Merge pull request #2806 from ChrisRackauckas-Claude/fix-autodiff-missing-imports

Use explicit imports

Author: ChrisRackauckas

.github/workflows/CI.yml

@@ -25,6 +25,7 @@ jobs:
           - Downstream
           - ODEInterfaceRegression
           - Multithreading
+          - QA
 
           - OrdinaryDiffEqAdamsBashforthMoulton
           - OrdinaryDiffEqBDF

Project.toml

@@ -3,46 +3,16 @@ uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 authors = ["Chris Rackauckas <[email protected]>", "Yingbo Ma <[email protected]>"]
 version = "6.101.0"
 
-[sources]
-OrdinaryDiffEqAdamsBashforthMoulton = {path = "lib/OrdinaryDiffEqAdamsBashforthMoulton"}
-OrdinaryDiffEqBDF = {path = "lib/OrdinaryDiffEqBDF"}
-OrdinaryDiffEqCore = {path = "lib/OrdinaryDiffEqCore"}
-OrdinaryDiffEqDefault = {path = "lib/OrdinaryDiffEqDefault"}
-OrdinaryDiffEqDifferentiation = {path = "lib/OrdinaryDiffEqDifferentiation"}
-OrdinaryDiffEqExplicitRK = {path = "lib/OrdinaryDiffEqExplicitRK"}
-OrdinaryDiffEqExponentialRK = {path = "lib/OrdinaryDiffEqExponentialRK"}
-OrdinaryDiffEqExtrapolation = {path = "lib/OrdinaryDiffEqExtrapolation"}
-OrdinaryDiffEqFIRK = {path = "lib/OrdinaryDiffEqFIRK"}
-OrdinaryDiffEqFeagin = {path = "lib/OrdinaryDiffEqFeagin"}
-OrdinaryDiffEqFunctionMap = {path = "lib/OrdinaryDiffEqFunctionMap"}
-OrdinaryDiffEqHighOrderRK = {path = "lib/OrdinaryDiffEqHighOrderRK"}
-OrdinaryDiffEqIMEXMultistep = {path = "lib/OrdinaryDiffEqIMEXMultistep"}
-OrdinaryDiffEqLinear = {path = "lib/OrdinaryDiffEqLinear"}
-OrdinaryDiffEqLowOrderRK = {path = "lib/OrdinaryDiffEqLowOrderRK"}
-OrdinaryDiffEqLowStorageRK = {path = "lib/OrdinaryDiffEqLowStorageRK"}
-OrdinaryDiffEqNonlinearSolve = {path = "lib/OrdinaryDiffEqNonlinearSolve"}
-OrdinaryDiffEqNordsieck = {path = "lib/OrdinaryDiffEqNordsieck"}
-OrdinaryDiffEqPDIRK = {path = "lib/OrdinaryDiffEqPDIRK"}
-OrdinaryDiffEqPRK = {path = "lib/OrdinaryDiffEqPRK"}
-OrdinaryDiffEqQPRK = {path = "lib/OrdinaryDiffEqQPRK"}
-OrdinaryDiffEqRKN = {path = "lib/OrdinaryDiffEqRKN"}
-OrdinaryDiffEqRosenbrock = {path = "lib/OrdinaryDiffEqRosenbrock"}
-OrdinaryDiffEqSDIRK = {path = "lib/OrdinaryDiffEqSDIRK"}
-OrdinaryDiffEqSSPRK = {path = "lib/OrdinaryDiffEqSSPRK"}
-OrdinaryDiffEqStabilizedIRK = {path = "lib/OrdinaryDiffEqStabilizedIRK"}
-OrdinaryDiffEqStabilizedRK = {path = "lib/OrdinaryDiffEqStabilizedRK"}
-OrdinaryDiffEqSymplecticRK = {path = "lib/OrdinaryDiffEqSymplecticRK"}
-OrdinaryDiffEqTsit5 = {path = "lib/OrdinaryDiffEqTsit5"}
-OrdinaryDiffEqVerner = {path = "lib/OrdinaryDiffEqVerner"}
-
 [deps]
 ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
 ArrayInterface = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
+CommonSolve = "38540f10-b2f7-11e9-35d8-d573e4eb0ff2"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 EnumX = "4e289a0a-7415-4d19-859d-a7e5c4648b56"
+ExplicitImports = "7d51a73a-1435-4ff3-83d9-f097790105c7"
 ExponentialUtilities = "d4d017d3-3776-5f7e-afef-a10c40355c18"
 FastBroadcast = "7034ab61-46d4-4ed7-9d0f-46aef9175898"
 FastClosures = "9aa1b823-49e4-5ca5-8b0f-3971ec8bab6a"
@@ -105,14 +75,48 @@ StaticArrayInterface = "0d7ed370-da01-4f52-bd93-41d350b8b718"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 TruncatedStacktraces = "781d530d-4396-4725-bb49-402e4bee1e77"
 
+[sources]
+OrdinaryDiffEqAdamsBashforthMoulton = {path = "lib/OrdinaryDiffEqAdamsBashforthMoulton"}
+OrdinaryDiffEqBDF = {path = "lib/OrdinaryDiffEqBDF"}
+OrdinaryDiffEqCore = {path = "lib/OrdinaryDiffEqCore"}
+OrdinaryDiffEqDefault = {path = "lib/OrdinaryDiffEqDefault"}
+OrdinaryDiffEqDifferentiation = {path = "lib/OrdinaryDiffEqDifferentiation"}
+OrdinaryDiffEqExplicitRK = {path = "lib/OrdinaryDiffEqExplicitRK"}
+OrdinaryDiffEqExponentialRK = {path = "lib/OrdinaryDiffEqExponentialRK"}
+OrdinaryDiffEqExtrapolation = {path = "lib/OrdinaryDiffEqExtrapolation"}
+OrdinaryDiffEqFIRK = {path = "lib/OrdinaryDiffEqFIRK"}
+OrdinaryDiffEqFeagin = {path = "lib/OrdinaryDiffEqFeagin"}
+OrdinaryDiffEqFunctionMap = {path = "lib/OrdinaryDiffEqFunctionMap"}
+OrdinaryDiffEqHighOrderRK = {path = "lib/OrdinaryDiffEqHighOrderRK"}
+OrdinaryDiffEqIMEXMultistep = {path = "lib/OrdinaryDiffEqIMEXMultistep"}
+OrdinaryDiffEqLinear = {path = "lib/OrdinaryDiffEqLinear"}
+OrdinaryDiffEqLowOrderRK = {path = "lib/OrdinaryDiffEqLowOrderRK"}
+OrdinaryDiffEqLowStorageRK = {path = "lib/OrdinaryDiffEqLowStorageRK"}
+OrdinaryDiffEqNonlinearSolve = {path = "lib/OrdinaryDiffEqNonlinearSolve"}
+OrdinaryDiffEqNordsieck = {path = "lib/OrdinaryDiffEqNordsieck"}
+OrdinaryDiffEqPDIRK = {path = "lib/OrdinaryDiffEqPDIRK"}
+OrdinaryDiffEqPRK = {path = "lib/OrdinaryDiffEqPRK"}
+OrdinaryDiffEqQPRK = {path = "lib/OrdinaryDiffEqQPRK"}
+OrdinaryDiffEqRKN = {path = "lib/OrdinaryDiffEqRKN"}
+OrdinaryDiffEqRosenbrock = {path = "lib/OrdinaryDiffEqRosenbrock"}
+OrdinaryDiffEqSDIRK = {path = "lib/OrdinaryDiffEqSDIRK"}
+OrdinaryDiffEqSSPRK = {path = "lib/OrdinaryDiffEqSSPRK"}
+OrdinaryDiffEqStabilizedIRK = {path = "lib/OrdinaryDiffEqStabilizedIRK"}
+OrdinaryDiffEqStabilizedRK = {path = "lib/OrdinaryDiffEqStabilizedRK"}
+OrdinaryDiffEqSymplecticRK = {path = "lib/OrdinaryDiffEqSymplecticRK"}
+OrdinaryDiffEqTsit5 = {path = "lib/OrdinaryDiffEqTsit5"}
+OrdinaryDiffEqVerner = {path = "lib/OrdinaryDiffEqVerner"}
+
 [compat]
 ADTypes = "1.16"
 Adapt = "3.0, 4"
 ArrayInterface = "7.15"
+CommonSolve = "0.2"
 DataStructures = "0.18, 0.19"
 DiffEqBase = "6.169.1"
 DocStringExtensions = "0.9"
 EnumX = "1"
+ExplicitImports = "1.13.1"
 ExponentialUtilities = "1"
 FastBroadcast = "0.2, 0.3"
 FastClosures = "0.3"
@@ -186,6 +190,7 @@ DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
 DiffEqDevTools = "f3b72e0c-5b89-59e1-b016-84e28bfd966d"
 DifferentiationInterface = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63"
 ElasticArrays = "fdbdab4c-e67f-52f5-8c3f-e7b388dad3d4"
+ExplicitImports = "7d51a73a-1435-4ff3-83d9-f097790105c7"
 IncompleteLU = "40713840-3770-5561-ab4c-a76e7d0d7895"
 InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 JLArrays = "27aeb0d3-9eb9-45fb-866b-73c2ecf80fcb"
@@ -210,4 +215,4 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
 [targets]
-test = ["Calculus", "ComponentArrays", "Symbolics", "AlgebraicMultigrid", "IncompleteLU", "DiffEqCallbacks", "DifferentiationInterface", "DiffEqDevTools", "ODEProblemLibrary", "ElasticArrays", "InteractiveUtils", "ParameterizedFunctions", "JLArrays", "PoissonRandom", "Printf", "Random", "ReverseDiff", "SafeTestsets", "SparseArrays", "Statistics", "StructArrays", "Test", "Unitful", "ModelingToolkit", "Pkg", "NLsolve", "RecursiveFactorization", "SparseConnectivityTracer", "SparseMatrixColorings"]
+test = ["Calculus", "ComponentArrays", "Symbolics", "AlgebraicMultigrid", "IncompleteLU", "DiffEqCallbacks", "DifferentiationInterface", "DiffEqDevTools", "ODEProblemLibrary", "ElasticArrays", "ExplicitImports", "InteractiveUtils", "ParameterizedFunctions", "JLArrays", "PoissonRandom", "Printf", "Random", "ReverseDiff", "SafeTestsets", "SparseArrays", "Statistics", "StructArrays", "Test", "Unitful", "ModelingToolkit", "Pkg", "NLsolve", "RecursiveFactorization", "SparseConnectivityTracer", "SparseMatrixColorings"]

lib/ImplicitDiscreteSolve/src/ImplicitDiscreteSolve.jl

@@ -11,7 +11,7 @@ import OrdinaryDiffEqCore: OrdinaryDiffEqAlgorithm, alg_cache, OrdinaryDiffEqMut
                            _initialize_dae!, DefaultInit, BrownFullBasicInit, OverrideInit
 
 using Reexport
-@reexport using DiffEqBase
+@reexport using SciMLBase
 
 """
     IDSolve()

lib/OrdinaryDiffEqAdamsBashforthMoulton/Project.toml

@@ -8,6 +8,8 @@ OrdinaryDiffEqCore = {path = "../OrdinaryDiffEqCore"}
 OrdinaryDiffEqLowOrderRK = {path = "../OrdinaryDiffEqLowOrderRK"}
 
 [deps]
+SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
+
 DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
 FastBroadcast = "7034ab61-46d4-4ed7-9d0f-46aef9175898"
 MuladdMacro = "46d2c3a1-f734-5fdb-9937-b9b9aeba4221"
@@ -33,6 +35,7 @@ Reexport = "1.2.2"
 SafeTestsets = "0.1.0"
 Static = "1.1.1"
 Test = "<0.0.1, 1"
+SciMLBase = "2"
 julia = "1.10"
 JET = "0.9.18, 0.10.4"
 Aqua = "0.8.11"

lib/OrdinaryDiffEqAdamsBashforthMoulton/src/OrdinaryDiffEqAdamsBashforthMoulton.jl

@@ -18,7 +18,7 @@ import Static: False
 import OrdinaryDiffEqCore
 
 using Reexport
-@reexport using DiffEqBase
+@reexport using SciMLBase
 
 include("algorithms.jl")
 include("alg_utils.jl")

lib/OrdinaryDiffEqBDF/Project.toml

@@ -4,6 +4,8 @@ authors = ["ParamThakkar123 <[email protected]>"]
 version = "1.7.0"
 
 [deps]
+SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
+
 ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
 ArrayInterface = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
 DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
@@ -57,6 +59,7 @@ SafeTestsets = "0.1.0"
 StaticArrays = "1.9.7"
 Test = "<0.0.1, 1"
 TruncatedStacktraces = "1.4.0"
+SciMLBase = "2"
 julia = "1.10"
 
 [extras]

lib/OrdinaryDiffEqBDF/src/OrdinaryDiffEqBDF.jl

@@ -24,21 +24,25 @@ import OrdinaryDiffEqCore: alg_order, calculate_residuals!,
                            _process_AD_choice
 using OrdinaryDiffEqSDIRK: ImplicitEulerConstantCache, ImplicitEulerCache
 
-using TruncatedStacktraces, MuladdMacro, MacroTools, FastBroadcast, RecursiveArrayTools
+using TruncatedStacktraces: @truncate_stacktrace
+using MuladdMacro: @muladd
+using MacroTools: @capture
+using FastBroadcast: @..
+using RecursiveArrayTools: recursivefill!
 import StaticArrays: SArray, MVector, SVector, @SVector, StaticArray, MMatrix, SA
 using LinearAlgebra: mul!, I
-using ArrayInterface
+import ArrayInterface
+using ArrayInterface: ismutable
 import OrdinaryDiffEqCore
 using OrdinaryDiffEqDifferentiation: UJacobianWrapper
 using OrdinaryDiffEqNonlinearSolve: NLNewton, du_alias_or_new, build_nlsolver,
                                     nlsolve!, nlsolvefail, isnewton, markfirststage!,
                                     set_new_W!, DIRK, compute_step!, COEFFICIENT_MULTISTEP,
                                     NonlinearSolveAlg
-import ADTypes
 import ADTypes: AutoForwardDiff, AutoFiniteDiff, AbstractADType
 
 using Reexport
-@reexport using DiffEqBase
+@reexport using SciMLBase
 
 include("algorithms.jl")
 include("alg_utils.jl")

lib/OrdinaryDiffEqBDF/src/algorithms.jl

@@ -444,7 +444,7 @@ function QNDF(; max_order::Val{MO} = Val{5}(), chunk_size = Val{0}(),
         extrapolant, kappa, controller, step_limiter!, AD_choice)
 end
 
-TruncatedStacktraces.@truncate_stacktrace QNDF
+@truncate_stacktrace QNDF
 
 @doc BDF_docstring("The second order Modified Extended BDF method,
     which has improved stability properties over the standard BDF.
@@ -549,7 +549,7 @@ function FBDF(; max_order::Val{MO} = Val{5}(), chunk_size = Val{0}(),
         controller, step_limiter!, AD_choice)
 end
 
-TruncatedStacktraces.@truncate_stacktrace FBDF
+@truncate_stacktrace FBDF
 
 """
 QBDF1: Multistep Method
@@ -773,4 +773,4 @@ function DFBDF(; max_order::Val{MO} = Val{5}(), chunk_size = Val{0}(),
         controller, AD_choice)
 end
 
-TruncatedStacktraces.@truncate_stacktrace DFBDF
+@truncate_stacktrace DFBDF

lib/OrdinaryDiffEqBDF/src/bdf_caches.jl

@@ -418,7 +418,7 @@ end
     step_limiter!::StepLimiter
 end
 
-TruncatedStacktraces.@truncate_stacktrace QNDFCache 1
+@truncate_stacktrace QNDFCache 1
 
 function alg_cache(alg::QNDF{MO}, u, rate_prototype, ::Type{uEltypeNoUnits},
         ::Type{uBottomEltypeNoUnits}, ::Type{tTypeNoUnits}, uprev, uprev2, f, t,
@@ -609,7 +609,7 @@ end
     step_limiter!::StepLimiter
 end
 
-TruncatedStacktraces.@truncate_stacktrace FBDFCache 1
+@truncate_stacktrace FBDFCache 1
 
 function alg_cache(alg::FBDF{MO}, u, rate_prototype, ::Type{uEltypeNoUnits},
         ::Type{uBottomEltypeNoUnits}, ::Type{tTypeNoUnits}, uprev, uprev2, f, t,

lib/OrdinaryDiffEqCore/src/OrdinaryDiffEqCore.jl

@@ -5,24 +5,27 @@ if isdefined(Base, :Experimental) &&
     @eval Base.Experimental.@max_methods 1
 end
 
-using DocStringExtensions
-using Reexport
-@reexport using DiffEqBase
+import DocStringExtensions
+import Reexport: @reexport
+using Reexport: @reexport
+@reexport using SciMLBase
+import DiffEqBase
 
-using Logging
+import Logging: @logmsg, LogLevel
 
-using MuladdMacro, FastClosures
+using MuladdMacro: @muladd
 
-using LinearAlgebra
+using LinearAlgebra: opnorm, I, UniformScaling, diag, rank, isdiag
 
-using PrecompileTools
+import PrecompileTools
 
 import FillArrays: Trues, Falses
 
-import FastPower
+import FastPower: fastpower
 
 # Interfaces
-import DiffEqBase: solve!, step!, initialize!, isadaptive
+import SciMLBase: solve!, step!, isadaptive
+import DiffEqBase: initialize!
 
 # Internal utils
 import DiffEqBase: ODE_DEFAULT_NORM,
@@ -36,25 +39,29 @@ import SciMLOperators: AbstractSciMLOperator, AbstractSciMLScalarOperator,
 
 using DiffEqBase: DEIntegrator
 
-import RecursiveArrayTools: chain, recursivecopy!
+import RecursiveArrayTools: chain, recursivecopy!, recursivecopy, recursive_bottom_eltype, recursive_unitless_bottom_eltype, recursive_unitless_eltype, copyat_or_push!, DiffEqArray
 
-using SimpleUnPack, RecursiveArrayTools, DataStructures, ArrayInterface
+using SimpleUnPack: @unpack
+import RecursiveArrayTools
+using DataStructures: BinaryHeap, FasterForward
+import DataStructures
+using ArrayInterface: ArrayInterface, issingular
 
-import TruncatedStacktraces
+import TruncatedStacktraces: @truncate_stacktrace, VERBOSE_MSG
 
 import StaticArraysCore: SArray, MVector, SVector, StaticArray, MMatrix,
                          StaticMatrix
 
 # Integrator Interface
-import DiffEqBase: resize!, deleteat!, addat!, full_cache, user_cache, u_cache, du_cache,
+import SciMLBase: resize!, deleteat!, addat!, full_cache, user_cache, u_cache, du_cache,
                    resize_non_user_cache!, deleteat_non_user_cache!, addat_non_user_cache!,
                    terminate!, get_du, get_dt, get_proposed_dt, set_proposed_dt!,
                    u_modified!, savevalues!,
                    add_tstop!, has_tstop, first_tstop, pop_tstop!,
                    add_saveat!, set_reltol!,
                    set_abstol!, postamble!, last_step_failed,
-                   isautodifferentiable,
-                   get_tstops, get_tstops_array, get_tstops_max
+                   isautodifferentiable
+import DiffEqBase: get_tstops, get_tstops_array, get_tstops_max
 
 using DiffEqBase: check_error!, @def, _vec, _reshape
 
@@ -65,21 +72,22 @@ using SciMLBase: NoInit, CheckInit, OverrideInit, AbstractDEProblem, _unwrap_val
 
 import SciMLBase: AbstractNonlinearProblem, alg_order, LinearAliasSpecifier
 
+import SciMLBase: unwrap_cache,
+                   islinear
 import DiffEqBase: calculate_residuals,
-                   calculate_residuals!, unwrap_cache,
-                   @tight_loop_macros,
-                   islinear, timedepentdtmin
+                   calculate_residuals!, @tight_loop_macros,
+                   timedepentdtmin
 
 import Polyester
-using MacroTools, Adapt
+# MacroTools and Adapt imported but not directly used in OrdinaryDiffEqCore
+# using MacroTools, Adapt
 import ADTypes: AutoFiniteDiff, AutoForwardDiff, AbstractADType, AutoSparse
 import Accessors: @reset
 
-using SciMLStructures: canonicalize, Tunable, isscimlstructure
+# SciMLStructures symbols imported but not directly used in OrdinaryDiffEqCore
+# using SciMLStructures: canonicalize, Tunable, isscimlstructure
 
-using SymbolicIndexingInterface: state_values, parameter_values, is_variable,
-                                 variable_index,
-                                 symbolic_type, NotSymbolic
+using SymbolicIndexingInterface: state_values, parameter_values
 
 const CompiledFloats = Union{Float32, Float64}
 import Preferences