QA: run_qa v1.6 form + ExplicitImports (#160)

* QA: run_qa v1.6 form + ExplicitImports

Replace the hand-rolled Aqua + ExplicitImports QA files (qa_tests.jl,
explicit_imports_tests.jl) with a single qa.jl on the SciMLTesting 1.6
`run_qa` form, with ExplicitImports enabled (all six checks).

- Aqua: `run_qa` runs the full `Aqua.test_all` (11 checks); no broken
  markers or aqua_kwargs tweaks needed — all pass.
- ExplicitImports: `explicit_imports = true`. Two checks needed ignore
  lists for third-party symbolic-stack internal names re-exported but not
  owned/public by ModelingToolkit/Symbolics (documented per source pkg);
  the other four checks pass unmodified.
- JET: `jet = false` in run_qa. Whole-package JET hits a toplevel
  `invalid redefinition of constant ModelOrderReduction.TSVD` (the exported
  `TSVD` struct collides with the `TSVD` dependency package under JET's
  toplevel virtualizer). The existing targeted `report_call` checks in
  jet_tests.jl provide the JET coverage and stay as a separate group file.

test/qa/Project.toml: drop ExplicitImports (transitive via SciMLTesting),
keep Aqua (ambiguities child-proc needs it direct) and JET (jet_tests.jl),
bump SciMLTesting compat to "1.6".

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

* Inline rhs extraction instead of internal Symbolics.rhss

`Symbolics.rhss` is an undocumented one-line internal helper
(`rhss(xs) = map(x->x.rhs, xs)`, not exported). Replace the single use in
deim.jl with the equivalent comprehension and drop its ExplicitImports
non-public allow-list entry, so we don't depend on a Symbolics internal.

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

* QA: strip redundant public-API EI ignores (SciMLTesting 1.7)

SciMLTesting 1.7 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 the base-lib make-public releases (ModelingToolkit
11.29, Symbolics 7.28+, SymbolicUtils 4.36, SciMLBase 3.24) marked most of the
previously-ignored names public.

Verified against registered releases on Julia 1.12: of the 13
all_qualified_accesses_are_public ignores, only :topsort_equations (still
non-public in ModelingToolkit) and :getname (re-exported by Symbolics from
SymbolicIndexingInterface, non-public) remain flagged. The other 11 are now
public and removed. QA group passes 17/17 on 1.12 and 15/15 on 1.10 (public
checks skipped on the LTS). The all_qualified_accesses_via_owners list is a
distinct (non public-API) check and is left untouched.

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

* QA: raise SciMLTesting compat floor to 1.7 for public-API EI gating

SciMLTesting 1.7 gates the two public-API ExplicitImports checks
(check_all_qualified_accesses_are_public / check_all_explicit_imports_are_public)
to Julia >= 1.11, which is the regime in which the stripped public-API
ignore lists are correct. Raising the floor from "1.6" to "1.7" ensures
CI resolves a SciMLTesting that runs those checks rather than potentially
an older release.

Verified against the registered releases (SciMLBase 3.27.0, DiffEqBase 7.6.0,
ModelingToolkit 11.29.0, Symbolics 7.29.0, SymbolicUtils 4.36.0,
SciMLTesting 1.7.0, ExplicitImports 1.15.0):

- Julia 1.12 (public-API checks run): emptying both public-API ignore lists
  leaves exactly two survivors flagged by all_qualified_accesses_are_public --
  topsort_equations (non-public in ModelingToolkit) and getname (re-exported
  by Symbolics from SymbolicIndexingInterface, non-public). Neither is a
  SciMLBase-owned name, so no DiffEqBase.X -> SciMLBase.X migration applies;
  both are restored. all_explicit_imports_are_public passes with an empty
  ignore list. QA group: 17/17 pass.
- Julia 1.10 (public-API checks skipped on the LTS): QA group 15/15 pass.

ModelOrderReduction's source makes no qualified SciMLBase/DiffEqBase accesses,
so steps 2 (caller-migrate) is a no-op for this package.

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

* QA: migrate re-export-gap accesses to public owners + drop now-public ignores

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>

* QA: thorough EI ignore re-clean (drop stale incl via_owners, migrate non-public re-exports)

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>

---------

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

Author: 3 people

Project.toml

@@ -11,6 +11,7 @@ PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
 RandomizedLinAlg = "0448d7d9-159c-5637-8537-fd72090fea46"
 Setfield = "efcf1570-3423-57d1-acb7-fd33fddbac46"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+SymbolicIndexingInterface = "2efcf032-c050-4f8e-a9bb-153293bab1f5"
 TSVD = "9449cd9e-2762-5aa3-a617-5413e99d722e"
 
 [compat]
@@ -21,5 +22,6 @@ PrecompileTools = "1.2.1"
 RandomizedLinAlg = "0.1"
 Setfield = "1.1.2"
 SparseArrays = "1"
+SymbolicIndexingInterface = "0.3.49"
 TSVD = "0.4.4"
 julia = "1.10"

src/ModelOrderReduction.jl

@@ -5,6 +5,7 @@ using DocStringExtensions: DocStringExtensions, FUNCTIONNAME, SIGNATURES, TYPEDS
 using ModelingToolkit: ModelingToolkit, @variables, Differential, Equation, Num, ODESystem,
     SymbolicUtils, Symbolics, arguments, build_function, complete,
     expand, substitute, tearing_substitution
+using SymbolicIndexingInterface: SymbolicIndexingInterface
 using LinearAlgebra: LinearAlgebra, /, \, mul!, qr, svd
 
 using Setfield: Setfield, @set!

src/deim.jl

@@ -143,10 +143,10 @@ function deim(
     var_name = gensym(:ŷ)
     ŷ = (@variables $var_name(iv)[1:pod_dim])[1]
     @set! sys.unknowns = Symbolics.value.(Symbolics.scalarize(ŷ)) # new variables from POD
-    ModelingToolkit.get_var_to_name(sys)[Symbolics.getname(ŷ)] = Symbolics.unwrap(ŷ)
+    ModelingToolkit.get_var_to_name(sys)[SymbolicIndexingInterface.getname(ŷ)] = Symbolics.unwrap(ŷ)
 
     deqs, eqs = get_deqs(sys) # split eqs into differential and non-differential equations
-    rhs = Symbolics.rhss(deqs)
+    rhs = [eq.rhs for eq in deqs]
     # a sparse matrix of coefficients for the linear part,
     # a vector of constant terms and a vector of nonlinear terms about dvs
     A, g, F = separate_terms(rhs, dvs, iv)

test/qa/Project.toml

@@ -1,6 +1,5 @@
 [deps]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
-ExplicitImports = "7d51a73a-1435-4ff3-83d9-f097790105c7"
 JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 ModelOrderReduction = "207801d6-6cee-43a9-ad0c-f0c64933efa0"
@@ -10,11 +9,10 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [compat]
 Aqua = "0.8"
-ExplicitImports = "1"
 JET = "0.9, 0.10, 0.11"
 LinearAlgebra = "1"
 SafeTestsets = "0.0.1, 0.1"
-SciMLTesting = "1"
+SciMLTesting = "1.7"
 Test = "1"
 
 [sources]

test/qa/explicit_imports_tests.jl

@@ -0,0 +1,27 @@
+using SciMLTesting, ModelOrderReduction, Test
+
+run_qa(
+    ModelOrderReduction;
+    explicit_imports = true,
+    # Whole-package JET (`report_package`/`test_package`) hits a toplevel
+    # `invalid redefinition of constant ModelOrderReduction.TSVD` error: the package
+    # exports a `TSVD` struct whose name collides with the `TSVD` dependency package
+    # under JET's toplevel virtualizer. JET coverage is provided by the targeted
+    # `report_call` checks in jet_tests.jl, which sidestep the toplevel re-eval.
+    jet = false,
+    ei_kwargs = (;
+        # `topsort_equations` is owned by ModelingToolkitBase, re-exported but not
+        # marked public by ModelingToolkit, and there is no make-public plan for it.
+        # `via_owners` flags the re-export; `are_public` flags the non-public status.
+        all_qualified_accesses_via_owners = (;
+            ignore = (
+                :topsort_equations,
+            ),
+        ),
+        all_qualified_accesses_are_public = (;
+            ignore = (
+                :topsort_equations,
+            ),
+        ),
+    )
+)