QA: run_qa v1.6 form + ExplicitImports (root + sublibs)#206
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ChrisRackauckas-Claude wants to merge 3 commits into
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QA: run_qa v1.6 form + ExplicitImports (root + sublibs)#206ChrisRackauckas-Claude wants to merge 3 commits into
ChrisRackauckas-Claude wants to merge 3 commits into
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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>
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>
…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>
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This PR should be ignored until reviewed by @ChrisRackauckas.
Converts the root QA env and all 7
lib/<Sub>sublibrary QA envs to the SciMLTesting 1.6run_qaform withexplicit_imports = true, in one branch.Per QA env
qa.jl→using SciMLTesting, <Module>, Test+run_qa(<Module>; explicit_imports = true, ...).test/qa/Project.toml: SciMLTesting[compat]bumped to"1.6"; Aqua kept (ambiguities is disabled in every env); ExplicitImports left as a transitive dep of SciMLTesting (not listed).[sources]/ develop wiring (sublib + umbrella-root pins,activate_group_env/develop_sources!<1.11backport) is preserved exactly.ExplicitImports: fixed, not suppressed (0 hard FAIL, no broken markers)
no_implicit_imports— each sublibrary's blanketusing <dep>is replaced with the explicit name list ExplicitImports recommends, e.g.using DiffEqBase: DiffEqBase, BVPFunction, BVProblem,using SpecialFunctions: SpecialFunctions, erfusing LinearAlgebra: LinearAlgebra, Diagonal, I, SymTridiagonal, diagind, ldiv!, mul!, rmul!, etc.using Catalyst: Catalyst, @reaction_network, @species, @parameters, @named, Num, Reaction, ReactionSystem, complete, default_t, hill, make_empty_network, species, unknownsall_qualified_accesses_are_public—JumpProblemLibraryandSDEProblemLibrarycall the non-publicRuntimeGeneratedFunctions.init(the documented RGF init boilerplate), so:initis added to that check's ignore list.Genuine Aqua disables preserved
ambiguities = falsein every env (including the root — its only ambiguities come from the imported dependency tree, since the umbrella owns no methods).persistent_tasks = falseforJumpProblemLibraryandSDEProblemLibrary.Root package
Project.tomlPkg[compat]entry (Aquadeps_compatextras check flagged it once Aqua started running on the root).[compat]to"1.6".Sublibs converted
BVProblemLibrary, DAEProblemLibrary, DDEProblemLibrary, JumpProblemLibrary, NonlinearProblemLibrary, ODEProblemLibrary, SDEProblemLibrary (7) + root.
Verification (Julia 1.11, released SciMLTesting 1.6.0)
Quality Assurance | 16 pass / 16 total(Aqua incl. persistent_tasks + deps_compat after the Pkg fix; ExplicitImports 6/6).initignore). Aqua per sublib unchanged from the prior hand-rolled call.🤖 Generated with Claude Code