QA: run_qa v1.6 form + ExplicitImports

Project.toml

@@ -21,7 +21,6 @@ Nemo = "2edaba10-b0f1-5616-af89-8c11ac63239a"
 Oscar = "f1435218-dba5-11e9-1e4d-f1a5fab5fc13"
 Polyhedra = "67491407-f73d-577b-9b50-8179a7c68029"
 PolynomialRoots = "3a141323-8675-5d76-9d11-e1df1406c778"
-PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
 ReactionNetworkImporters = "b4db0fb7-de2a-5028-82bf-5021f5cfa881"
 SBMLToolkit = "86080e66-c8ac-44c2-a1a0-9adaadfe4a4e"
 Satisfiability = "160ab843-0bc6-4ba4-9585-b7478b70f443"
@@ -47,7 +46,6 @@ Nemo = "0.47, 0.54, 0.56"
 Oscar = "1.1.1, 1.7"
 Polyhedra = "0.7.8, 0.8"
 PolynomialRoots = "1.0.0"
-PrecompileTools = "1.2.1"
 ReactionNetworkImporters = "0.15.1, 1.3"
 SBMLImporter = "4"
 SBMLToolkit = "0.1.29"

src/CatalystNetworkAnalysis.jl

@@ -1,7 +1,5 @@
 module CatalystNetworkAnalysis
 
-using PrecompileTools: @setup_workload, @compile_workload
-
 using Catalyst
 using Satisfiability # For siphon detection
 
@@ -23,6 +21,8 @@ using MixedSubdivisions, DynamicPolynomials
 using Polyhedra
 import CDDLib
 
+import SymbolicUtils
+
 include("persistence.jl")
 export ispersistent, minimalsiphons, iscritical, isconservative, isconsistent
 include("concordance.jl")

src/utils.jl

@@ -133,7 +133,7 @@ function ratematrix(rs::ReactionSystem, rates::Vector{T} = reactionrates(rs)) wh
     complexes, D = reactioncomplexes(rs)
     n = length(complexes)
     rxns = reactions(rs)
-    ratematrix = (T <: Symbolics.BasicSymbolic) ? zeros(Any, n, n) : zeros(T, n, n)
+    ratematrix = (T <: SymbolicUtils.BasicSymbolic) ? zeros(Any, n, n) : zeros(T, n, n)
 
     for r in 1:length(rxns)
         rxn = rxns[r]

test/qa/Project.toml

@@ -2,7 +2,6 @@
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 CatalystNetworkAnalysis = "5fe4a9df-d2e2-44a6-8bda-0abe10269b5a"
 JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
-SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
 SciMLTesting = "09d9d899-5365-40a9-917a-5f67fddea283"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
@@ -12,7 +11,6 @@ CatalystNetworkAnalysis = {path = "../.."}
 [compat]
 Aqua = "0.8"
 JET = "0.9, 0.10, 0.11"
-SafeTestsets = "0.0.1, 0.1"
-SciMLTesting = "1"
+SciMLTesting = "1.6"
 Test = "1"
 julia = "1.10"

test/qa/qa.jl

@@ -1,26 +1,46 @@
-using CatalystNetworkAnalysis, Aqua, JET
+using SciMLTesting, CatalystNetworkAnalysis, JET
 using Test
 
-@testset "Aqua" begin
-    # undefined_exports, stale_deps and the deps_compat extras check disabled:
-    # genuine findings tracked in https://github.com/SciML/CatalystNetworkAnalysis.jl/issues/70
-    # (marked @test_broken below). All other Aqua sub-checks still run and pass.
-    Aqua.test_all(
-        CatalystNetworkAnalysis;
-        undefined_exports = false,
-        stale_deps = false,
-        deps_compat = (check_extras = false,),
-    )
-    @test_broken false  # Aqua undefined_exports: symbolic_steady_states — tracked in https://github.com/SciML/CatalystNetworkAnalysis.jl/issues/70
-    @test_broken false  # Aqua stale_deps: ReactionNetworkImporters, PolynomialRoots, ModelingToolkit, SBMLToolkit — tracked in https://github.com/SciML/CatalystNetworkAnalysis.jl/issues/70
-    @test_broken false  # Aqua deps_compat extras: Pkg missing [compat] — tracked in https://github.com/SciML/CatalystNetworkAnalysis.jl/issues/70
-end
-
-@testset "JET" begin
-    # JET reports genuine errors (Nemo.ZZMatrix no-matching-method, undefined
-    # bindings) tracked in https://github.com/SciML/CatalystNetworkAnalysis.jl/issues/70 —
-    # run in report mode and @test_broken the assertion so QA stays green and
-    # auto-flags once fixed.
-    rep = JET.report_package(CatalystNetworkAnalysis; target_defined_modules = true)
-    @test_broken isempty(JET.get_reports(rep))  # JET: 12 possible errors — tracked in https://github.com/SciML/CatalystNetworkAnalysis.jl/issues/70
-end
+# deps_compat keeps deps/weakdeps/julia checks running but disables the extras
+# check: no [compat] for the `Pkg` extra — tracked in
+# https://github.com/SciML/CatalystNetworkAnalysis.jl/issues/70
+#
+# aqua_broken sub-checks (tracked in issue #70):
+#   undefined_exports: symbolic_steady_states exported but flagged undefined
+#   stale_deps: ReactionNetworkImporters, PolynomialRoots, ModelingToolkit, SBMLToolkit
+#
+# jet_broken: ~14 possible errors (report mode + @test_broken) — issue #70
+#
+# ExplicitImports:
+#   no_implicit_imports is ei_broken — the package `using`s several large
+#   dependencies (Catalyst, Oscar, JuMP, Graphs, DynamicPolynomials,
+#   Satisfiability, ...) and relies on ~75 of their exported names implicitly;
+#   making every one explicit is a large refactor tracked in issue #70.
+#   The qualified-access ignore-lists below are names that are not public in
+#   their *source* packages (other people's packages) but are accessed
+#   intentionally via Mod.name; ignored per ExplicitImports' public-API checks.
+run_qa(
+    CatalystNetworkAnalysis;
+    explicit_imports = true,
+    # jet_broken uses report_package; match the original invocation
+    # (target_defined_modules only, no target_modules narrowing) so the genuine
+    # ~14 reports are still surfaced as @test_broken rather than filtered out.
+    jet_kwargs = (; target_defined_modules = true),
+    aqua_kwargs = (; deps_compat = (check_extras = false,)),
+    aqua_broken = (:undefined_exports, :stale_deps),
+    jet_broken = true,
+    ei_kwargs = (;
+        all_qualified_accesses_are_public = (;
+            ignore = (
+                :Library,              # CDDLib
+                :Optimizer,            # HiGHS
+                :assemble_oderhs,      # Catalyst
+                :cycles,               # Catalyst
+                :get_networkproperties, # Catalyst
+                :n_positive_roots,     # Hecke
+                :symmap_to_varmap,     # Catalyst
+            ),
+        ),
+    ),
+    ei_broken = (:no_implicit_imports,),
+)