QA: run_qa v1.6 form + ExplicitImports

.github/workflows/Test.yml

@@ -32,6 +32,7 @@ jobs:
           - Hybrid
           - Misc
           - Spatial
+          - QA
     uses: "SciML/.github/.github/workflows/tests.yml@v1"
     with:
       julia-version: "${{ matrix.version }}"

Project.toml

@@ -54,13 +54,13 @@ DocStringExtensions = "0.8, 0.9"
 DynamicPolynomials = "0.6"
 DynamicQuantities = "1"
 EnumX = "1"
-ExplicitImports = "1.15"
 GraphMakie = "0.5, 0.6"
 Graphs = "1.4"
 HomotopyContinuation = "2.9"
 JumpProcesses = "9.23"
 LaTeXStrings = "1.3.0"
 Latexify = "0.16.6"
+LinearAlgebra = "1.10"
 MacroTools = "0.5.5"
 Makie = "0.22.1, 0.23, 0.24"
 ModelingToolkitBase = "1.17"
@@ -77,6 +77,7 @@ RuntimeGeneratedFunctions = "0.5.12"
 SciMLBase = "2.84, 3"
 SciMLPublic = "1"
 Setfield = "1"
+SparseArrays = "1.10"
 StochasticDiffEq = "6.101, 7"
 StructuralIdentifiability = "0.5.11"
 SymbolicIndexingInterface = "0.3"
@@ -89,7 +90,6 @@ DataInterpolations = "82cc6244-b520-54b8-b5a6-8a565e85f1d0"
 DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
 DiffEqNoiseProcess = "77a26b50-5914-5dd7-bc55-306e6241c503"
 DomainSets = "5b8099bc-c8ec-5219-889f-1d9e522a28bf"
-ExplicitImports = "7d51a73a-1435-4ff3-83d9-f097790105c7"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
@@ -112,7 +112,7 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
 test = ["DataInterpolations", "DiffEqCallbacks", "DiffEqNoiseProcess", "DomainSets",
-    "ExplicitImports", "Logging", "NonlinearSolve", "OrdinaryDiffEqBDF", "OrdinaryDiffEqCore", "OrdinaryDiffEqDefault",
+    "Logging", "NonlinearSolve", "OrdinaryDiffEqBDF", "OrdinaryDiffEqCore", "OrdinaryDiffEqDefault",
     "OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqTsit5", "OrdinaryDiffEqVerner",
     "Pkg", "Plots", "Random", "SafeTestsets", "StableRNGs",
     "StaticArrays", "Statistics", "SteadyStateDiffEq", "StochasticDiffEq", "Test"]

src/Catalyst.jl

@@ -48,7 +48,7 @@ import ModelingToolkitBase: check_variables, check_parameters,
 # Import from owner module (SymbolicUtils) per ExplicitImports.jl audit
 import SymbolicUtils: _iszero, unwrap
 
-import Base: (==), hash, size, getindex, setindex, isless, Sort.defalg, length, show
+import Base: ==, hash, size, getindex, setindex, isless, Sort.defalg, length, show
 import MacroTools, Graphs
 using MacroTools: striplines
 import Graphs: DiGraph, SimpleGraph, SimpleDiGraph, vertices, edges, add_vertices!, nv, ne
@@ -200,7 +200,7 @@ export isedgeparameter
 include("spatial_reaction_systems/discrete_space_reaction_systems.jl")
 export DiscreteSpaceReactionSystem
 export spatial_species, vertex_parameters, edge_parameters
-export CartesianGrid, CartesianGridReJ # (Implemented in JumpProcesses)
+export CartesianGrid, CartesianGridRej # (Implemented in JumpProcesses)
 export has_cartesian_dspace, has_masked_dspace, has_grid_dspace, has_graph_dspace,
        grid_dims, grid_size
 export make_edge_p_values, make_directed_edge_values

test/qa/Project.toml

@@ -0,0 +1,10 @@
+[deps]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
+Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83"
+JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
+SciMLTesting = "09d9d899-5365-40a9-917a-5f67fddea283"
+
+[compat]
+Aqua = "0.8"
+JET = "0.9, 0.10, 0.11"
+SciMLTesting = "1.6"

test/qa/qa.jl

@@ -0,0 +1,70 @@
+using SciMLTesting, Catalyst, Test
+
+# JET is a SciMLTesting weak dependency: `using JET` registers it and turns the JET
+# check on. JET 0.11 crashes (UndefRefError in `collect_callee_reports!`) when run
+# under the Julia 1.13 prerelease `Compiler.jl`, so only load it on the Julia versions
+# JET supports. Aqua and ExplicitImports still run on every version. Re-enable JET on
+# 1.13 once a JET release analyses cleanly there. Tracked in SciML/Catalyst.jl#1496.
+@static if VERSION < v"1.13-"
+    using JET
+end
+
+# ExplicitImports cannot fully analyze `Catalyst` (the `PhysicalScale` EnumX enum
+# parses as an unanalyzable submodule), so the per-module checks are told to allow it.
+const EI_ALLOW_UNANALYZABLE = (Catalyst, Catalyst.PhysicalScale)
+
+# JET typo-mode surfaces 5 pre-existing latent findings (see the `jet_broken` comment
+# below). They are only reported by JET 0.11 (the version resolved on Julia 1.12+); the
+# lts lane resolves JET 0.9, which reports nothing, so the JET check must stay a hard
+# (un-broken) `test_package` there. `jet_broken` is therefore only enabled on the Julia
+# versions whose JET surfaces the findings, otherwise the lts lane would flip to an
+# Unexpected Pass. Gating on `VERSION` (not on a JET version query) keeps this a
+# compile-time `@static` choice that matches the JET-load gate above.
+const JET_BROKEN = VERSION >= v"1.12-"
+
+run_qa(
+    Catalyst;
+    explicit_imports = true,
+    # Test-only [extras] in the root Project.toml intentionally carry no [compat]
+    # entries (they are pinned via the resolver, not declared bounds).
+    aqua_kwargs = (; deps_compat = (; check_extras = false)),
+    # Pre-existing Aqua findings tracked in SciML/Catalyst.jl#1496:
+    #   - ambiguities:       55 method ambiguities across the API surface
+    #   - unbound_args:      GridLattice `Union{Array{Bool,N}, CartesianGridRej{N,T}}`
+    #                        methods leave `T` unbound on the Array branch
+    #   - undefined_exports: `Variable` is reexported (via `@reexport using
+    #                        ModelingToolkitBase`) but no longer defined upstream
+    aqua_broken = (:ambiguities, :unbound_args, :undefined_exports),
+    # Pre-existing JET typo-mode findings tracked in SciML/Catalyst.jl#1496. They are
+    # latent on master (reproduce byte-identical on the unmodified base) and were never
+    # caught before because Catalyst had no JET check. JET surfaces them only on the
+    # Julia 1 lane (JET 0.11 on Julia 1.12); the lts lane runs JET 0.9 and does not
+    # flag them. `report_package(Catalyst; mode = :typo)` reports 5 names:
+    #   - `metadata_entries` (src/dsl.jl:436) and `reaction`
+    #     (src/chemistry_functionality.jl:400): wrong variable names interpolated into
+    #     `error(...)` strings on already-error paths (should be `metadata_i` / `rx`).
+    #   - `clipboard` x2 (src/latexify_recipes.jl:65, 161): `clipboard` (InteractiveUtils)
+    #     is not imported; only reachable when `Latexify.COPY_TO_CLIPBOARD` is set.
+    #   - `V` (src/reactionsystem.jl:78): the unparameterised `NetworkProperties()`
+    #     `@kwdef` keyword constructor references the type parameter `V` in its
+    #     `Set{V}()`/`Dict{V,Int}()` defaults; that bare constructor is never called
+    #     (only `NetworkProperties{Int, SymbolicT}()` is), so it is a latent dead path.
+    # `jet_broken` runs `report_package` and asserts the reports are non-empty, so it
+    # auto-flags an Unexpected Pass once the source typos are fixed and the bare
+    # constructor is removed/parameterised.
+    jet_broken = JET_BROKEN,
+    ei_kwargs = (;
+        no_implicit_imports = (; allow_unanalyzable = EI_ALLOW_UNANALYZABLE),
+        no_stale_explicit_imports = (; allow_unanalyzable = EI_ALLOW_UNANALYZABLE),
+    ),
+    # Pre-existing ExplicitImports public-API findings tracked in
+    # SciML/Catalyst.jl#1496: Catalyst pervasively imports/accesses internal (not
+    # `public`/exported) names of ModelingToolkitBase, Symbolics, SymbolicUtils,
+    # SciMLBase, DiffEqBase, JumpProcesses, Latexify, Graphs and Base. These go green
+    # as the upstream packages mark the names public; tracked-broken until then.
+    ei_broken = (
+        :all_qualified_accesses_via_owners,
+        :all_qualified_accesses_are_public,
+        :all_explicit_imports_are_public,
+    ),
+)

test/runtests.jl

@@ -12,6 +12,12 @@ function activate_extensions_env()
     Pkg.instantiate()
 end
 
+function activate_qa_env()
+    Pkg.activate("qa")
+    Pkg.develop(PackageSpec(path = dirname(@__DIR__)))
+    Pkg.instantiate()
+end
+
 ### Run Tests ###
 @time begin
     if GROUP == "All" || GROUP == "Modeling"
@@ -66,11 +72,18 @@ end
 
     if GROUP == "All" || GROUP == "Misc"
         @time @safetestset "ReactionSystem Serialisation" begin include("miscellaneous_tests/reactionsystem_serialisation.jl") end
-        @time @safetestset "Explicit Imports" begin include("miscellaneous_tests/explicit_imports.jl") end
         # BROKEN
         #@time @safetestset "Latexify" begin include("visualisation/latexify.jl") end # https://github.com/SciML/Catalyst.jl/issues/1352
     end
 
+    # Quality assurance (Aqua, JET, ExplicitImports) via the SciMLTesting harness.
+    # Runs in its own `test/qa` sub-environment so the heavier QA tooling does not
+    # constrain the main test environment's resolution.
+    if GROUP == "QA"
+        activate_qa_env()
+        include("qa/qa.jl")
+    end
+
     if GROUP == "All" || GROUP == "Spatial"
         # Tests spatial modelling and simulations.
         @time @safetestset "PDE Systems Simulations" begin include("spatial_modelling/simulate_PDEs.jl") end