SciML · ChrisRackauckas · Jul 3, 2026 · Jun 25, 2026 · Jun 27, 2026 · Jun 29, 2026
diff --git a/Project.toml b/Project.toml
@@ -13,7 +13,6 @@ MLUtils = "f1d291b0-491e-4a28-83b9-f70985020b54"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
 PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
-ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
 QuadGK = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
@@ -38,7 +37,6 @@ OrdinaryDiffEqTsit5 = "1, 2"
 Parameters = "0.12.1, 0.13"
 Pkg = "1"
 PrecompileTools = "1"
-ProgressMeter = "1.6"
 QuadGK = "2.4"
 Random = "1"
 RecipesBase = "1"

diff --git a/lib/DataDrivenDMD/src/DataDrivenDMD.jl b/lib/DataDrivenDMD/src/DataDrivenDMD.jl
@@ -5,14 +5,12 @@ using DataDrivenDiffEq
 using DataDrivenDiffEq: AbstractBasis
 using DataDrivenDiffEq: AbstractDataDrivenAlgorithm
 using DataDrivenDiffEq: AbstractDataDrivenResult
-using DataDrivenDiffEq: AbstractDataDrivenProblem
 using DataDrivenDiffEq: DDReturnCode, ABSTRACT_CONT_PROB, ABSTRACT_DISCRETE_PROB
 using DataDrivenDiffEq: InternalDataDrivenProblem
 using DataDrivenDiffEq: is_implicit, is_controlled
 
 using DataDrivenDiffEq.DocStringExtensions
 using DataDrivenDiffEq.CommonSolve
-using DataDrivenDiffEq.CommonSolve: solve!
 using DataDrivenDiffEq.StatsBase
 using DataDrivenDiffEq.Parameters
 

diff --git a/lib/DataDrivenDMD/test/qa/Project.toml b/lib/DataDrivenDMD/test/qa/Project.toml
@@ -2,6 +2,7 @@
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 DataDrivenDMD = "3c9adf31-5280-42ff-b439-b71cc6b07807"
 JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
+SciMLTesting = "09d9d899-5365-40a9-917a-5f67fddea283"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [sources]
@@ -10,5 +11,6 @@ DataDrivenDMD = {path = "../.."}
 [compat]
 Aqua = "0.8"
 JET = "0.9, 0.10, 0.11"
+SciMLTesting = "1.6"
 Test = "1"
 julia = "1.10"
diff --git a/lib/DataDrivenDMD/test/qa/qa.jl b/lib/DataDrivenDMD/test/qa/qa.jl
@@ -1,13 +1,33 @@
+using SciMLTesting
 using DataDrivenDMD
-using Aqua
 using JET
 using Test
 
-@testset "QA" begin
-    @testset "Aqua" begin
-        Aqua.test_all(DataDrivenDMD)
-    end
-    @testset "JET" begin
-        JET.test_package(DataDrivenDMD; target_defined_modules = true)
-    end
-end
+run_qa(
+    DataDrivenDMD;
+    explicit_imports = true,
+    # `get_trainerror`/`get_testerror` are listed in `export` (src/DataDrivenDMD.jl) but
+    # no method is ever defined for them (dead exports from the #371 refactor). Aqua was
+    # never run before this conversion, so this is pre-existing and surfaced, not
+    # introduced; marked broken rather than silenced.
+    aqua_broken = (:undefined_exports,),
+    ei_kwargs = (;
+        # DataDrivenDiffEq exposes these names as the (non-`export`ed) extension API its
+        # own sublibraries build on. They are used deliberately; declaring them `public`
+        # upstream is tracked separately.
+        all_explicit_imports_are_public = (;
+            ignore = (
+                :AbstractBasis, :AbstractDataDrivenAlgorithm, :AbstractDataDrivenResult,
+                :ABSTRACT_CONT_PROB, :ABSTRACT_DISCRETE_PROB,
+                :InternalDataDrivenProblem, :is_controlled, :is_implicit,
+            ),
+        ),
+        all_qualified_accesses_are_public = (;
+            ignore = (:__EMPTY_MATRIX, :__construct_basis, :get_fit_targets),
+        ),
+    ),
+    # The umbrella `using DataDrivenDiffEq` (plus the `using DataDrivenDiffEq.<submodule>`
+    # re-exports) pulls the DataDrivenDiffEq public surface in implicitly; making every
+    # name explicit is a large refactor tracked separately.
+    ei_broken = (:no_implicit_imports,)
+)
diff --git a/lib/DataDrivenLux/Project.toml b/lib/DataDrivenLux/Project.toml
@@ -1,6 +1,6 @@
 name = "DataDrivenLux"
 uuid = "47881146-99d0-492a-8425-8f2f33327637"
-version = "0.2.4"
+version = "0.2.5"
 authors = ["JuliusMartensen <julius.martensen@gmail.com>"]
 
 [deps]
@@ -45,13 +45,13 @@ Distributions = "0.25.123"
 DistributionsAD = "0.6"
 DocStringExtensions = "0.9.3"
 ForwardDiff = "0.10, 1"
-IntervalArithmetic = "0.22, 0.23, 1"
+IntervalArithmetic = "0.22.10, 0.23, 1"
 InverseFunctions = "0.1"
 LinearAlgebra = "1.10"
 Logging = "1.10"
 Lux = "1"
 LuxCore = "1"
-Optim = "1.7, 2"
+Optim = "2"
 Optimisers = "0.3, 0.4"
 OrdinaryDiffEq = "6, 7"
 Pkg = "1.10"

diff --git a/lib/DataDrivenLux/src/DataDrivenLux.jl b/lib/DataDrivenLux/src/DataDrivenLux.jl
@@ -3,13 +3,12 @@ module DataDrivenLux
 using DataDrivenDiffEq
 
 # Load specific (abstract) types
-using DataDrivenDiffEq: AbstractBasis, AbstractDataDrivenAlgorithm,
+using DataDrivenDiffEq: AbstractDataDrivenAlgorithm,
     AbstractDataDrivenResult, AbstractDataDrivenProblem, DDReturnCode,
-    ABSTRACT_CONT_PROB, ABSTRACT_DISCRETE_PROB,
-    InternalDataDrivenProblem, is_implicit, is_controlled
+    InternalDataDrivenProblem
 
 using DocStringExtensions: DocStringExtensions, FIELDS, TYPEDEF, SIGNATURES
-using CommonSolve: CommonSolve, solve!
+using CommonSolve: CommonSolve
 using ConcreteStructs: @concrete
 using Setfield: Setfield, @set!
 
@@ -25,7 +24,7 @@ using TransformVariables: TransformVariables, as, transform_logdensity
 using Distributions: Distributions, Distribution, Normal, Uniform, Univariate, dof,
     loglikelihood, logpdf, mean, mode, quantile, scale, truncated
 using DistributionsAD: DistributionsAD
-using StatsBase: StatsBase, aicc, nobs, nullloglikelihood, r2, rss, sum, weights
+using StatsBase: StatsBase, aicc, nobs, nullloglikelihood, r2, rss, sum
 
 using ChainRulesCore: @ignore_derivatives
 using ComponentArrays: ComponentArrays, ComponentVector

diff --git a/lib/DataDrivenLux/test/qa/Project.toml b/lib/DataDrivenLux/test/qa/Project.toml
@@ -3,6 +3,7 @@ Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 DataDrivenDiffEq = "2445eb08-9709-466a-b3fc-47e12bd697a2"
 DataDrivenLux = "47881146-99d0-492a-8425-8f2f33327637"
 JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
+SciMLTesting = "09d9d899-5365-40a9-917a-5f67fddea283"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [sources]
@@ -12,5 +13,6 @@ DataDrivenLux = {path = "../.."}
 [compat]
 Aqua = "0.8"
 JET = "0.9, 0.10, 0.11"
+SciMLTesting = "1.6"
 Test = "1"
 julia = "1.10"
diff --git a/lib/DataDrivenLux/test/qa/qa.jl b/lib/DataDrivenLux/test/qa/qa.jl
@@ -1,13 +1,44 @@
+using SciMLTesting
 using DataDrivenLux
-using Aqua
 using JET
 using Test
 
-@testset "QA" begin
-    @testset "Aqua" begin
-        Aqua.test_all(DataDrivenLux)
-    end
-    @testset "JET" begin
-        JET.test_package(DataDrivenLux; target_defined_modules = true)
-    end
-end
+run_qa(
+    DataDrivenLux;
+    explicit_imports = true,
+    ei_kwargs = (;
+        all_explicit_imports_are_public = (;
+            ignore = (
+                # DataDrivenDiffEq non-`export`ed extension API its sublibraries build on.
+                :AbstractDataDrivenAlgorithm, :AbstractDataDrivenProblem,
+                :AbstractDataDrivenResult, :InternalDataDrivenProblem,
+                # External non-public names, used deliberately.
+                :AbstractBackend, :ForwardDiffBackend, :gradient,  # AbstractDifferentiation
+                :converged, :Options,                              # Optim
+                :isempty,                                          # IntervalArithmetic
+                :square,                                           # InverseFunctions
+            ),
+        ),
+        all_explicit_imports_via_owners = (;
+            ignore = (:isempty,),  # IntervalArithmetic.isempty (owner Base)
+        ),
+        all_qualified_accesses_are_public = (;
+            ignore = (
+                # DataDrivenDiffEq internals accessed qualified.
+                :get_f, :get_fit_targets, :get_implicit_data, :get_oop_args,
+                :remake_problem, :_set_default_val, :AbstractDataDrivenResult,
+                :getdefaultval,                          # Symbolics
+                :isvariable,                             # ModelingToolkit
+                :promote_eltype,                         # Base
+                :AbstractBackend, :ForwardDiffBackend, :gradient,  # AbstractDifferentiation
+                :converged, :Options,                    # Optim
+            ),
+        ),
+        all_qualified_accesses_via_owners = (;
+            ignore = (:isvariable,),  # ModelingToolkit.isvariable (owner ModelingToolkitBase)
+        ),
+    ),
+    # The umbrella `using DataDrivenDiffEq` pulls its public surface in implicitly;
+    # making every name explicit is a large refactor tracked separately.
+    ei_broken = (:no_implicit_imports,)
+)
diff --git a/lib/DataDrivenSR/src/DataDrivenSR.jl b/lib/DataDrivenSR/src/DataDrivenSR.jl
@@ -2,17 +2,14 @@ module DataDrivenSR
 
 using DataDrivenDiffEq
 # Load specific (abstract) types
-using DataDrivenDiffEq: AbstractBasis, Difference
+using DataDrivenDiffEq: Difference
 using DataDrivenDiffEq: AbstractDataDrivenAlgorithm
 using DataDrivenDiffEq: AbstractDataDrivenResult
-using DataDrivenDiffEq: AbstractDataDrivenProblem
-using DataDrivenDiffEq: DDReturnCode, ABSTRACT_CONT_PROB, ABSTRACT_DISCRETE_PROB
+using DataDrivenDiffEq: DDReturnCode
 using DataDrivenDiffEq: InternalDataDrivenProblem
-using DataDrivenDiffEq: is_implicit, is_controlled
 
 using DataDrivenDiffEq.DocStringExtensions
 using DataDrivenDiffEq.CommonSolve
-using DataDrivenDiffEq.CommonSolve: solve!
 using DataDrivenDiffEq.StatsBase
 using DataDrivenDiffEq.Parameters
 

diff --git a/lib/DataDrivenSR/test/qa/Project.toml b/lib/DataDrivenSR/test/qa/Project.toml
@@ -3,6 +3,7 @@ Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 DataDrivenDiffEq = "2445eb08-9709-466a-b3fc-47e12bd697a2"
 DataDrivenSR = "7fed8a53-d475-4873-af3a-ba53cceea094"
 JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
+SciMLTesting = "09d9d899-5365-40a9-917a-5f67fddea283"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [sources]
@@ -12,5 +13,6 @@ DataDrivenSR = {path = "../.."}
 [compat]
 Aqua = "0.8"
 JET = "0.9, 0.10, 0.11"
+SciMLTesting = "1.6"
 Test = "1"
 julia = "1.10"
diff --git a/lib/DataDrivenSR/test/qa/qa.jl b/lib/DataDrivenSR/test/qa/qa.jl
@@ -1,13 +1,35 @@
+using SciMLTesting
 using DataDrivenSR
-using Aqua
 using JET
 using Test
 
-@testset "QA" begin
-    @testset "Aqua" begin
-        Aqua.test_all(DataDrivenSR)
-    end
-    @testset "JET" begin
-        JET.test_package(DataDrivenSR; target_defined_modules = true)
-    end
-end
+run_qa(
+    DataDrivenSR;
+    explicit_imports = true,
+    ei_kwargs = (;
+        all_explicit_imports_are_public = (;
+            # DataDrivenDiffEq non-`export`ed extension API its sublibraries build on.
+            ignore = (
+                :AbstractDataDrivenAlgorithm, :AbstractDataDrivenResult,
+                :InternalDataDrivenProblem,
+            ),
+        ),
+        all_qualified_accesses_are_public = (;
+            ignore = (
+                # DataDrivenDiffEq internals accessed qualified.
+                :assert_lhs, :get_implicit_data, :remake_problem, :_set_default_val,
+                :setdefaultval,  # Symbolics
+                :Sym,            # SymbolicUtils
+                :toparam,        # ModelingToolkit
+            ),
+        ),
+        all_qualified_accesses_via_owners = (;
+            ignore = (:toparam,),  # ModelingToolkit.toparam (owner ModelingToolkitBase)
+        ),
+    ),
+    # The umbrella `using DataDrivenDiffEq` and `@reexport using SymbolicRegression`
+    # (plus the `using DataDrivenDiffEq.<submodule>` re-exports) pull those public
+    # surfaces in implicitly; making every name explicit is a large refactor tracked
+    # separately.
+    ei_broken = (:no_implicit_imports,)
+)
diff --git a/lib/DataDrivenSparse/src/DataDrivenSparse.jl b/lib/DataDrivenSparse/src/DataDrivenSparse.jl
@@ -2,13 +2,10 @@ module DataDrivenSparse
 
 using DataDrivenDiffEq
 # Load specific (abstract) types
-using DataDrivenDiffEq: AbstractBasis
 using DataDrivenDiffEq: AbstractDataDrivenAlgorithm
 using DataDrivenDiffEq: AbstractDataDrivenResult
-using DataDrivenDiffEq: AbstractDataDrivenProblem
-using DataDrivenDiffEq: DDReturnCode, ABSTRACT_CONT_PROB, ABSTRACT_DISCRETE_PROB
+using DataDrivenDiffEq: DDReturnCode
 using DataDrivenDiffEq: InternalDataDrivenProblem
-using DataDrivenDiffEq: is_implicit, is_controlled
 
 using DataDrivenDiffEq.DocStringExtensions
 using DataDrivenDiffEq.CommonSolve

diff --git a/lib/DataDrivenSparse/src/algorithms/proximals.jl b/lib/DataDrivenSparse/src/algorithms/proximals.jl
@@ -136,7 +136,7 @@ ClippedAbsoluteDeviation() = ClippedAbsoluteDeviation(NaN)
 end
 
 function (s::ClippedAbsoluteDeviation)(x::AbstractArray, λ::T) where {T <: Real}
-    @unpack ρ = h
+    @unpack ρ = s
     ρ = isnan(ρ) ? convert(T, 5) * λ : convert(T, ρ)
     for i in eachindex(x)
         x[i] = abs(x[i]) > ρ ? x[i] : sign(x[i]) * max(abs(x[i]) - λ, 0)

diff --git a/lib/DataDrivenSparse/src/result.jl b/lib/DataDrivenSparse/src/result.jl
@@ -20,7 +20,7 @@ is_success(k::SparseRegressionResult) = getfield(k, :retcode) == DDReturnCode(1)
 l2error(k::SparseRegressionResult) = is_success(k) ? getfield(k, :testerror) : Inf
 
 function l2error(k::SparseRegressionResult{<:Any, <:Any, Nothing})
-    return is_success(k) ? getfield(k, :traineerror) : Inf
+    return is_success(k) ? getfield(k, :trainerror) : Inf
 end
 
 get_coefficients(k::SparseRegressionResult) = getfield(k, :coefficients)
diff --git a/lib/DataDrivenSparse/test/qa/Project.toml b/lib/DataDrivenSparse/test/qa/Project.toml
@@ -2,6 +2,7 @@
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 DataDrivenSparse = "5b588203-7d8b-4fab-a537-c31a7f73f46b"
 JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
+SciMLTesting = "09d9d899-5365-40a9-917a-5f67fddea283"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [sources]
@@ -10,5 +11,6 @@ DataDrivenSparse = {path = "../.."}
 [compat]
 Aqua = "0.8"
 JET = "0.9, 0.10, 0.11"
+SciMLTesting = "1.6"
 Test = "1"
 julia = "1.10"
diff --git a/lib/DataDrivenSparse/test/qa/qa.jl b/lib/DataDrivenSparse/test/qa/qa.jl
@@ -1,13 +1,32 @@
+using SciMLTesting
 using DataDrivenSparse
-using Aqua
 using JET
 using Test
 
-@testset "QA" begin
-    @testset "Aqua" begin
-        Aqua.test_all(DataDrivenSparse)
-    end
-    @testset "JET" begin
-        JET.test_package(DataDrivenSparse; target_defined_modules = true)
-    end
-end
+run_qa(
+    DataDrivenSparse;
+    explicit_imports = true,
+    # The `unique!`/`deleteat!` Basis methods that DataDrivenDiffEq defines on
+    # `Symbolics.Num`/`Symbolics.Arr` vectors are ambiguous against `Base.unique!`/
+    # `Base.deleteat!`; the ambiguity is inherited from the parent package (it predates
+    # this conversion and Aqua was never run before), so it is marked broken here.
+    aqua_broken = (:ambiguities,),
+    ei_kwargs = (;
+        # DataDrivenDiffEq exposes these names as the (non-`export`ed) extension API its
+        # own sublibraries build on; declaring them `public` upstream is tracked separately.
+        all_explicit_imports_are_public = (;
+            ignore = (
+                :AbstractDataDrivenAlgorithm, :AbstractDataDrivenResult,
+                :InternalDataDrivenProblem,
+            ),
+        ),
+        all_qualified_accesses_are_public = (;
+            # __construct_basis/is_implicit: DataDrivenDiffEq internals; transform: StatsBase.
+            ignore = (:__construct_basis, :is_implicit, :transform),
+        ),
+    ),
+    # The umbrella `using DataDrivenDiffEq` (plus the `using DataDrivenDiffEq.<submodule>`
+    # re-exports) pulls the DataDrivenDiffEq public surface in implicitly; making every
+    # name explicit is a large refactor tracked separately.
+    ei_broken = (:no_implicit_imports,)
+)
diff --git a/src/DataDrivenDiffEq.jl b/src/DataDrivenDiffEq.jl
@@ -6,7 +6,7 @@ module DataDrivenDiffEq
 using LinearAlgebra
 
 using DiffEqBase
-using SciMLBase: SciMLBase, AbstractTimeseriesSolution
+using SciMLBase: SciMLBase
 using CommonSolve
 using Reexport