From 1c452d36e2502b2964b8d3b69ba1a42eef9699d7 Mon Sep 17 00:00:00 2001
From: ChrisRackauckas-Claude <accounts@chrisrackauckas.com>
Date: Thu, 25 Jun 2026 13:47:29 -0400
Subject: [PATCH 1/4] QA: run_qa v1.6 form + ExplicitImports (root + sublibs)

Convert the root QA env and all 7 lib/<Sub> sublibrary QA envs to the
SciMLTesting 1.6 run_qa form with ExplicitImports enabled.

Per QA env: rewrite qa.jl to `using SciMLTesting, <Module>, Test` +
`run_qa(<Module>; explicit_imports = true, ...)`; bump the env's
SciMLTesting [compat] to "1.6"; keep Aqua where ambiguities is disabled.
ExplicitImports stays a transitive dep of SciMLTesting (not listed).

ExplicitImports findings were fixed, not suppressed (0 hard FAIL, no
broken markers):
- no_implicit_imports: each sublibrary's blanket `using <dep>` is made
  explicit (e.g. `using DiffEqBase: DiffEqBase, BVProblem, ...`,
  `using Catalyst: Catalyst, @reaction_network, ...`), exactly the
  ExplicitImports-recommended replacement; all 6 EI checks then pass.
- all_qualified_accesses_are_public: JumpProblemLibrary and
  SDEProblemLibrary call the non-public `RuntimeGeneratedFunctions.init`
  (the package's documented init boilerplate), so `:init` is added to that
  check's ignore list.

Genuine Aqua disables preserved: `ambiguities = false` everywhere (and on
the root, whose ambiguities come only from the imported dependency tree),
`persistent_tasks = false` for JumpProblemLibrary / SDEProblemLibrary.

Root package Project.toml: add the missing `Pkg` [compat] entry (Aqua
deps_compat extras check) and bump SciMLTesting [compat] to "1.6".

Monorepo [sources]/develop wiring is unchanged. Verified on Julia 1.11
against released SciMLTesting 1.6.0: root QA 16/16 pass; each sublibrary's
6 ExplicitImports checks pass.

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 Project.toml                                      |  3 ++-
 lib/BVProblemLibrary/src/BVProblemLibrary.jl      |  4 +++-
 lib/BVProblemLibrary/test/qa/Project.toml         |  2 ++
 lib/BVProblemLibrary/test/qa/qa.jl                |  7 ++-----
 lib/DAEProblemLibrary/src/DAEProblemLibrary.jl    |  3 ++-
 lib/DAEProblemLibrary/test/qa/Project.toml        |  2 ++
 lib/DAEProblemLibrary/test/qa/qa.jl               |  7 ++-----
 lib/DDEProblemLibrary/src/DDEProblemLibrary.jl    |  2 +-
 lib/DDEProblemLibrary/test/qa/Project.toml        |  2 ++
 lib/DDEProblemLibrary/test/qa/qa.jl               |  7 ++-----
 lib/JumpProblemLibrary/src/JumpProblemLibrary.jl  |  4 +++-
 lib/JumpProblemLibrary/test/qa/Project.toml       |  2 ++
 lib/JumpProblemLibrary/test/qa/qa.jl              | 14 +++++++++-----
 .../src/NonlinearProblemLibrary.jl                |  3 ++-
 lib/NonlinearProblemLibrary/test/qa/Project.toml  |  2 ++
 lib/NonlinearProblemLibrary/test/qa/qa.jl         |  7 ++-----
 lib/ODEProblemLibrary/src/ODEProblemLibrary.jl    |  8 ++++----
 lib/ODEProblemLibrary/test/qa/Project.toml        |  2 ++
 lib/ODEProblemLibrary/test/qa/qa.jl               |  7 ++-----
 lib/SDEProblemLibrary/src/SDEProblemLibrary.jl    |  3 ++-
 lib/SDEProblemLibrary/test/qa/Project.toml        |  2 ++
 lib/SDEProblemLibrary/test/qa/qa.jl               | 14 +++++++++-----
 test/qa/Project.toml                              |  4 +---
 test/qa/qa.jl                                     | 15 +++++----------
 24 files changed, 67 insertions(+), 59 deletions(-)

diff --git a/Project.toml b/Project.toml
index d4bd8f3..3bcc69b 100644
--- a/Project.toml
+++ b/Project.toml
@@ -28,8 +28,9 @@ DDEProblemLibrary = "0.1"
 JumpProblemLibrary = "1, 2.0"
 NonlinearProblemLibrary = "0.1"
 ODEProblemLibrary = "1"
+Pkg = "1.10"
 SafeTestsets = "0.1"
-SciMLTesting = "1"
+SciMLTesting = "1.6"
 SDEProblemLibrary = "1"
 Test = "1.10"
 julia = "1.10"
diff --git a/lib/BVProblemLibrary/src/BVProblemLibrary.jl b/lib/BVProblemLibrary/src/BVProblemLibrary.jl
index 09067f5..2070818 100644
--- a/lib/BVProblemLibrary/src/BVProblemLibrary.jl
+++ b/lib/BVProblemLibrary/src/BVProblemLibrary.jl
@@ -1,6 +1,8 @@
 module BVProblemLibrary
 
-using DiffEqBase, Markdown, SpecialFunctions
+using DiffEqBase: DiffEqBase, BVPFunction, BVProblem
+using Markdown: Markdown
+using SpecialFunctions: SpecialFunctions, erf
 
 include("linear.jl")
 include("nonlinear.jl")
diff --git a/lib/BVProblemLibrary/test/qa/Project.toml b/lib/BVProblemLibrary/test/qa/Project.toml
index 3b6a6c9..0303815 100644
--- a/lib/BVProblemLibrary/test/qa/Project.toml
+++ b/lib/BVProblemLibrary/test/qa/Project.toml
@@ -1,6 +1,7 @@
 [deps]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 BVProblemLibrary = "ded0fc24-dfea-4565-b1d9-79c027d14d84"
+SciMLTesting = "09d9d899-5365-40a9-917a-5f67fddea283"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [sources]
@@ -9,5 +10,6 @@ BVProblemLibrary = {path = "../.."}
 [compat]
 Aqua = "0.8"
 BVProblemLibrary = "0.1"
+SciMLTesting = "1.6"
 Test = "1.10"
 julia = "1.10"
diff --git a/lib/BVProblemLibrary/test/qa/qa.jl b/lib/BVProblemLibrary/test/qa/qa.jl
index 36a36a3..d0cdafb 100644
--- a/lib/BVProblemLibrary/test/qa/qa.jl
+++ b/lib/BVProblemLibrary/test/qa/qa.jl
@@ -1,6 +1,3 @@
-using BVProblemLibrary
-using Aqua
+using SciMLTesting, BVProblemLibrary, Test
 
-@testset "Aqua" begin
-    Aqua.test_all(BVProblemLibrary; ambiguities = false)
-end
+run_qa(BVProblemLibrary; explicit_imports = true, aqua_kwargs = (; ambiguities = false))
diff --git a/lib/DAEProblemLibrary/src/DAEProblemLibrary.jl b/lib/DAEProblemLibrary/src/DAEProblemLibrary.jl
index 383121f..5d6644b 100644
--- a/lib/DAEProblemLibrary/src/DAEProblemLibrary.jl
+++ b/lib/DAEProblemLibrary/src/DAEProblemLibrary.jl
@@ -1,6 +1,7 @@
 module DAEProblemLibrary
 
-using DiffEqBase, Markdown
+using DiffEqBase: DiffEqBase, DAEProblem
+using Markdown: Markdown, @doc_str
 
 #DAE Example Problems
 export prob_dae_resrob, prob_dae_transamp
diff --git a/lib/DAEProblemLibrary/test/qa/Project.toml b/lib/DAEProblemLibrary/test/qa/Project.toml
index 5883ba1..47f8873 100644
--- a/lib/DAEProblemLibrary/test/qa/Project.toml
+++ b/lib/DAEProblemLibrary/test/qa/Project.toml
@@ -1,6 +1,7 @@
 [deps]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 DAEProblemLibrary = "dfb8ca35-80a1-48ba-a605-84916a45b4f8"
+SciMLTesting = "09d9d899-5365-40a9-917a-5f67fddea283"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [sources]
@@ -9,5 +10,6 @@ DAEProblemLibrary = {path = "../.."}
 [compat]
 Aqua = "0.8"
 DAEProblemLibrary = "0.1"
+SciMLTesting = "1.6"
 Test = "1.10"
 julia = "1.10"
diff --git a/lib/DAEProblemLibrary/test/qa/qa.jl b/lib/DAEProblemLibrary/test/qa/qa.jl
index 0bb41bc..19f7b6c 100644
--- a/lib/DAEProblemLibrary/test/qa/qa.jl
+++ b/lib/DAEProblemLibrary/test/qa/qa.jl
@@ -1,6 +1,3 @@
-using DAEProblemLibrary
-using Aqua
+using SciMLTesting, DAEProblemLibrary, Test
 
-@testset "Aqua" begin
-    Aqua.test_all(DAEProblemLibrary; ambiguities = false)
-end
+run_qa(DAEProblemLibrary; explicit_imports = true, aqua_kwargs = (; ambiguities = false))
diff --git a/lib/DDEProblemLibrary/src/DDEProblemLibrary.jl b/lib/DDEProblemLibrary/src/DDEProblemLibrary.jl
index 3284271..efc1a67 100644
--- a/lib/DDEProblemLibrary/src/DDEProblemLibrary.jl
+++ b/lib/DDEProblemLibrary/src/DDEProblemLibrary.jl
@@ -1,6 +1,6 @@
 module DDEProblemLibrary
 
-using DiffEqBase
+using DiffEqBase: DiffEqBase, DDEFunction, DDEProblem, remake
 # DDE Example Problems
 
 # examples with constant delays
diff --git a/lib/DDEProblemLibrary/test/qa/Project.toml b/lib/DDEProblemLibrary/test/qa/Project.toml
index 233d74a..2806b3c 100644
--- a/lib/DDEProblemLibrary/test/qa/Project.toml
+++ b/lib/DDEProblemLibrary/test/qa/Project.toml
@@ -1,6 +1,7 @@
 [deps]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 DDEProblemLibrary = "f42792ee-6ffc-4e2a-ae83-8ee2f22de800"
+SciMLTesting = "09d9d899-5365-40a9-917a-5f67fddea283"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [sources]
@@ -9,5 +10,6 @@ DDEProblemLibrary = {path = "../.."}
 [compat]
 Aqua = "0.8"
 DDEProblemLibrary = "0.1"
+SciMLTesting = "1.6"
 Test = "1.10"
 julia = "1.10"
diff --git a/lib/DDEProblemLibrary/test/qa/qa.jl b/lib/DDEProblemLibrary/test/qa/qa.jl
index ce167c0..10c3fbb 100644
--- a/lib/DDEProblemLibrary/test/qa/qa.jl
+++ b/lib/DDEProblemLibrary/test/qa/qa.jl
@@ -1,6 +1,3 @@
-using DDEProblemLibrary
-using Aqua
+using SciMLTesting, DDEProblemLibrary, Test
 
-@testset "Aqua" begin
-    Aqua.test_all(DDEProblemLibrary; ambiguities = false)
-end
+run_qa(DDEProblemLibrary; explicit_imports = true, aqua_kwargs = (; ambiguities = false))
diff --git a/lib/JumpProblemLibrary/src/JumpProblemLibrary.jl b/lib/JumpProblemLibrary/src/JumpProblemLibrary.jl
index f5700b5..9263e67 100644
--- a/lib/JumpProblemLibrary/src/JumpProblemLibrary.jl
+++ b/lib/JumpProblemLibrary/src/JumpProblemLibrary.jl
@@ -1,6 +1,8 @@
 module JumpProblemLibrary
 
-using Catalyst
+using Catalyst: Catalyst, @named, @parameters, @reaction_network, @species, Num,
+    Reaction, ReactionSystem, complete, default_t, hill, make_empty_network,
+    species, unknowns
 
 import RuntimeGeneratedFunctions
 RuntimeGeneratedFunctions.init(@__MODULE__)
diff --git a/lib/JumpProblemLibrary/test/qa/Project.toml b/lib/JumpProblemLibrary/test/qa/Project.toml
index 4d15c00..84983a9 100644
--- a/lib/JumpProblemLibrary/test/qa/Project.toml
+++ b/lib/JumpProblemLibrary/test/qa/Project.toml
@@ -1,6 +1,7 @@
 [deps]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 JumpProblemLibrary = "faf0f6d7-8cee-47cb-b27c-1eb80cef534e"
+SciMLTesting = "09d9d899-5365-40a9-917a-5f67fddea283"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [sources]
@@ -9,5 +10,6 @@ JumpProblemLibrary = {path = "../.."}
 [compat]
 Aqua = "0.8"
 JumpProblemLibrary = "2"
+SciMLTesting = "1.6"
 Test = "1.10"
 julia = "1.10"
diff --git a/lib/JumpProblemLibrary/test/qa/qa.jl b/lib/JumpProblemLibrary/test/qa/qa.jl
index 3d703ee..377d194 100644
--- a/lib/JumpProblemLibrary/test/qa/qa.jl
+++ b/lib/JumpProblemLibrary/test/qa/qa.jl
@@ -1,6 +1,10 @@
-using JumpProblemLibrary
-using Aqua
+using SciMLTesting, JumpProblemLibrary, Test
 
-@testset "Aqua" begin
-    Aqua.test_all(JumpProblemLibrary; ambiguities = false, persistent_tasks = false)
-end
+# `RuntimeGeneratedFunctions.init(@__MODULE__)` qualified-accesses the non-public
+# `RuntimeGeneratedFunctions.init` (the package's documented init boilerplate), so it
+# is ignored for the public-API qualified-access check.
+run_qa(
+    JumpProblemLibrary; explicit_imports = true,
+    aqua_kwargs = (; ambiguities = false, persistent_tasks = false),
+    ei_kwargs = (; all_qualified_accesses_are_public = (; ignore = (:init,)))
+)
diff --git a/lib/NonlinearProblemLibrary/src/NonlinearProblemLibrary.jl b/lib/NonlinearProblemLibrary/src/NonlinearProblemLibrary.jl
index ae5c52f..397aa7d 100644
--- a/lib/NonlinearProblemLibrary/src/NonlinearProblemLibrary.jl
+++ b/lib/NonlinearProblemLibrary/src/NonlinearProblemLibrary.jl
@@ -1,6 +1,7 @@
 module NonlinearProblemLibrary
 
-using SciMLBase, LinearAlgebra
+using SciMLBase: SciMLBase, NonlinearProblem
+using LinearAlgebra: LinearAlgebra
 
 # Implementation of the 23 test problems in
 # [test_nonlin](https://people.sc.fsu.edu/~jburkardt/m_src/test_nonlin/test_nonlin.html)
diff --git a/lib/NonlinearProblemLibrary/test/qa/Project.toml b/lib/NonlinearProblemLibrary/test/qa/Project.toml
index 5ee5061..8b49b35 100644
--- a/lib/NonlinearProblemLibrary/test/qa/Project.toml
+++ b/lib/NonlinearProblemLibrary/test/qa/Project.toml
@@ -2,6 +2,7 @@
 AllocCheck = "9b6a8646-10ed-4001-bbdc-1d2f46dfbb1a"
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 NonlinearProblemLibrary = "b7050fa9-e91f-4b37-bcee-a89a063da141"
+SciMLTesting = "09d9d899-5365-40a9-917a-5f67fddea283"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [sources]
@@ -11,5 +12,6 @@ NonlinearProblemLibrary = {path = "../.."}
 AllocCheck = "0.2"
 Aqua = "0.8"
 NonlinearProblemLibrary = "0.1"
+SciMLTesting = "1.6"
 Test = "1"
 julia = "1.10"
diff --git a/lib/NonlinearProblemLibrary/test/qa/qa.jl b/lib/NonlinearProblemLibrary/test/qa/qa.jl
index 5274826..5c4dc61 100644
--- a/lib/NonlinearProblemLibrary/test/qa/qa.jl
+++ b/lib/NonlinearProblemLibrary/test/qa/qa.jl
@@ -1,6 +1,3 @@
-using NonlinearProblemLibrary
-using Aqua
+using SciMLTesting, NonlinearProblemLibrary, Test
 
-@testset "Aqua" begin
-    Aqua.test_all(NonlinearProblemLibrary; ambiguities = false)
-end
+run_qa(NonlinearProblemLibrary; explicit_imports = true, aqua_kwargs = (; ambiguities = false))
diff --git a/lib/ODEProblemLibrary/src/ODEProblemLibrary.jl b/lib/ODEProblemLibrary/src/ODEProblemLibrary.jl
index 243c4d0..bf022ee 100644
--- a/lib/ODEProblemLibrary/src/ODEProblemLibrary.jl
+++ b/lib/ODEProblemLibrary/src/ODEProblemLibrary.jl
@@ -1,9 +1,9 @@
 module ODEProblemLibrary
 
-using DiffEqBase
-using LinearAlgebra
-using Markdown
-using Random
+using DiffEqBase: DiffEqBase, ODEFunction, ODEProblem
+using LinearAlgebra: LinearAlgebra, Diagonal, I, SymTridiagonal, diagind, ldiv!, mul!, rmul!
+using Markdown: Markdown, @doc_str
+using Random: Random
 
 Random.seed!(100)
 
diff --git a/lib/ODEProblemLibrary/test/qa/Project.toml b/lib/ODEProblemLibrary/test/qa/Project.toml
index d52ff29..ff7b19a 100644
--- a/lib/ODEProblemLibrary/test/qa/Project.toml
+++ b/lib/ODEProblemLibrary/test/qa/Project.toml
@@ -1,6 +1,7 @@
 [deps]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 ODEProblemLibrary = "fdc4e326-1af4-4b90-96e7-779fcce2daa5"
+SciMLTesting = "09d9d899-5365-40a9-917a-5f67fddea283"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [sources]
@@ -9,5 +10,6 @@ ODEProblemLibrary = {path = "../.."}
 [compat]
 Aqua = "0.8"
 ODEProblemLibrary = "1"
+SciMLTesting = "1.6"
 Test = "1.10"
 julia = "1.10"
diff --git a/lib/ODEProblemLibrary/test/qa/qa.jl b/lib/ODEProblemLibrary/test/qa/qa.jl
index cdfb145..f5b5bb5 100644
--- a/lib/ODEProblemLibrary/test/qa/qa.jl
+++ b/lib/ODEProblemLibrary/test/qa/qa.jl
@@ -1,6 +1,3 @@
-using ODEProblemLibrary
-using Aqua
+using SciMLTesting, ODEProblemLibrary, Test
 
-@testset "Aqua" begin
-    Aqua.test_all(ODEProblemLibrary; ambiguities = false)
-end
+run_qa(ODEProblemLibrary; explicit_imports = true, aqua_kwargs = (; ambiguities = false))
diff --git a/lib/SDEProblemLibrary/src/SDEProblemLibrary.jl b/lib/SDEProblemLibrary/src/SDEProblemLibrary.jl
index 4b577d5..b463129 100644
--- a/lib/SDEProblemLibrary/src/SDEProblemLibrary.jl
+++ b/lib/SDEProblemLibrary/src/SDEProblemLibrary.jl
@@ -1,6 +1,7 @@
 module SDEProblemLibrary
 
-using DiffEqBase, Markdown
+using DiffEqBase: DiffEqBase, SDEFunction, SDEProblem
+using Markdown: Markdown, @doc_str
 
 import RuntimeGeneratedFunctions
 RuntimeGeneratedFunctions.init(@__MODULE__)
diff --git a/lib/SDEProblemLibrary/test/qa/Project.toml b/lib/SDEProblemLibrary/test/qa/Project.toml
index 2cdb197..90732b1 100644
--- a/lib/SDEProblemLibrary/test/qa/Project.toml
+++ b/lib/SDEProblemLibrary/test/qa/Project.toml
@@ -1,6 +1,7 @@
 [deps]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 SDEProblemLibrary = "c72e72a9-a271-4b2b-8966-303ed956772e"
+SciMLTesting = "09d9d899-5365-40a9-917a-5f67fddea283"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [sources]
@@ -9,5 +10,6 @@ SDEProblemLibrary = {path = "../.."}
 [compat]
 Aqua = "0.8"
 SDEProblemLibrary = "1"
+SciMLTesting = "1.6"
 Test = "1.10"
 julia = "1.10"
diff --git a/lib/SDEProblemLibrary/test/qa/qa.jl b/lib/SDEProblemLibrary/test/qa/qa.jl
index faf5dfb..396ed6d 100644
--- a/lib/SDEProblemLibrary/test/qa/qa.jl
+++ b/lib/SDEProblemLibrary/test/qa/qa.jl
@@ -1,6 +1,10 @@
-using SDEProblemLibrary
-using Aqua
+using SciMLTesting, SDEProblemLibrary, Test
 
-@testset "Aqua" begin
-    Aqua.test_all(SDEProblemLibrary; ambiguities = false, persistent_tasks = false)
-end
+# `RuntimeGeneratedFunctions.init(@__MODULE__)` qualified-accesses the non-public
+# `RuntimeGeneratedFunctions.init` (the package's documented init boilerplate), so it
+# is ignored for the public-API qualified-access check.
+run_qa(
+    SDEProblemLibrary; explicit_imports = true,
+    aqua_kwargs = (; ambiguities = false, persistent_tasks = false),
+    ei_kwargs = (; all_qualified_accesses_are_public = (; ignore = (:init,)))
+)
diff --git a/test/qa/Project.toml b/test/qa/Project.toml
index 7037fbf..78e8c4e 100644
--- a/test/qa/Project.toml
+++ b/test/qa/Project.toml
@@ -1,6 +1,5 @@
 [deps]
 DiffEqProblemLibrary = "a077e3f3-b75c-5d7f-a0c6-6bc4c8ec64a9"
-ExplicitImports = "7d51a73a-1435-4ff3-83d9-f097790105c7"
 SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
 SciMLTesting = "09d9d899-5365-40a9-917a-5f67fddea283"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
@@ -10,8 +9,7 @@ DiffEqProblemLibrary = {path = "../.."}
 
 [compat]
 DiffEqProblemLibrary = "5"
-ExplicitImports = "1"
 SafeTestsets = "0.0.1, 0.1"
-SciMLTesting = "1"
+SciMLTesting = "1.6"
 Test = "1.10"
 julia = "1.10"
diff --git a/test/qa/qa.jl b/test/qa/qa.jl
index 8c77d8f..454dc48 100644
--- a/test/qa/qa.jl
+++ b/test/qa/qa.jl
@@ -1,11 +1,6 @@
-# The root umbrella package's own test: it re-exports each sublibrary,
-# so the test is that the whole thing builds with no implicit or stale
-# explicit imports.
-using DiffEqProblemLibrary
-using ExplicitImports
-using Test
+using SciMLTesting, DiffEqProblemLibrary, Test
 
-@testset "ExplicitImports" begin
-    @test check_no_implicit_imports(DiffEqProblemLibrary) === nothing
-    @test check_no_stale_explicit_imports(DiffEqProblemLibrary) === nothing
-end
+# The root umbrella package re-exports each sublibrary; it owns no methods of its own,
+# so the reported method ambiguities all come from the imported dependency tree
+# (DiffEqBase / SciMLBase / Catalyst), matching the `ambiguities = false` each sublib uses.
+run_qa(DiffEqProblemLibrary; explicit_imports = true, aqua_kwargs = (; ambiguities = false))

From aceb07b233bde5b4ebbd4fc633de9af567e4e9cc Mon Sep 17 00:00:00 2001
From: ChrisRackauckas-Claude <accounts@chrisrackauckas.com>
Date: Fri, 26 Jun 2026 15:29:29 -0400
Subject: [PATCH 2/4] QA: drop now-redundant RuntimeGeneratedFunctions.init
 public-API ignore

SciMLTesting 1.7.0 runs the two public-API ExplicitImports checks
(check_all_qualified_accesses_are_public / check_all_explicit_imports_are_public)
only on Julia >= 1.11, and RuntimeGeneratedFunctions made `init` public
(Base.ispublic(RuntimeGeneratedFunctions, :init) === true as of v0.5.21).

The `RuntimeGeneratedFunctions.init(@__MODULE__)` boilerplate in
JumpProblemLibrary and SDEProblemLibrary therefore no longer trips the
qualified-access public-API check, so the per-repo `:init` ignore on
`all_qualified_accesses_are_public` is now inert and is removed. Both qa.jl
calls reduce to the plain `run_qa(...; explicit_imports = true, aqua_kwargs = ...)`
form with no EI ignore-lists.

Verified against the registered releases (no dev):
- Julia 1.12 (>= 1.11, public checks run): SDEProblemLibrary EI runs 6/6 with
  the emptied ignore-list (SciMLTesting 1.7.0). JumpProblemLibrary uses the
  identical init pattern and already passed EI 6/6 on CI; init being public
  makes the ignore unnecessary.
- Julia 1.10 (lts, public checks skipped by 1.7): SDE/Jump EI 4/4, root QA 14/14.

SciMLTesting [compat] "1.6" already admits 1.7 (caret), so no compat bump
needed. No `if VERSION < v"1.11"` ignore blocks existed to remove. No names
required restoring -- the public-API ignore-lists are now fully empty.

Note: the sublibrary QA (Julia 1) lanes still fail on a pre-existing,
unrelated Aqua deps_compat issue (`Pkg` listed in [extras] without a [compat]
bound in DAE/DDE/Jump/Nonlinear/ODE/SDE, identical on master); that is out of
scope for this EI ignore sweep and left for a separate focused fix.

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 lib/JumpProblemLibrary/test/qa/qa.jl | 6 +-----
 lib/SDEProblemLibrary/test/qa/qa.jl  | 6 +-----
 2 files changed, 2 insertions(+), 10 deletions(-)

diff --git a/lib/JumpProblemLibrary/test/qa/qa.jl b/lib/JumpProblemLibrary/test/qa/qa.jl
index 377d194..ed40700 100644
--- a/lib/JumpProblemLibrary/test/qa/qa.jl
+++ b/lib/JumpProblemLibrary/test/qa/qa.jl
@@ -1,10 +1,6 @@
 using SciMLTesting, JumpProblemLibrary, Test
 
-# `RuntimeGeneratedFunctions.init(@__MODULE__)` qualified-accesses the non-public
-# `RuntimeGeneratedFunctions.init` (the package's documented init boilerplate), so it
-# is ignored for the public-API qualified-access check.
 run_qa(
     JumpProblemLibrary; explicit_imports = true,
-    aqua_kwargs = (; ambiguities = false, persistent_tasks = false),
-    ei_kwargs = (; all_qualified_accesses_are_public = (; ignore = (:init,)))
+    aqua_kwargs = (; ambiguities = false, persistent_tasks = false)
 )
diff --git a/lib/SDEProblemLibrary/test/qa/qa.jl b/lib/SDEProblemLibrary/test/qa/qa.jl
index 396ed6d..0a4e0d8 100644
--- a/lib/SDEProblemLibrary/test/qa/qa.jl
+++ b/lib/SDEProblemLibrary/test/qa/qa.jl
@@ -1,10 +1,6 @@
 using SciMLTesting, SDEProblemLibrary, Test
 
-# `RuntimeGeneratedFunctions.init(@__MODULE__)` qualified-accesses the non-public
-# `RuntimeGeneratedFunctions.init` (the package's documented init boilerplate), so it
-# is ignored for the public-API qualified-access check.
 run_qa(
     SDEProblemLibrary; explicit_imports = true,
-    aqua_kwargs = (; ambiguities = false, persistent_tasks = false),
-    ei_kwargs = (; all_qualified_accesses_are_public = (; ignore = (:init,)))
+    aqua_kwargs = (; ambiguities = false, persistent_tasks = false)
 )

From 2db9cd47ce294f8c312a55e89597c1467dc43f6a Mon Sep 17 00:00:00 2001
From: ChrisRackauckas-Claude <accounts@chrisrackauckas.com>
Date: Sat, 27 Jun 2026 00:28:37 -0400
Subject: [PATCH 3/4] QA: SciMLTesting 1.7 floor + missing Pkg extras compat
 (green public-API EI)

Finish the run_qa/ExplicitImports conversion against the now-released
public-API surfaces (SciMLBase 3.27.0, DiffEqBase 7.6.0, ArrayInterface
7.26.0) and SciMLTesting 1.7.0 (which gates the two public-API EI checks
-- all_qualified_accesses_are_public / all_explicit_imports_are_public --
to Julia >= 1.11).

Compat:
- Bump SciMLTesting "1.6" -> "1.7" in the root [compat] and every QA
  sub-env (root test/qa + all 7 lib/*/test/qa). "1.6" already admits
  1.7.0 by caret, but the public-API checks are unconditional in 1.6 and
  only gained the >= 1.11 gate in 1.7; pinning the floor at 1.7 guarantees
  the gating version so the LTS (1.10) lane skips the backport-incompatible
  public checks instead of spuriously flagging backported-public names.

QA fix (the QA / Julia 1 reds):
- Add the missing `Pkg = "1.10"` [compat] entry to the six sublibraries
  that list `Pkg` in [extras] without a [compat] bound (DAE/DDE/Jump/
  Nonlinear/ODE/SDE). Aqua's deps_compat extras check (Aqua 0.8 via
  SciMLTesting) hard-fails on `Pkg` extras lacking compat; BVProblemLibrary
  already carries this entry and its QA lane was the only green one. This
  matches BVProblemLibrary exactly -- a real missing bound, not a silenced
  check.

No EI ignore-lists, `ei_broken`, or `VERSION < v"1.11"` blocks exist to
strip (the qa.jl files were already in the bare run_qa form), and no
`DiffEqBase.X` qualified accesses of SciMLBase-owned public names exist in
src/ to migrate -- the source uses explicit imports (`using DiffEqBase:
ODEProblem`, ...) which pass all_explicit_imports_are_public unchanged.

Verified against the registered releases (Pkg resolve, no dev of deps):
  Julia 1.12 (public checks run): root 16/16, ODEProblemLibrary 16/16,
    SDEProblemLibrary 15/15, NonlinearProblemLibrary 16/16,
    DAEProblemLibrary 16/16, JumpProblemLibrary 15/15 -- all green, 0 Fail.
  Julia 1.10 (public checks skipped by the 1.7 gate): ODEProblemLibrary
    14/14 (= 16 minus the 2 skipped public checks); root EI runs 4/4.

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 Project.toml                                     | 2 +-
 lib/BVProblemLibrary/test/qa/Project.toml        | 2 +-
 lib/DAEProblemLibrary/Project.toml               | 1 +
 lib/DAEProblemLibrary/test/qa/Project.toml       | 2 +-
 lib/DDEProblemLibrary/Project.toml               | 1 +
 lib/DDEProblemLibrary/test/qa/Project.toml       | 2 +-
 lib/JumpProblemLibrary/Project.toml              | 1 +
 lib/JumpProblemLibrary/test/qa/Project.toml      | 2 +-
 lib/NonlinearProblemLibrary/Project.toml         | 1 +
 lib/NonlinearProblemLibrary/test/qa/Project.toml | 2 +-
 lib/ODEProblemLibrary/Project.toml               | 1 +
 lib/ODEProblemLibrary/test/qa/Project.toml       | 2 +-
 lib/SDEProblemLibrary/Project.toml               | 1 +
 lib/SDEProblemLibrary/test/qa/Project.toml       | 2 +-
 test/qa/Project.toml                             | 2 +-
 15 files changed, 15 insertions(+), 9 deletions(-)

diff --git a/Project.toml b/Project.toml
index 3bcc69b..b68846a 100644
--- a/Project.toml
+++ b/Project.toml
@@ -30,7 +30,7 @@ NonlinearProblemLibrary = "0.1"
 ODEProblemLibrary = "1"
 Pkg = "1.10"
 SafeTestsets = "0.1"
-SciMLTesting = "1.6"
+SciMLTesting = "1.7"
 SDEProblemLibrary = "1"
 Test = "1.10"
 julia = "1.10"
diff --git a/lib/BVProblemLibrary/test/qa/Project.toml b/lib/BVProblemLibrary/test/qa/Project.toml
index 0303815..7245dbb 100644
--- a/lib/BVProblemLibrary/test/qa/Project.toml
+++ b/lib/BVProblemLibrary/test/qa/Project.toml
@@ -10,6 +10,6 @@ BVProblemLibrary = {path = "../.."}
 [compat]
 Aqua = "0.8"
 BVProblemLibrary = "0.1"
-SciMLTesting = "1.6"
+SciMLTesting = "1.7"
 Test = "1.10"
 julia = "1.10"
diff --git a/lib/DAEProblemLibrary/Project.toml b/lib/DAEProblemLibrary/Project.toml
index 1492602..28555f9 100644
--- a/lib/DAEProblemLibrary/Project.toml
+++ b/lib/DAEProblemLibrary/Project.toml
@@ -9,6 +9,7 @@ Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
 [compat]
 DiffEqBase = "6, 7"
 Markdown = "1.10"
+Pkg = "1.10"
 SafeTestsets = "0.1"
 Test = "1.10"
 julia = "1.10"
diff --git a/lib/DAEProblemLibrary/test/qa/Project.toml b/lib/DAEProblemLibrary/test/qa/Project.toml
index 47f8873..1c0a85d 100644
--- a/lib/DAEProblemLibrary/test/qa/Project.toml
+++ b/lib/DAEProblemLibrary/test/qa/Project.toml
@@ -10,6 +10,6 @@ DAEProblemLibrary = {path = "../.."}
 [compat]
 Aqua = "0.8"
 DAEProblemLibrary = "0.1"
-SciMLTesting = "1.6"
+SciMLTesting = "1.7"
 Test = "1.10"
 julia = "1.10"
diff --git a/lib/DDEProblemLibrary/Project.toml b/lib/DDEProblemLibrary/Project.toml
index 6621d19..8751596 100644
--- a/lib/DDEProblemLibrary/Project.toml
+++ b/lib/DDEProblemLibrary/Project.toml
@@ -7,6 +7,7 @@ DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
 
 [compat]
 DiffEqBase = "6, 7"
+Pkg = "1.10"
 SafeTestsets = "0.1"
 Test = "1.10"
 julia = "1.10"
diff --git a/lib/DDEProblemLibrary/test/qa/Project.toml b/lib/DDEProblemLibrary/test/qa/Project.toml
index 2806b3c..feb7f93 100644
--- a/lib/DDEProblemLibrary/test/qa/Project.toml
+++ b/lib/DDEProblemLibrary/test/qa/Project.toml
@@ -10,6 +10,6 @@ DDEProblemLibrary = {path = "../.."}
 [compat]
 Aqua = "0.8"
 DDEProblemLibrary = "0.1"
-SciMLTesting = "1.6"
+SciMLTesting = "1.7"
 Test = "1.10"
 julia = "1.10"
diff --git a/lib/JumpProblemLibrary/Project.toml b/lib/JumpProblemLibrary/Project.toml
index f595ccd..ea7e7fb 100644
--- a/lib/JumpProblemLibrary/Project.toml
+++ b/lib/JumpProblemLibrary/Project.toml
@@ -8,6 +8,7 @@ RuntimeGeneratedFunctions = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47"
 
 [compat]
 Catalyst = "16"
+Pkg = "1.10"
 RuntimeGeneratedFunctions = "0.5"
 SafeTestsets = "0.1"
 Test = "1.10"
diff --git a/lib/JumpProblemLibrary/test/qa/Project.toml b/lib/JumpProblemLibrary/test/qa/Project.toml
index 84983a9..eca6aca 100644
--- a/lib/JumpProblemLibrary/test/qa/Project.toml
+++ b/lib/JumpProblemLibrary/test/qa/Project.toml
@@ -10,6 +10,6 @@ JumpProblemLibrary = {path = "../.."}
 [compat]
 Aqua = "0.8"
 JumpProblemLibrary = "2"
-SciMLTesting = "1.6"
+SciMLTesting = "1.7"
 Test = "1.10"
 julia = "1.10"
diff --git a/lib/NonlinearProblemLibrary/Project.toml b/lib/NonlinearProblemLibrary/Project.toml
index bc377fc..e72686a 100644
--- a/lib/NonlinearProblemLibrary/Project.toml
+++ b/lib/NonlinearProblemLibrary/Project.toml
@@ -8,6 +8,7 @@ SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 
 [compat]
 LinearAlgebra = "1.6"
+Pkg = "1.10"
 SafeTestsets = "0.1"
 SciMLBase = "2, 3"
 Test = "1"
diff --git a/lib/NonlinearProblemLibrary/test/qa/Project.toml b/lib/NonlinearProblemLibrary/test/qa/Project.toml
index 8b49b35..053f135 100644
--- a/lib/NonlinearProblemLibrary/test/qa/Project.toml
+++ b/lib/NonlinearProblemLibrary/test/qa/Project.toml
@@ -12,6 +12,6 @@ NonlinearProblemLibrary = {path = "../.."}
 AllocCheck = "0.2"
 Aqua = "0.8"
 NonlinearProblemLibrary = "0.1"
-SciMLTesting = "1.6"
+SciMLTesting = "1.7"
 Test = "1"
 julia = "1.10"
diff --git a/lib/ODEProblemLibrary/Project.toml b/lib/ODEProblemLibrary/Project.toml
index 7d70379..717daae 100644
--- a/lib/ODEProblemLibrary/Project.toml
+++ b/lib/ODEProblemLibrary/Project.toml
@@ -12,6 +12,7 @@ Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 DiffEqBase = "6, 7"
 LinearAlgebra = "1.10"
 Markdown = "1.10"
+Pkg = "1.10"
 Random = "1.10"
 SafeTestsets = "0.1"
 Test = "1.10"
diff --git a/lib/ODEProblemLibrary/test/qa/Project.toml b/lib/ODEProblemLibrary/test/qa/Project.toml
index ff7b19a..5b386cd 100644
--- a/lib/ODEProblemLibrary/test/qa/Project.toml
+++ b/lib/ODEProblemLibrary/test/qa/Project.toml
@@ -10,6 +10,6 @@ ODEProblemLibrary = {path = "../.."}
 [compat]
 Aqua = "0.8"
 ODEProblemLibrary = "1"
-SciMLTesting = "1.6"
+SciMLTesting = "1.7"
 Test = "1.10"
 julia = "1.10"
diff --git a/lib/SDEProblemLibrary/Project.toml b/lib/SDEProblemLibrary/Project.toml
index 61614d8..8a37076 100644
--- a/lib/SDEProblemLibrary/Project.toml
+++ b/lib/SDEProblemLibrary/Project.toml
@@ -11,6 +11,7 @@ SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 [compat]
 DiffEqBase = "6, 7"
 Markdown = "1.10"
+Pkg = "1.10"
 RuntimeGeneratedFunctions = "0.5"
 SafeTestsets = "0.1"
 SciMLBase = "2.0.1, 3"
diff --git a/lib/SDEProblemLibrary/test/qa/Project.toml b/lib/SDEProblemLibrary/test/qa/Project.toml
index 90732b1..c48efef 100644
--- a/lib/SDEProblemLibrary/test/qa/Project.toml
+++ b/lib/SDEProblemLibrary/test/qa/Project.toml
@@ -10,6 +10,6 @@ SDEProblemLibrary = {path = "../.."}
 [compat]
 Aqua = "0.8"
 SDEProblemLibrary = "1"
-SciMLTesting = "1.6"
+SciMLTesting = "1.7"
 Test = "1.10"
 julia = "1.10"
diff --git a/test/qa/Project.toml b/test/qa/Project.toml
index 78e8c4e..31a8d0e 100644
--- a/test/qa/Project.toml
+++ b/test/qa/Project.toml
@@ -10,6 +10,6 @@ DiffEqProblemLibrary = {path = "../.."}
 [compat]
 DiffEqProblemLibrary = "5"
 SafeTestsets = "0.0.1, 0.1"
-SciMLTesting = "1.6"
+SciMLTesting = "1.7"
 Test = "1.10"
 julia = "1.10"

From 4c37ef5e4fa8c7b0034556ce625b59004af24953 Mon Sep 17 00:00:00 2001
From: ChrisRackauckas-Claude <accounts@chrisrackauckas.com>
Date: Sun, 28 Jun 2026 18:21:50 -0400
Subject: [PATCH 4/4] QA: develop qa env [sources] on Julia <1.11 so checks
 test the working tree
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

The root QA env (test/qa) pins `DiffEqProblemLibrary = {path = "../.."}` in
[sources], but on Julia <1.11 Pkg ignores [sources]; `activate_qa_env`'s plain
`Pkg.activate` + `Pkg.instantiate` therefore resolved DiffEqProblemLibrary to the
registered release v5.2.1 instead of the working copy. The run_qa conversion runs
`Aqua.test_all` (which the old qa.jl did not), so its deps_compat extras check ran
against the registry Project.toml — which lacks the `Pkg` extras [compat] entry
this branch adds — failing the Downgrade Core (lts/1.10) lane while the fix on the
branch went unexercised.

Develop the qa env's local path [sources] on Julia <1.11 before instantiating,
mirroring the existing sublibrary branch in this file, so the QA checks run against
the working tree (where `Pkg = "1.10"` is already declared).

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
---
 test/runtests.jl | 25 +++++++++++++++++++------
 1 file changed, 19 insertions(+), 6 deletions(-)

diff --git a/test/runtests.jl b/test/runtests.jl
index afc51fa..5465d62 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -5,13 +5,26 @@ using SciMLTesting
 const GROUP = current_group()
 const LIB_DIR = joinpath(dirname(@__DIR__), "lib")
 
-# The root umbrella package's own QA env activation. It is kept as an explicit
-# helper (rather than `run_tests`'s `env =` group spec) so the activate/instantiate
-# behavior — in particular NOT `Pkg.develop`-ing the root or transitively developing
-# the env's `[sources]` on Julia < 1.11 — stays byte-for-byte identical to the
-# previous hand-written runtests.jl.
+# The root umbrella package's own QA env activation. On Julia < 1.11 the env's
+# `[sources]` table is ignored by Pkg, so `DiffEqProblemLibrary = {path = "../.."}`
+# would silently resolve to the registered release instead of the working copy —
+# meaning the QA checks (Aqua.test_all etc.) run against the registry version, not
+# the branch under CI. Develop the env's local path sources first, mirroring the
+# sublibrary branch below, so the checks test the working tree.
 function activate_qa_env()
-    Pkg.activate(joinpath(@__DIR__, "qa"))
+    qa_dir = joinpath(@__DIR__, "qa")
+    Pkg.activate(qa_dir)
+    if VERSION < v"1.11.0-DEV.0"
+        toml = Pkg.TOML.parsefile(joinpath(qa_dir, "Project.toml"))
+        specs = Pkg.PackageSpec[]
+        for (_, source_spec) in get(toml, "sources", Dict())
+            if source_spec isa Dict && haskey(source_spec, "path")
+                dep_path = normpath(joinpath(qa_dir, source_spec["path"]))
+                isdir(dep_path) && push!(specs, Pkg.PackageSpec(path = dep_path))
+            end
+        end
+        isempty(specs) || Pkg.develop(specs)
+    end
     return Pkg.instantiate()
 end