QA: run_qa v1.6 form + ExplicitImports (#96)

* QA: run_qa v1.6 form + ExplicitImports

Convert the hand-rolled test/qa/qa.jl to the SciMLTesting 1.6 run_qa
form and enable the ExplicitImports check group.

- qa.jl: replace the manual Aqua/JET testset (which carried two
  @test_broken placeholders) with run_qa(FiniteVolumeMethod1D;
  explicit_imports = true, ...).
- The Aqua deps_compat finding (#84) is fixed at the source rather than
  marked broken: add SparseArrays = "1" to the root [compat]. Aqua
  test_all (incl. deps_compat) now passes.
- The JET finding (#84) does not reproduce under run_qa's canonical
  config (mode = :typo, target_modules = (FiniteVolumeMethod1D,)); the
  original 4 reports were artifacts of target_defined_modules = true.
  JET.test_package now runs and passes, so no jet_broken is needed.
- ExplicitImports: all six checks run. Four pass clean; two non-public
  names from other packages are ignored until they go public:
  all_qualified_accesses_are_public ignores AutoSpecialize (SciMLBase)
  and init (CommonSolve); all_explicit_imports_are_public ignores solve
  (CommonSolve, re-exported). All ignores are other-package non-public
  names, documented inline with their source package.
- Drop ExplicitImports from the root [extras]/[targets].test and the
  test/ env, and remove the legacy test/explicit_imports.jl (its two
  checks are subsumed by the QA group's six). ExplicitImports is now a
  transitive dep via SciMLTesting.
- test/qa/Project.toml: bump SciMLTesting compat to "1.6"; keep
  SafeTestsets (the folder-model @safetestset wrapper needs it as a
  direct dep of the group env) and Aqua/JET.

Verified locally on Julia 1.10 against released SciMLTesting 1.6.0 via
GROUP=QA runtests.jl: QA/qa.jl 18/18 pass, 0 fail/error/broken.

Closes #84.

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* QA: drop now-public EI ignores (SciMLTesting 1.7 + base-lib public APIs)

SciMLTesting 1.7.0 runs the two public-API ExplicitImports checks
(check_all_qualified_accesses_are_public and
check_all_explicit_imports_are_public) only on Julia >= 1.11 and skips
them on the lts. Combined with the base-lib public-API releases
(SciMLBase 3.24.0, CommonSolve 0.2.9), the per-repo public-API ignore
entries this PR carried are now redundant.

Empty both public-API ignore-lists in test/qa/qa.jl: the previously
ignored AutoSpecialize (SciMLBase), init (CommonSolve), and solve
(CommonSolve) are all recognized as public on the registered releases,
so run_qa(...; explicit_imports = true) passes with no ei_kwargs at all.

Verified against registered releases (no dev of base libs; FVM dev'd
from this working tree):
- Julia 1.12 (public-API checks RUN): QA group 18/18 pass, 0 fail/
  error/broken; resolved SciMLTesting 1.7.0, SciMLBase 3.24.0,
  CommonSolve 0.2.9, ExplicitImports 1.15.0.
- Julia 1.10 lts (public-API checks skipped by SciMLTesting 1.7):
  QA group 16/16 pass, 0 fail/error/broken.

No names needed restoring; the ignore-lists are now empty.

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* QA: pin SciMLTesting compat floor to 1.7 (public-API EI gate)

The two public-API ExplicitImports checks
(check_all_qualified_accesses_are_public,
check_all_explicit_imports_are_public) are gated to Julia >= 1.11 only
from SciMLTesting 1.7.0. With the now-empty public-API ignore-lists in
qa.jl, the QA group relies on that gate so the LTS (1.10) does not
spuriously flag public-backported names. Raise the qa-env compat floor
from "1.6" to "1.7" so the resolved SciMLTesting always carries the gate.

Verified against registered releases (FVM dev'd via [sources], no dev of
base libs):
- Julia 1.12 (public-API checks RUN, no ignores): QA group 18/18 pass,
  0 fail/error/broken. Resolved SciMLBase 3.27.0, SciMLTesting 1.7.0,
  CommonSolve 0.2.9, ExplicitImports 1.15.0, JET 0.11.5, Aqua 0.8.16.
- Julia 1.10 lts (public-API checks skipped by the 1.7 gate): QA group
  16/16 pass, 0 fail/error/broken (the 2-test delta is exactly the two
  gated public-API checks).

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Author: 3 people

.gitignore

@@ -1,3 +1,4 @@
 /Manifest.toml
 /test/Manifest.toml
+/test/qa/Manifest.toml
 /docs/build/

Project.toml

@@ -11,15 +11,14 @@ SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [compat]
 CommonSolve = "0.2"
-ExplicitImports = "1"
 PrecompileTools = "1"
 SciMLBase = "2.146, 3.1"
+SparseArrays = "1"
 Test = "1"
 julia = "1.10"
 
 [extras]
-ExplicitImports = "7d51a73a-1435-4ff3-83d9-f097790105c7"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["ExplicitImports", "Test"]
+test = ["Test"]

test/Project.toml

@@ -1,7 +1,6 @@
 [deps]
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 DomainSets = "5b8099bc-c8ec-5219-889f-1d9e522a28bf"
-ExplicitImports = "7d51a73a-1435-4ff3-83d9-f097790105c7"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 LinearSolve = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
 MethodOfLines = "94925ecb-adb7-4558-8ed8-f975c56a0bf4"

test/explicit_imports.jl

@@ -13,6 +13,6 @@ FiniteVolumeMethod1D = {path = "../.."}
 Aqua = "0.8"
 JET = "0.9,0.10,0.11"
 SafeTestsets = "0.0.1, 0.1"
-SciMLTesting = "1"
+SciMLTesting = "1.7"
 Test = "1"
 julia = "1.10"

test/qa/Project.toml

@@ -1,20 +1,7 @@
-using FiniteVolumeMethod1D
-using Aqua
+using SciMLTesting, FiniteVolumeMethod1D, Test
 using JET
-using Test
 
-@testset "Quality Assurance" begin
-    @testset "Aqua" begin
-        # All Aqua sub-checks pass except deps_compat, which is marked broken below.
-        Aqua.test_all(FiniteVolumeMethod1D; deps_compat = false)
-        # deps_compat fails: SparseArrays is a dep with no [compat] entry.
-        # See https://github.com/SciML/FiniteVolumeMethod1D.jl/issues/84
-        @test_broken false  # Aqua deps_compat: SparseArrays missing [compat] — see #84
-    end
-    @testset "JET" begin
-        # JET.report_package reports 4 possible errors (Dirichlet/Neumann kwdef
-        # inner ctors and CommonSolve.init on the constructed ODEProblem).
-        # See https://github.com/SciML/FiniteVolumeMethod1D.jl/issues/84
-        @test_broken false  # JET: report_package errors — see #84
-    end
-end
+run_qa(
+    FiniteVolumeMethod1D;
+    explicit_imports = true,
+)