Canonical CI: grouped-tests.yml + root test/test_groups.toml

.github/workflows/CI.yml

@@ -11,16 +11,5 @@ concurrency:
   cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
 jobs:
   tests:
-    name: "Tests"
-    strategy:
-      fail-fast: false
-      matrix:
-        group:
-          - Core
-        version:
-          - '1'
-    uses: "SciML/.github/.github/workflows/tests.yml@v1"
-    with:
-      group: "${{ matrix.group }}"
-      julia-version: "${{ matrix.version }}"
+    uses: "SciML/.github/.github/workflows/grouped-tests.yml@v1"
     secrets: "inherit"

Project.toml

@@ -49,20 +49,25 @@ 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"
 SafeTestsets = "0.1.0"
 Satisfiability = "0.2"
 SparseArrays = "1"
+StableRNGs = "1"
 StaticArrays = "1.9.8"
 SymbolicUtils = "3.7.2, 4"
+Test = "1"
+UnPack = "1"
 julia = "1.10"
 
 [extras]
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 SBMLImporter = "210efffb-c3c8-456d-a807-6f55560b12fe"
 SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
 StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed"
 
 [targets]
-test = ["Test", "SBMLImporter", "SafeTestsets", "StableRNGs", "UnPack"]
+test = ["Test", "SBMLImporter", "SafeTestsets", "StableRNGs", "UnPack", "Pkg"]

test/qa/Project.toml

@@ -0,0 +1,16 @@
+[deps]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
+CatalystNetworkAnalysis = "5fe4a9df-d2e2-44a6-8bda-0abe10269b5a"
+JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[sources]
+CatalystNetworkAnalysis = {path = "../.."}
+
+[compat]
+Aqua = "0.8"
+JET = "0.9, 0.10, 0.11"
+Pkg = "1"
+Test = "1"
+julia = "1.10"

test/qa/qa.jl

@@ -0,0 +1,26 @@
+using CatalystNetworkAnalysis, Aqua, 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

test/runtests.jl

@@ -1,32 +1,53 @@
-using CatalystNetworkAnalysis
+using Pkg
 using SafeTestsets, Test
+using CatalystNetworkAnalysis
 using UnPack, SBMLImporter, SBMLToolkit
 
-@testset "CatalystNetworkAnalysis.jl" begin
-    # Write your tests here.
+const GROUP = get(ENV, "GROUP", "All")
 
-    @time @safetestset "Concentration Robustness" begin
-        include("ACR.jl")
-    end
-    @time @safetestset "Concordance Helpers" begin
-        include("concordancehelpers.jl")
-    end
-    @time @safetestset "Siphons" begin
-        include("siphons.jl")
-    end
-    @time @safetestset "Persistence" begin
-        include("persistence.jl")
-    end
-    @time @safetestset "Deficiency One Algorithm" begin
-        include("deficiencyone.jl")
-    end
-    @time @safetestset "Specific Stoichiometric Compatibility Class Functionality" begin
-        include("specificscc.jl")
-    end
-    @time @safetestset "Linear programming utilities" begin
-        include("lp_utils.jl")
+# QA (Aqua + JET) runs in an isolated environment (test/qa) so its tooling deps
+# never enter the main test target's resolve. On Julia < 1.11 the [sources] table
+# is ignored, so develop the package by path to test the PR branch code.
+function activate_qa_env()
+    Pkg.activate(joinpath(@__DIR__, "qa"))
+    if VERSION < v"1.11.0-DEV.0"
+        Pkg.develop(PackageSpec(path = dirname(@__DIR__)))
+    end
+    return Pkg.instantiate()
+end
+
+if GROUP == "All" || GROUP == "Core"
+    @testset "CatalystNetworkAnalysis.jl" begin
+        @time @safetestset "Concentration Robustness" begin
+            include("ACR.jl")
+        end
+        @time @safetestset "Concordance Helpers" begin
+            include("concordancehelpers.jl")
+        end
+        @time @safetestset "Siphons" begin
+            include("siphons.jl")
+        end
+        @time @safetestset "Persistence" begin
+            include("persistence.jl")
+        end
+        @time @safetestset "Deficiency One Algorithm" begin
+            include("deficiencyone.jl")
+        end
+        @time @safetestset "Specific Stoichiometric Compatibility Class Functionality" begin
+            include("specificscc.jl")
+        end
+        @time @safetestset "Linear programming utilities" begin
+            include("lp_utils.jl")
+        end
+        @time @safetestset "Network Translation" begin
+            include("network_translation.jl")
+        end
     end
-    @time @safetestset "Network Translation" begin
-        include("network_translation.jl")
+end
+
+if GROUP == "QA"
+    activate_qa_env()
+    @time @safetestset "Quality Assurance" begin
+        include("qa/qa.jl")
     end
 end

test/test_groups.toml

@@ -0,0 +1,5 @@
+[Core]
+versions = ["lts", "1", "pre"]
+
+[QA]
+versions = ["lts", "1"]