tutorial examples giving MethodError: no method matching keys(::Catlab.ColumnImplementations.DenseAttr{Union{Float64, Int64, AbstractString, Expr, Function, Symbol}})

[anandijain]

Hello, thanks for the package!

I wanted to play around with some of the tutorials and see how it compares with Catalyst.jl and ModelingToolkit.jl, however, I ran into an issue. (I should note that I haven't really used Catlab, so maybe the solution is obvious)

I started with https://github.com/Merck/ReactiveDynamics.jl/blob/main/tutorial/example.jl
When I ran the following using the main branch of ReactiveDynamics :

using ReactiveDynamics

# acs as a model : incomplete dynamics
sir_acs = @ReactionNetwork

I got

ERROR: MethodError: no method matching keys(::Catlab.ColumnImplementations.DenseAttr{Union{Float64, Int64, AbstractString, Expr, Function, Symbol}})
Closest candidates are:
  keys(::Union{Tables.AbstractColumns, Tables.AbstractRow}) at ~/.julia/packages/Tables/T7rHm/src/Tables.jl:189
  keys(::DataStructures.Accumulator) at ~/.julia/packages/DataStructures/59MD0/src/accumulator.jl:58
  keys(::ComponentArrays.AbstractAxis) at ~/.julia/packages/ComponentArrays/D6i2q/src/axis.jl:146
  ...
Stacktrace:
 [1] eachindex(itrs::Catlab.ColumnImplementations.DenseAttr{Union{Float64, Int64, AbstractString, Expr, Function, Symbol}})
   @ Base ./abstractarray.jl:282
 [2] assign_defaults!(acs::ReactiveDynamics.FoldedReactionNetworkType{Symbol, Union{Missing, String, Symbol}, Union{Float64, Int64, AbstractString, Expr, Function, Symbol}, Set{Symbol}, ReactiveDynamics.FoldedObservable, Any})
   @ ReactiveDynamics ~/.julia/dev/ReactiveDynamics.jl/src/ReactiveDynamics.jl:99
 [3] merge_acs!(acs::ReactiveDynamics.FoldedReactionNetworkType{Symbol, Union{Missing, String, Symbol}, Union{Float64, Int64, AbstractString, Expr, Function, Symbol}, Set{Symbol}, ReactiveDynamics.FoldedObservable, Any}, transitions::Vector{Any}, reactants::Vector{Any}, obs::Vector{Any}, events::Vector{Any})
   @ ReactiveDynamics ~/.julia/dev/ReactiveDynamics.jl/src/ReactiveDynamics.jl:137
 [4] ReactiveDynamics.FoldedReactionNetworkType{Symbol, Union{Missing, String, Symbol}, Union{Float64, Int64, AbstractString, Expr, Function, Symbol}, Set{Symbol}, ReactiveDynamics.FoldedObservable, Any}(transitions::Vector{Any}, reactants::Vector{Any}, obs::Vector{Any}, events::Vector{Any})
   @ ReactiveDynamics ~/.julia/dev/ReactiveDynamics.jl/src/ReactiveDynamics.jl:111
 [5] top-level scope
   @ ~/.julia/dev/ReactiveDynamics.jl/tutorial/example.jl:4

Thanks

[thevolatilebit]

Many thanks for pointing this out! The issue here is that accessing subparts in Catlab.jl has changed lately; a new version of ReactiveDynamics.jl will address the problem (and it is already on its way to the general registry).

[thevolatilebit]

This is solved by d303952.

However, there's a Catlab.jl hack,

ReactiveDynamics.jl/src/ReactiveDynamics.jl

Lines 147 to 150 in a64d86f

	# Catlab.jl hack: bypass @isdefined check
	function Base.getindex(m::Catlab.ColumnImplementations.PartialVecMap, x::Int)
	m.v[x]
	end

versus

function Base.getindex(m::PartialVecMap, x::Int)
  @assert m.defined[x]
  m.v[x]
end

This is alright since I always perform isdefined checks manually. Anyway, I plan to drop the Catlab backend in an upcoming release.

[anandijain]

Thanks!