Support Catalyst v17 / SciMLBase v3 / OrdinaryDiffEq v7 ecosystem

[ChrisRackauckas-Claude]

Summary

Allows PEtab to be used with the Catalyst v17 / SciMLBase v3 / OrdinaryDiffEq v7 ecosystem release that's currently rolling out across SciML.

Compat changes

Package	Before	After
Catalyst	"16"	"16, 17"
DiffEqBase	"6.183.0"	"6.183.0, 7"
OrdinaryDiffEqBDF	"1.0"	"1.0, 2"
OrdinaryDiffEqRosenbrock	"1.0"	"1.0, 2"
OrdinaryDiffEqSDIRK	"1.0"	"1.0, 2"
OrdinaryDiffEqTsit5	"1.9.0"	"1.9.0, 2"
SciMLBase	"2"	"2, 3"
SciMLLogging (new)	—	"1"

SciMLLogging is added as a regular (non-extension) dep because it's used in the verbose kwarg compat shim that needs to be defined at module load time on both v6 and v7 codepaths.

Source changes

Two SciMLBase v3 / OrdinaryDiffEq v7 breaking changes are exercised by PEtab's source. Both are gated with @static if so PEtab works on both v2 and v3.

1. SciMLAlgorithm → AbstractSciMLAlgorithm (SciMLBase v3 rename, no deprecation shim)

Used as a type annotation in ODESolver's solver/solver_adj fields and in several method signatures (solve.jl, helper.jl, petab_odeproblem.jl). Aliased back to the old name at the top of PEtab.jl:

@static if isdefined(SciMLBase, :SciMLAlgorithm)
    using SciMLBase: SciMLAlgorithm
else
    const SciMLAlgorithm = SciMLBase.AbstractSciMLAlgorithm
end

2. verbose = false no longer accepted on solve (DiffEqBase v7)

DiffEqBase v7 requires a verbosity object from SciMLLogging (e.g. None(), Standard()) instead of Bool. PEtab's ODESolver.verbose::Bool is passed straight through to solve in solve/solve.jl and solve/steady_state.jl. Wrapped via _verbose_kwarg:

@static if isdefined(DiffEqBase, :DEVerbosity)
    _verbose_kwarg(b::Bool) = b ? SciMLLogging.Standard() : SciMLLogging.None()
else
    _verbose_kwarg(b::Bool) = b
end

PEtab's user-facing ODESolver(...; verbose = true|false) API is unchanged.

Other v3 breaking changes checked and not used

I went through OrdinaryDiffEq.jl's NEWS.md and grepped for each migration. None of these patterns are used in PEtab's source:

• sol[i] linear indexing on ODESolution (RAT v4 makes it scalar)
• length(sol) / eachindex(sol) / iterate(sol) / for u in sol on a SciML solution
• EnsembleSolution iteration via for sol in es
• prob_func(prob, i, repeat) ensemble signature (PEtab doesn't construct EnsembleProblems)
• u_modified! → derivative_discontinuity!
• sol.destats / has_destats field/trait renames
• DEAlgorithm / DEProblem / DESolution abstract type renames
• sol.retcode == :Symbol Symbol-based retcode comparisons
• concrete_solve / alias_u0 / alias_du0
• Old controller kwargs (gamma, beta1, beta2, qmin, etc.)
• chunk_size / standardtag / diff_type AD kwargs

Verified

julia> using Pkg; Pkg.activate(".");
       Pkg.develop(path="path/to/Catalyst.jl@v17");
       Pkg.develop(path="path/to/SBMLImporter#widen-compat-catalyst17");
       using PEtab
loaded OK
v"5.1.1"

Resolves with: Catalyst 17.0.0 / SciMLBase 3.9.1 / DiffEqBase 7.3.0 / OrdinaryDiffEq{BDF,Rosenbrock,SDIRK,Tsit5} v2.

Context

Unblocks SciML/Catalyst.jl#1466 (Catalyst v17 release), where PEtab is in docs/Project.toml and currently blocks the doc build.

Depends on: sebapersson/SBMLImporter.jl#155 (PEtab depends on SBMLImporter).

Please ignore until reviewed by @sebapersson.

🤖 Generated with Claude Code

[ChrisRackauckas]

This exists on the pre-v3 too

[ChrisRackauckas]

The real thing here is to just always use SciMLBase.AbstractSciMLAlgorithm on both v2 and v3: SciMLAlgorithm was deprecated a long ways back.