QA: run_qa v1.6 form + ExplicitImports

src/MethodOfLines.jl

@@ -3,13 +3,12 @@ using LinearAlgebra
 using SciMLBase
 using DiffEqBase
 using ModelingToolkit
-using ModelingToolkit: variable, get_unknowns,
-    parameters, varmap_to_vars, get_eqs, get_bcs, get_dvs,
+using ModelingToolkit: get_unknowns,
+    get_eqs, get_bcs, get_dvs,
     get_ivs
 using SymbolicIndexingInterface
 using SymbolicUtils, Symbolics
-using Symbolics: unwrap, symbolic_linear_solve, expand_derivatives, diff2term, setname,
-    rename
+using Symbolics: unwrap, symbolic_linear_solve, expand_derivatives, diff2term
 using SymbolicUtils: operation, arguments, iscall, getmetadata, unwrap_const
 using IfElse
 using StaticArrays
@@ -26,8 +25,7 @@ using PDEBase: unitindices, unitindex, remove, insert, sym_dot, VariableMap, dep
     d_orders, vcat!, update_varmap!, get_ops
 
 # staggered changes
-using PDEBase: cardinalize_eqs!, make_pdesys_compatible, parse_bcs, generate_system,
-    Interval
+using PDEBase: Interval
 using PDEBase: error_analysis, add_metadata!
 
 # To Extend

test/qa/Project.toml

@@ -1,19 +1,14 @@
 [deps]
-Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
 MethodOfLines = "94925ecb-adb7-4558-8ed8-f975c56a0bf4"
-Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
-SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
 SciMLTesting = "09d9d899-5365-40a9-917a-5f67fddea283"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [sources]
 MethodOfLines = {path = "../.."}
 
 [compat]
-Aqua = "0.8"
 JET = "0.9,0.10,0.11"
-SafeTestsets = "0.0.1, 0.1"
-SciMLTesting = "1"
+SciMLTesting = "1.7"
 Test = "1"
 julia = "1.10"

test/qa/qa.jl

@@ -1,20 +1,76 @@
-using MethodOfLines, Aqua, JET, Test
+using SciMLTesting, MethodOfLines, Test
+using JET
 
-# Aqua/JET findings tracked at https://github.com/SciML/MethodOfLines.jl/issues/574
-@testset "Aqua" begin
-    # Passing sub-checks run normally.
-    Aqua.test_unbound_args(MethodOfLines)
-    Aqua.test_project_extras(MethodOfLines)
-    Aqua.test_persistent_tasks(MethodOfLines)
-
-    # Failing sub-checks marked broken pending fixes.
-    @test_broken false  # Aqua ambiguities: 48 method ambiguities — see https://github.com/SciML/MethodOfLines.jl/issues/574
-    @test_broken false  # Aqua undefined_exports: MethodOfLines.grid_align — see https://github.com/SciML/MethodOfLines.jl/issues/574
-    @test_broken false  # Aqua stale_deps: OrdinaryDiffEq — see https://github.com/SciML/MethodOfLines.jl/issues/574
-    @test_broken false  # Aqua deps_compat: LinearAlgebra has no compat entry — see https://github.com/SciML/MethodOfLines.jl/issues/574
-    @test_broken false  # Aqua piracies: PDEBase.AbstractBoundary/InterfaceBoundary call ops in interface_boundary.jl — see https://github.com/SciML/MethodOfLines.jl/issues/574
-end
-
-@testset "JET" begin
-    @test_broken false  # JET: 10 possible errors (DiscreteSpace fields, otherderivmaps, staggered_discretize) — see https://github.com/SciML/MethodOfLines.jl/issues/574
-end
+# Aqua/JET/ExplicitImports findings tracked at
+# https://github.com/SciML/MethodOfLines.jl/issues/574
+run_qa(
+    MethodOfLines;
+    explicit_imports = true,
+    # Aqua sub-checks with genuine findings, marked broken pending fixes (issue #574):
+    #   :ambiguities       — 48 method ambiguities involving MethodOfLines methods
+    #   :undefined_exports — MethodOfLines.grid_align (a kwarg/field name, not a binding)
+    #   :stale_deps        — OrdinaryDiffEq declared but not loaded (uses split subpackages)
+    #   :deps_compat       — LinearAlgebra has no [compat] entry
+    #   :piracies          — call-operator methods on PDEBase.InterfaceBoundary /
+    #                        PDEBase.AbstractBoundary in interface_boundary.jl
+    aqua_broken = (:ambiguities, :undefined_exports, :stale_deps, :deps_compat, :piracies),
+    # JET: still reports possible errors on Julia 1.11/1.12 (the CI `julia 1` lane):
+    # DiscreteSpace getproperty `.time`/`.ps` FieldErrors via ivs/params,
+    # `MethodOfLines.otherderivmaps` not defined, and `f_analytic` possibly-undefined in
+    # MOL_discretization.jl. Kept broken there pending issue #574. JET is clean on the
+    # LTS (1.10) lane, so only mark broken on 1.11+; `report_package` auto-flags an
+    # Unexpected Pass once JET is clean on 1.11+ too.
+    jet_broken = VERSION >= v"1.11",
+    # ExplicitImports per-check ignore-lists (names owned by / non-public in other
+    # packages; they become clean once those packages export/declare-public these names).
+    ei_kwargs = (;
+        all_explicit_imports_via_owners = (;
+            ignore = (
+                :Interval,                       # owner IntervalSets, re-exported by PDEBase
+                :get_bcs, :get_dvs, :get_eqs,    # owner ModelingToolkitBase, re-exported by ModelingToolkit
+                :get_ivs, :get_unknowns,
+                :unwrap,                         # owner SymbolicUtils, re-exported by Symbolics
+            ),
+        ),
+        all_qualified_accesses_via_owners = (;
+            ignore = (
+                :ProblemTypeCtx,                 # owner ModelingToolkitBase, accessed via ModelingToolkit
+                :unwrap,                         # owner SymbolicUtils, accessed via Symbolics
+            ),
+        ),
+        all_explicit_imports_are_public = (;
+            ignore = (
+                # non-public in PDEBase:
+                :Interval, :add_metadata!, :error_analysis, :get_ops, :insert, :remove,
+                :sym_dot, :unitindex, :unitindices, :update_varmap!, :vcat!,
+                # non-public in Symbolics:
+                :diff2term,
+            ),
+        ),
+        all_qualified_accesses_are_public = (;
+            ignore = (
+                # non-public in Base:
+                :AbstractCartesianIndex,
+                # non-public in SciMLBase:
+                :AbstractDiscretizationMetadata, :AbstractODESolution, :AbstractPDESolution,
+                :PDESolution, :observed,
+                # non-public in PDEBase:
+                :EquationState, :cardinalize_eqs!, :check_boundarymap,
+                :construct_differential_discretizer, :construct_disc_state,
+                :construct_discrete_space, :construct_var_equation_mapping,
+                :discretize_equation!, :generate_ic_defaults, :generate_metadata,
+                :get_discvars, :get_eqvar, :interface_errors, :parse_bcs,
+                :should_transform, :transform_pde_system!,
+                # non-public in ModelingToolkit:
+                :ProblemTypeCtx,
+                # non-public in IfElse:
+                :ifelse,
+            ),
+        ),
+    ),
+    # no_implicit_imports: ~80 names reach MethodOfLines via `using <BigDep>` (SciMLBase,
+    # DiffEqBase, ModelingToolkit, Symbolics, SymbolicUtils, PDEBase, DomainSets,
+    # Interpolations, ...). Making them all explicit is a large, risky refactor; kept
+    # broken pending issue #574.
+    ei_broken = (:no_implicit_imports,),
+)