Gatlab Migration

[jpfairbanks]

We need to check that we can run against Catlab#main.

[epatters]

@jpfairbanks, are we still targeting a Catlab major release with Gatlab integration for next week? If so, we should start sorting this out ASAP. I can help with this issue if needed.

[jpfairbanks]

Yes @quffaro tested it and found a bug with the catalyst integration that needs tracking down. Reproducing is just running the tests on main.

[epatters]

OK, I will take a look this afternoon.

[epatters]

Possibly related to #162, the Catalyst tests fail even on Catlab v0.15.5:

Catalyst Package Extension: Error During Test at /home/epatters/Local/algjulia/algpetri/test/ext/extensions.jl:3
  Got exception outside of a @test
  LoadError: MethodError: no method matching CartesianIndices(::Tuple{Vector{Int64}})
  
  Closest candidates are:
    CartesianIndices(::CartesianIndex)
     @ Base multidimensional.jl:255
    CartesianIndices(::AbstractArray)
     @ Base multidimensional.jl:259
    CartesianIndices(::Tuple{})
     @ Base multidimensional.jl:249
    ...
  
  Stacktrace:
    [1] getindex(x::SymbolicUtils.BasicSymbolic{Vector{Real}}, idx::Int64)
      @ Symbolics ~/.julia/packages/Symbolics/gBKZv/src/array-lib.jl:24
    [2] getindex(x::Symbolics.Arr{Symbolics.Num, 1}, idx::Int64)
      @ Symbolics ~/.julia/packages/Symbolics/gBKZv/src/array-lib.jl:90
    [3] (::AlgebraicPetriCatalystExt.var"#4#7")(i::Int64)
      @ AlgebraicPetriCatalystExt ./none:0
    [4] iterate
      @ ./generator.jl:47 [inlined]
    [5] collect(itr::Base.Generator{Vector{Int64}, AlgebraicPetriCatalystExt.var"#4#7"})
      @ Base ./array.jl:782
    [6] (::AlgebraicPetriCatalystExt.var"#3#6"{AlgebraicPetri.PetriNet, Symbolics.Arr{Symbolics.Num, 1}})(t::Int64)
      @ AlgebraicPetriCatalystExt ~/Local/algjulia/algpetri/ext/AlgebraicPetriCatalystExt.jl:27
    [7] iterate
      @ ./generator.jl:47 [inlined]
    [8] _collect(c::UnitRange{Int64}, itr::Base.Generator{UnitRange{Int64}, AlgebraicPetriCatalystExt.var"#3#6"{AlgebraicPetri.PetriNet, Symbolics.Arr{Symbolics.Num, 1}}}, #unused#::Base.EltypeUnknown, isz::Base.HasShape{1})
      @ Base ./array.jl:802
    [9] collect_similar
      @ ./array.jl:711 [inlined]
   [10] map
      @ ./abstractarray.jl:3263 [inlined]
   [11] Catalyst.ReactionSystem(pn::AlgebraicPetri.PetriNet)
      @ AlgebraicPetriCatalystExt ~/Local/algjulia/algpetri/ext/AlgebraicPetriCatalystExt.jl:22
   [12] top-level scope
      @ ~/Local/algjulia/algpetri/test/ext/AlgebraicPetriCatalystExt.jl:9
   [13] include(fname::String)
      @ Base.MainInclude ./client.jl:478
   [14] macro expansion
      @ ~/Local/algjulia/algpetri/test/ext/extensions.jl:4 [inlined]
   [15] macro expansion
      @ ~/.julia/juliaup/julia-1.9.3+0.x64.linux.gnu/share/julia/stdlib/v1.9/Test/src/Test.jl:1498 [inlined]
   [16] top-level scope
      @ ~/Local/algjulia/algpetri/test/ext/extensions.jl:4
   [17] include(fname::String)
      @ Base.MainInclude ./client.jl:478
   [18] macro expansion
      @ ~/Local/algjulia/algpetri/test/runtests.jl:28 [inlined]
   [19] macro expansion
      @ ~/.julia/juliaup/julia-1.9.3+0.x64.linux.gnu/share/julia/stdlib/v1.9/Test/src/Test.jl:1498 [inlined]
   [20] top-level scope
      @ ~/Local/algjulia/algpetri/test/runtests.jl:28
   [21] include(mod::Module, _path::String)
      @ Base ./Base.jl:457
   [22] exec_options(opts::Base.JLOptions)
      @ Base ./client.jl:307
   [23] _start()
      @ Base ./client.jl:522
  in expression starting at /home/epatters/Local/algjulia/algpetri/test/ext/AlgebraicPetriCatalystExt.jl:1
Test Summary:                       | Pass  Error  Total   Time
Package Extensions                  |    4      1      5  49.9s
  Catalyst Package Extension        |           1      1  38.2s
  ModelingToolkit Package Extension |    4             4  11.7s
ERROR: LoadError: Some tests did not pass: 4 passed, 0 failed, 1 errored, 0 broken.
in expression starting at /home/epatters/Local/algjulia/algpetri/test/runtests.jl:27