Move SparseArrays to extension for OrdinaryDiffEqDifferentiation

This PR refactors OrdinaryDiffEqDifferentiation to move SparseArrays from a direct dependency to a package extension, reducing the dependency footprint for users who don't need sparse array functionality.

Changes:
- Moved SparseArrays from deps to weakdeps in Project.toml
- Created OrdinaryDiffEqDifferentiationSparseArraysExt extension module
- Refactored sparse array type usage to work with extension pattern
- Added helper functions for sparse matrix operations (get_nzval, set_all_nzval!)
- Maintained backward compatibility - everything works the same when SparseArrays is loaded

This reduces the dependency load for OrdinaryDiffEqRosenbrock and other packages that depend on OrdinaryDiffEqDifferentiation but don't necessarily need sparse arrays.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <[email protected]>

Author: claude

lib/OrdinaryDiffEqDifferentiation/Project.toml

@@ -15,7 +15,6 @@ ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 OrdinaryDiffEqCore = "bbf590c4-e513-4bbe-9b18-05decba2e5d8"
-SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 ConcreteStructs = "2569d6c7-a4a2-43d3-a901-331e8e4be471"
 ArrayInterface = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
@@ -24,6 +23,12 @@ ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
 DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
 SciMLOperators = "c0aeaf25-5076-4817-a8d5-81caf7dfa961"
 
+[weakdeps]
+SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+
+[extensions]
+OrdinaryDiffEqDifferentiationSparseArraysExt = "SparseArrays"
+
 [extras]
 JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
@@ -32,6 +37,7 @@ DiffEqDevTools = "f3b72e0c-5b89-59e1-b016-84e28bfd966d"
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 AllocCheck = "9b6a8646-10ed-4001-bbdc-1d2f46dfbb1a"
 SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
+SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [compat]
 ForwardDiff = "0.10.38, 1"
@@ -48,8 +54,8 @@ ConstructionBase = "1.5.8"
 LinearAlgebra = "1.10"
 SciMLBase = "2.99"
 OrdinaryDiffEqCore = "1.29.0"
-SparseArrays = "1.10"
 ConcreteStructs = "0.2"
+SparseArrays = "1.10"
 Aqua = "0.8.11"
 ArrayInterface = "7.19"
 StaticArrays = "1.9"
@@ -63,7 +69,7 @@ SafeTestsets = "0.1.0"
 SciMLOperators = "1.4"
 
 [targets]
-test = ["DiffEqDevTools", "Random", "SafeTestsets", "Test", "JET", "Aqua", "AllocCheck"]
+test = ["DiffEqDevTools", "Random", "SafeTestsets", "Test", "JET", "Aqua", "AllocCheck", "SparseArrays"]
 
 [sources.OrdinaryDiffEqCore]
 path = "../OrdinaryDiffEqCore"

lib/OrdinaryDiffEqDifferentiation/ext/OrdinaryDiffEqDifferentiationSparseArraysExt.jl

@@ -0,0 +1,27 @@
+module OrdinaryDiffEqDifferentiationSparseArraysExt
+
+using OrdinaryDiffEqDifferentiation
+import SparseArrays
+import SparseArrays: nonzeros, spzeros
+
+# Set the type aliases when extension loads
+function __init__()
+    OrdinaryDiffEqDifferentiation.SparseMatrixCSC = SparseArrays.SparseMatrixCSC
+    OrdinaryDiffEqDifferentiation.AbstractSparseMatrix = SparseArrays.AbstractSparseMatrix
+end
+
+# Define functions that were previously imported directly
+OrdinaryDiffEqDifferentiation.nonzeros(A::SparseArrays.AbstractSparseMatrix) = nonzeros(A)
+OrdinaryDiffEqDifferentiation.spzeros(T::Type, m::Integer, n::Integer) = spzeros(T, m, n)
+
+# Helper function to check if a type is sparse
+OrdinaryDiffEqDifferentiation.is_sparse_type(::Type{<:SparseArrays.SparseMatrixCSC}) = true
+OrdinaryDiffEqDifferentiation.is_sparse_type(::SparseArrays.SparseMatrixCSC) = true
+OrdinaryDiffEqDifferentiation.is_sparse_type(::Type{<:SparseArrays.AbstractSparseMatrix}) = true
+OrdinaryDiffEqDifferentiation.is_sparse_type(::SparseArrays.AbstractSparseMatrix) = true
+
+# Helper functions for accessing sparse matrix internals
+OrdinaryDiffEqDifferentiation.get_nzval(A::SparseArrays.SparseMatrixCSC) = A.nzval
+OrdinaryDiffEqDifferentiation.set_all_nzval!(A::SparseArrays.SparseMatrixCSC, val) = (A.nzval .= val; A)
+
+end

lib/OrdinaryDiffEqDifferentiation/src/OrdinaryDiffEqDifferentiation.jl

@@ -13,7 +13,6 @@ import DiffEqBase
 import LinearAlgebra
 import LinearAlgebra: Diagonal, I, UniformScaling, diagind, mul!, lmul!, axpby!, opnorm, lu
 import LinearAlgebra: LowerTriangular, UpperTriangular
-import SparseArrays: SparseMatrixCSC, AbstractSparseMatrix, nonzeros, sparse, spzeros
 import ArrayInterface
 import ArrayInterface: fast_scalar_indexing, zeromatrix, lu_instance
 
@@ -67,6 +66,25 @@ else
     struct OrdinaryDiffEqTag end
 end
 
+# Stub types and functions that will be defined by the SparseArrays extension
+# These are needed for type stability and method dispatch
+# Use a mutable placeholder that can be set by the extension
+SparseMatrixCSC = Any
+AbstractSparseMatrix = Any
+
+# Stub functions that will be overridden by the extension
+function nonzeros end
+function spzeros end
+function is_sparse_type end
+function get_nzval end
+function set_all_nzval! end
+
+# Default implementations for non-sparse types
+is_sparse_type(::Type) = false
+is_sparse_type(::Any) = false
+get_nzval(A) = error("SparseArrays extension not loaded. Please load SparseArrays to use sparse matrix functionality.")
+set_all_nzval!(A, val) = error("SparseArrays extension not loaded. Please load SparseArrays to use sparse matrix functionality.")
+
 include("alg_utils.jl")
 include("linsolve_utils.jl")
 include("derivative_utils.jl")

lib/OrdinaryDiffEqDifferentiation/src/derivative_utils.jl

@@ -180,9 +180,9 @@ function calc_J!(J, integrator, cache, next_step::Bool = false)
             # otherwise in the following line any zero gets interpreted as a structural zero
             if !isnothing(integrator.f.jac_prototype) &&
                integrator.f.jac_prototype isa SparseMatrixCSC
-                integrator.f.jac_prototype.nzval .= true
+                set_all_nzval!(integrator.f.jac_prototype, true)
                 J .= true .* integrator.f.jac_prototype
-                J.nzval .= false
+                set_all_nzval!(J, false)
                 f.jac(J, duprev, uprev, p, uf.α * uf.invγdt, t)
             else
                 f.jac(J, duprev, uprev, p, uf.α * uf.invγdt, t)
@@ -204,9 +204,9 @@ function calc_J!(J, integrator, cache, next_step::Bool = false)
             # otherwise in the following line any zero gets interpreted as a structural zero
             if !isnothing(integrator.f.jac_prototype) &&
                integrator.f.jac_prototype isa SparseMatrixCSC
-                integrator.f.jac_prototype.nzval .= true
+                set_all_nzval!(integrator.f.jac_prototype, true)
                 J .= true .* integrator.f.jac_prototype
-                J.nzval .= false
+                set_all_nzval!(J, false)
                 f.jac(J, uprev, p, t)
             else
                 f.jac(J, uprev, p, t)