Comments (4)
@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.
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Yes @quffaro tested it and found a bug with the catalyst integration that needs tracking down. Reproducing is just running the tests on main.
from algebraicpetri.jl.
OK, I will take a look this afternoon.
from algebraicpetri.jl.
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
from algebraicpetri.jl.
Related Issues (20)
- `mca_help` within `mca` in SubACSets.jl doesn't recurse.
- It appears MCA recursion can StackOverflow
- `mca` not searching in order of size HOT 2
- `one_removed_subobs` does not remove arcs from Petri net
- Have `mca` find the morphisms and return the spans HOT 1
- Generalize `mca` to work for more than two input ACSets HOT 1
- `vectorfield_expr` only works with LabelledArrays HOT 6
- Utilize PrecompileTools.jl for Caching HOT 1
- Use cascading delete provided by Catlab HOT 1
- `prim_petri` of TypedPetri.jl not labeling types of states correctly
- AlgebraicPetri v0.9
- Issues when running stratified model HOT 1
- oapply_typed results in wrong wiring HOT 2
- Precompilation warnings in package extensions HOT 11
- Core Files in docs build HOT 3
- suggestions for documentation improvement HOT 1
- Use color to distinguish morphisms of Petri nets HOT 2
- Update Comparison tests to Catlab > v0.16.9 HOT 1
- Incorrect generation of state names?
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