QA: run_qa v1.6 form + ExplicitImports

Project.toml

@@ -4,7 +4,6 @@ version = "2.4.0"
 authors = ["Chris Rackauckas <accounts@chrisrackauckas.com>"]
 
 [deps]
-Calculus = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9"
 CommonSolve = "38540f10-b2f7-11e9-35d8-d573e4eb0ff2"
 Dierckx = "39dd38d3-220a-591b-8e3c-4c3a8c710a94"
 DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
@@ -19,14 +18,13 @@ StatsAPI = "82ae8749-77ed-4fe6-ae5f-f523153014b0"
 
 [compat]
 BlackBoxOptim = "0.6"
-Calculus = "0.5.2"
 CommonSolve = "0.2.6"
 DelayDiffEq = "5.63, 6"
 Dierckx = "0.5"
 DiffEqBase = "6.213, 7"
 Distributions = "0.25.87"
-ExplicitImports = "1"
 ForwardDiff = "0.10.38"
+LinearAlgebra = "1.10"
 Logging = "1"
 NLopt = "0.6, 1"
 Optim = "1"
@@ -55,7 +53,6 @@ julia = "1.10"
 [extras]
 BlackBoxOptim = "a134a8b2-14d6-55f6-9291-3336d3ab0209"
 DelayDiffEq = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb"
-ExplicitImports = "7d51a73a-1435-4ff3-83d9-f097790105c7"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 NLopt = "76087f3c-5699-56af-9a33-bf431cd00edd"
@@ -76,4 +73,4 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [targets]
-test = ["Test", "ExplicitImports", "BlackBoxOptim", "DelayDiffEq", "ForwardDiff", "Logging", "NLopt", "Optim", "Optimization", "OptimizationBBO", "OptimizationNLopt", "OptimizationOptimJL", "OrdinaryDiffEq", "Random", "SafeTestsets", "SciMLSensitivity", "SciMLTesting", "StochasticDiffEq", "SteadyStateDiffEq", "Sundials", "Zygote"]
+test = ["Test", "BlackBoxOptim", "DelayDiffEq", "ForwardDiff", "Logging", "NLopt", "Optim", "Optimization", "OptimizationBBO", "OptimizationNLopt", "OptimizationOptimJL", "OrdinaryDiffEq", "Random", "SafeTestsets", "SciMLSensitivity", "SciMLTesting", "StochasticDiffEq", "SteadyStateDiffEq", "Sundials", "Zygote"]

src/cost_functions.jl

@@ -33,14 +33,14 @@ struct L2Loss{T, D, U, W, G, B} <: DiffEqBase.DECostFunction
     du_buf::B
 end
 
-function (f::L2Loss)(sol::DiffEqBase.AbstractNoTimeSolution)
+function (f::L2Loss)(sol::SciMLBase.AbstractNoTimeSolution)
     data = f.data
     weight = f.data_weight
     diff_weight = f.differ_weight
     colloc_grad = f.colloc_grad
     dudt = f.dudt
 
-    if sol isa DiffEqBase.AbstractEnsembleSolution
+    if sol isa SciMLBase.AbstractEnsembleSolution
         failure = any(!SciMLBase.successful_retcode(s.retcode) for s in sol.u)
     else
         failure = !SciMLBase.successful_retcode(sol.retcode)
@@ -73,7 +73,7 @@ function (f::L2Loss)(sol::SciMLBase.AbstractSciMLSolution)
     colloc_grad = f.colloc_grad
     dudt = f.dudt
 
-    if sol isa DiffEqBase.AbstractEnsembleSolution
+    if sol isa SciMLBase.AbstractEnsembleSolution
         failure = any(!SciMLBase.successful_retcode(s.retcode) for s in sol.u)
     else
         failure = !SciMLBase.successful_retcode(sol.retcode)
@@ -172,7 +172,7 @@ function L2Loss(
     )
 end
 
-function (f::L2Loss)(sol::DiffEqBase.AbstractEnsembleSolution)
+function (f::L2Loss)(sol::SciMLBase.AbstractEnsembleSolution)
     return mean(f.(sol.u))
 end
 
@@ -200,7 +200,7 @@ end
 
 function (f::LogLikeLoss)(sol::SciMLBase.AbstractSciMLSolution)
     distributions = f.data_distributions
-    if sol isa DiffEqBase.AbstractEnsembleSolution
+    if sol isa SciMLBase.AbstractEnsembleSolution
         failure = any(!SciMLBase.successful_retcode(s.retcode) for s in sol.u)
     else
         failure = !SciMLBase.successful_retcode(sol.retcode)
@@ -248,7 +248,7 @@ function (f::LogLikeLoss)(sol::SciMLBase.AbstractSciMLSolution)
     return ll
 end
 
-function (f::LogLikeLoss)(sol::DiffEqBase.AbstractEnsembleSolution)
+function (f::LogLikeLoss)(sol::SciMLBase.AbstractEnsembleSolution)
     distributions = f.data_distributions
     failure = any(!SciMLBase.successful_retcode(s.retcode) for s in sol.u)
     failure && return Inf

src/multiple_shooting_objective.jl

@@ -57,7 +57,7 @@ function multiple_shooting_objective(
         u = [uc for k in 1:K for uc in (k == K ? sol[k].u : sol[k].u[1:(end - 1)])]
         t = [tc for k in 1:K for tc in (k == K ? sol[k].t : sol[k].t[1:(end - 1)])]
         sol_loss = Merged_Solution(u, t, sol)
-        sol_new = DiffEqBase.build_solution(
+        sol_new = SciMLBase.build_solution(
             prob, alg, sol_loss.t, sol_loss.u,
             retcode = ReturnCode.Success
         )

test/qa/Project.toml

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

test/qa/qa.jl

@@ -1,13 +1,14 @@
-using DiffEqParamEstim, Aqua, JET, Test
+using SciMLTesting, DiffEqParamEstim, JET, Test
 
-@testset "Aqua" begin
-    # stale_deps and deps_compat disabled: genuine findings tracked in
-    # https://github.com/SciML/DiffEqParamEstim.jl/issues/306
-    Aqua.test_all(DiffEqParamEstim; stale_deps = false, deps_compat = false)
-    @test_broken false  # Aqua stale_deps: Calculus is a stale dep — tracked in https://github.com/SciML/DiffEqParamEstim.jl/issues/306
-    @test_broken false  # Aqua deps_compat: LinearAlgebra dep + Pkg extra missing compat entries — tracked in https://github.com/SciML/DiffEqParamEstim.jl/issues/306
-end
-
-@testset "JET" begin
-    JET.test_package(DiffEqParamEstim; target_defined_modules = true)
-end
+run_qa(
+    DiffEqParamEstim;
+    explicit_imports = true,
+    ei_kwargs = (
+        # NoAD is owned by SciMLBase but not (yet) declared public there.
+        all_qualified_accesses_are_public = (;
+            ignore = (
+                :NoAD,  # SciMLBase
+            ),
+        ),
+    ),
+)