QA: Aqua/JET findings marked @test_broken pending fix

[ChrisRackauckas-Claude]

The QA group (Aqua + JET) of MethodOfLines.jl has genuine findings that are being marked @test_broken so the QA CI group is GREEN. These should be fixed and un-@test_brokened. All findings were reproduced locally on Julia 1.11 against branch grouped-tests-ci.

The QA driver (test/qa/qa.jl) now keeps the passing Aqua sub-checks running normally and marks each failing check @test_broken. Each @test_broken line references this issue.

Aqua findings (Aqua.test_all)

1. Method ambiguities — Aqua.test_ambiguities reports 48 ambiguities involving MethodOfLines methods.
2. Undefined exports — Aqua.test_undefined_exports reports MethodOfLines.grid_align is exported but not a defined binding (it is a keyword/field name, not a module-level binding). src/MethodOfLines.jl:122 exports grid_align.
3. Stale dependencies — Aqua.test_stale_deps reports OrdinaryDiffEq is declared in [deps] but not actually loaded (the package uses split OrdinaryDiffEq subpackages).
4. Deps compat — Aqua.test_deps_compat reports LinearAlgebra (used via using LinearAlgebra in src/MethodOfLines.jl:2) has no [compat] entry in the root Project.toml.
5. Type piracy — Aqua.test_piracies reports two call-operator methods defined on PDEBase-owned types in src/discretization/interface_boundary.jl:
   • (b::PDEBase.InterfaceBoundary)(I, s, jx) (line 23)
   • (b::PDEBase.AbstractBoundary)(I, s, jx) (line 24)

The passing Aqua sub-checks (unbound type parameters, project_extras, julia compat, extras/weakdeps compat, persistent tasks) continue to run normally.

JET findings (JET.test_package)

JET.test_package(MethodOfLines; target_defined_modules = true) reports 10 possible errors:

• DiscreteSpace has no field ps — getproperty/params at src/discretization/discretize_vars.jl:212,278.
• DiscreteSpace has no field time — getproperty/ivs at src/discretization/discretize_vars.jl:212,295 (reached from generate_cartesian_rules and boundary_value_maps).
• MethodOfLines.otherderivmaps is not defined — boundary_value_maps at src/discretization/generate_bc_eqs.jl:156.
• Staggered grid discretize: no matching kwcall for NonlinearProblem / ODEProblem construction at src/discretization/staggered_discretize.jl:12,21.
• symbolic_trace: no matching method found arguments(::Bool) at src/discretization/staggered_discretize.jl:34,37.
• symbolic_trace: no matching method found getindex(::Expr, ::Int64) at src/discretization/staggered_discretize.jl:46,47.

Status

These are @test_broken so CI is green; they should be investigated and fixed, then the @test_broken markers removed (restored to passing assertions). Ignore until reviewed by @ChrisRackauckas.

[ChrisRackauckas-Claude]

Update from #580 (run_qa v1.6 conversion)

test/qa/qa.jl was converted to the SciMLTesting 1.6 run_qa form with ExplicitImports enabled. Status of the tracked findings:

Aqua — still broken (preserved as aqua_broken):

• :ambiguities, :undefined_exports (grid_align), :stale_deps (OrdinaryDiffEq), :deps_compat (LinearAlgebra), :piracies (PDEBase call-ops in interface_boundary.jl). All still reproduce; left as tracked @test_broken placeholders.

JET — RESOLVED, un-broken.
The 10 possible errors (DiscreteSpace ps/time fields, otherderivmaps, staggered_discretize kwcall/arguments(::Bool)/getindex(::Expr,::Int)) no longer reproduce on the current ModelingToolkit 11.28 / SciMLBase 3.22 stack — JET.report_package returns zero reports. JET.test_package now runs as a hard check (passes). No JET items remain.

ExplicitImports (newly enabled):

• no_stale_explicit_imports — FIXED: removed 9 unused explicit imports (variable, parameters, varmap_to_vars, setname, rename, cardinalize_eqs!, make_pdesys_compatible, parse_bcs, generate_system).
• no_implicit_imports — new tracked-broken item. ~80 names reach MethodOfLines via heavy using <BigDep> (SciMLBase, DiffEqBase, ModelingToolkit, Symbolics, SymbolicUtils, PDEBase, DomainSets, Interpolations, IfElse, StaticArrays, Latexify, PrecompileTools, RuntimeGeneratedFunctions, SymbolicIndexingInterface). Making them explicit is a large refactor; kept ei_broken = (:no_implicit_imports,). To clear: convert the using X lines to using X: name1, name2, ... for the listed names, then drop :no_implicit_imports from ei_broken.
• owners / public checks pass via per-check ignore-lists for other packages' non-public / re-exported names (they will go clean once those packages export/declare-public the names).