Catalyst V15 todo

[isaacsas]

• Uncap SciMLBase, DiffEqBase (See Uncap those bases #1127)
• Some of the mtk_structure_indexing.jl when using Symbols (broken with SciMLBase > 2.57.1) (Seems fixed now)
• Stability computation (broken with SciMLBase > 2.57.1, currently disabled)
• Serialisation (disabled)
• StructuralIdentifiability (disabled, add when works on 10.5 and up)
• spatial_modelling/lattice_reaction_systems.jl (disabled)
• Bifkit disabled due to crashes.
• add rebuild
• update HISTORY.md and docs with changes (rebuild for example).
• fix Latex display?

[isaacsas]

The first two seem to be due to SciML/SciMLBase.jl#832

[isaacsas]

I’ve capped SciMLBase till the remake issues are fixed.

[AayushSabharwal]

https://github.com/SciML/Catalyst.jl/actions/runs/11560966175/job/32178950735?pr=1098#step:6:1033

The breakage here is because p is a map from Symbol to value. u0 contains the mapping Z => Z0, and p contains :Z0 => 10.0, but it can't substitute the Symbol into the BasicSymbolic. This used to work because remake would reason that since the values in p are all numbers (no symbolics) it can create the parameter buffer, and then use getu to get the values in u0. That approach was abandoned because if p contains a value for a parameter dependency, it won't necessarily be reflected in the parameter object and any u0 depending on it would get an incorrect value. This is analogous to the mass conservation case where Gamma[1] => X + Y, but Y is an observed variable and thus not present in the instantiated u0 vector, leading to incorrect values for Gamma.

I'll try and think of a way to resolve this.

[AayushSabharwal]

SciML/SciMLBase.jl#837

[isaacsas]

Chris asked me to update this post as of today (11/4). Here is the current state of things as I understand it:

Serialization and spatial are disabled in tests, but were both failing when I last tested them:

Catalyst.jl/test/runtests.jl

Line 60 in bef4566

# @time @safetestset "ReactionSystem Serialisation" begin include("miscellaneous_tests/reactionsystem_serialisation.jl") end

Catalyst.jl/test/runtests.jl

Line 77 in bef4566

#@time @safetestset "Lattice Reaction Systems" begin include("spatial_modelling/lattice_reaction_systems.jl") end

I capped SciMLBase at 2.57.1 in the Project.toml so we could still get stuff merged. If it is uncapped then one or both of these were failing for me:

Catalyst.jl/test/runtests.jl

Lines 54 to 55 in bef4566

	@time @safetestset "MTK Structure Indexing" begin include("upstream/mtk_structure_indexing.jl") end
	@time @safetestset "MTK Problem Inputs" begin include("upstream/mtk_problem_inputs.jl") end

When uncapping it this was also failing for me:

Catalyst.jl/test/runtests.jl

Line 95 in bef4566

@time @safetestset "Steady State Stability Computations" begin include("extensions/stability_computation.jl") end

The MTK indexing test failures were symbol-related issues I think (i.e. using symbols instead of symbolics), maybe remake too. The stability computation stuff I didn’t into dig much but I think it was breaking on remake and/or initialization related stuff for the conservation laws (but it previously worked on 2.57.1 and earlier). Neither of these is actually disabled currently as they work with SciMLBase <= 2.57.1.

[AayushSabharwal]

"ReactionSystem Serialization" test failures are due to the changes in SciML/ModelingToolkit.jl#3149. Specifically, sys.subsys.var syntax requires the subsystems to be present in MTK.get_systems(sys) or MTK.get_systems(MTK.get_parent(sys)). flatten(sys::ReactionSystem) loses the systems information, and since ReactionSystem doesn't have a parent field the latter approach doesn't work either.

complete now calls flatten because it's the correct approach to enable the parameter reordering it does subsequently. Without it, parameters of subsystems end up duplicated in the root system. The only reason parameters(sys) still works is because it calls unique on the returned vector.

There are two ways to fix this:

• Only flatten if the system has a parent field. This would still duplicate parameters, and rely on the unique call.
• Add the parent field to ReactionSystem

[AayushSabharwal]

In "Lattice Reaction Systems", the only failure is

Catalyst.jl/test/spatial_modelling/lattice_reaction_systems.jl

Line 260 in bef4566

@test_throws ArgumentError LatticeReactionSystem(rs2, [TransportReaction(D, X)], CartesianGrid((2,2)))

. I'm not sure what error that's testing and why it should error.

[isaacsas]

I hadn't seen the change that complete now flattens. That is nice in that we can now get rid of lots of places where we flatten (like in system conversion or conservation law detection).

Specifically, sys.subsys.var syntax requires the subsystems to be present in MTK.get_systems(sys) or MTK.get_systems(MTK.get_parent(sys)). flatten(sys::ReactionSystem) loses the systems information, and since ReactionSystem doesn't have a parent field the latter approach doesn't work either.

We can update ReactionSystems to have parent fields. Beyond adding the field what do we need to do with it here (for example, we have our own dispatches of flatten, compose and extend, do they need to do anything with it?).

Also though, isn't this change in indexing behavior after calling complete breaking (i.e. it was added post 9.0.0 right?).

[AayushSabharwal]

Beyond adding the field what do we need to do with it here (for example, we have our own dispatches of flatten, compose and extend, do they need to do anything with it?).

They shouldn't have anything to do with it. complete denotes that the system won't be modified, so compose and extend are immaterial at that point.

Also though, isn't this change in indexing behavior after calling complete breaking

Yeah it was accidental. Instead of calling flatten then checking has_parent, it should only have flattened if has_parent.

[AayushSabharwal]

MTK structure indexing tests are fixed on SciMLBase#master

[isaacsas]

Yeah it was accidental. Instead of calling flatten then checking has_parent, it should only have flattened if has_parent.

Will that get a fix then in MTK? Otherwise that bug will still impact released Catalyst versions.

MTK structure indexing tests are fixed on SciMLBase#master

OK, great. I'm swamped today but if I have time tomorrow I will test against MTK and SciMLBase masters to see where things are at then.

[AayushSabharwal]

With MTK problem inputs tests, why does the value of p keep changing in https://github.com/SciML/Catalyst.jl/blob/master/test/upstream/mtk_problem_inputs.jl#L258? Later, you test that the solution of the problem from remake is identical to the original solution (

Catalyst.jl/test/upstream/mtk_problem_inputs.jl

Line 303 in bef4566

# @test base_sol == solve(oprob, Tsit5(); saveat = 1.0)

) but this won't be the case if the parameters are different.