol ? (ex,) : Base.isexpr(ex, :tuple) ? ex.args : error("malformed input to `@public`: $ex")
+        args = ex isa Symbol ? (ex,) : Base.isexpr(ex, :tuple) ? ex.args :
+            error("malformed input to `@public`: $ex")
         esc(Expr(:public, args...))
     else
         nothing
@@ -190,7 +191,9 @@ function initialize_input end
 When a `Subsystem` is connected to multiple other subsystems, all of the inputs sent to that `Subsystem` via the connections must be `combine`'d together into one input representing the accumulation of all of the inputs. `combine` is the function used to accumulate these inputs together at each step. Defaults to addition, but can have methods added to it for more exotic input types.
 """
 combine(x::Number, y::Number) = x + y
-combine(x::NamedTuple, y::NamedTuple) = typeof(x)(combine.(Tuple(x), Tuple(y)))
+function combine(x::NamedTuple{names}, y::NamedTuple{names}) where {names}
+    NamedTuple{names}(combine.(Tuple(x), Tuple(y)))
+end
 
 
 """
@@ -224,7 +227,7 @@ end
 """
     event_times(::T) = ()
 
-add methods to this function if a subsystem or connection type has a discrete event that triggers at pre-defined times. This will be used to add `tstops` to the `ODEProblem` or `SDEProblem` automatically.
+add methods to this function if a subsystem or connection type has a discrete event that triggers at pre-defined times. This will be used to add `tstops` to the `ODEProblem` or `SDEProblem` automatically during `GraphSystem` construction. This is vital for discrete events which only trigger at a specific time.
 """
 event_times(::Any) = ()
 

src/subsystems.jl

@@ -201,19 +201,30 @@ Base.eltype(::Type{<:Subsystem{<:Any, T}}) where {T} = T
 struct VectorOfSubsystemStates{States, Mat <: AbstractMatrix} <: AbstractVector{States}
     data::Mat
 end
-VectorOfSubsystemStates{States}(v::Mat) where {States, Mat} = VectorOfSubsystemStates{States, Mat}(v)
+function VectorOfSubsystemStates{SubsystemStates{Name, T, NamedTuple{snames, Tup}}}(
+    v::AbstractMatrix{U}
+    ) where {Name, T, U, snames, Tup}
+    V = promote_type(T,U)
+    States = SubsystemStates{Name, V, NamedTuple{snames, NTuple{length(snames), V}}}
+    VectorOfSubsystemStates{States, typeof(v)}(v)
+end
 
 Base.size(v::VectorOfSubsystemStates{States}) where {States} = (size(v.data, 2),)
 
 @propagate_inbounds function Base.getindex(v::VectorOfSubsystemStates{States}, idx::Integer) where {States <: SubsystemStates}
     l = length(States)
-    #@boundscheck checkbounds(v.data, 1:l, idx)
+    @boundscheck checkbounds(v.data, 1:l, idx)
     @inbounds States(view(v.data, 1:l, idx))
 end
+
+@noinline function sym_not_found_error(::Type{SubsystemStates{Name, T, NamedTuple{names}}}, s::Symbol) where {Name, T, names}
+    error("SubsystemStates{$Name} does not have a field $s, valid fields are $names")
+end
+
 @propagate_inbounds function Base.getindex(v::VectorOfSubsystemStates{States}, s::Symbol, idx::Integer) where {States <: SubsystemStates}
     i = state_ind(States, s)
     if isnothing(i)
-        error("Something helpful")
+        sym_not_found_error(States, s)
     end
     v.data[i, idx]
 end
@@ -231,7 +242,7 @@ end
                                             idx::Integer) where {States <: SubsystemStates}
     i = state_ind(States, s)
     if isnothing(i)
-        error("Something helpful")
+        sym_not_found_error(States, s)
     end
     v.data[i, idx] = val
 end