Fix deprecation warnings (#122)

Co-authored-by: ChrisRackauckas-Claude <noreply@anthropic.com>

Author: ChrisRackauckas-Claude

Project.toml

@@ -26,6 +26,7 @@ SparseDiffTools = "47a9eef4-7e08-11e9-0b38-333d64bd3804"
 MultiScaleArraysSparseDiffToolsExt = "SparseDiffTools"
 
 [compat]
+ADTypes = "1"
 DiffEqBase = "6.5"
 DifferentiationInterface = "0.7.7"
 FiniteDiff = "2.3"
@@ -43,10 +44,11 @@ StochasticDiffEq = "6.13"
 julia = "1.10"
 
 [extras]
+ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
 JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["JET", "OrdinaryDiffEq", "SafeTestsets", "Test"]
+test = ["ADTypes", "JET", "OrdinaryDiffEq", "SafeTestsets", "Test"]

test/dynamic_diffeq.jl

@@ -1,5 +1,6 @@
 using MultiScaleArrays
 using OrdinaryDiffEq, DiffEqBase, Test, StochasticDiffEq, Statistics
+using ADTypes
 
 struct Cell{B} <: AbstractMultiScaleArrayLeaf{B}
     values::Vector{B}
@@ -64,9 +65,12 @@ prob = ODEProblem(f, embryo, (0.0, 1.0))
 test_embryo = deepcopy(embryo)
 
 sol = solve(prob, Tsit5(), callback = growing_cb, tstops = tstop)
-sol = solve(prob, Rosenbrock23(autodiff = false), tstops = tstop)
-sol = solve(prob, Rosenbrock23(autodiff = false), callback = growing_cb, tstops = tstop)
-sol = solve(prob, Rosenbrock23(chunk_size = 1), callback = growing_cb, tstops = tstop)
+sol = solve(prob, Rosenbrock23(autodiff = AutoFiniteDiff()), tstops = tstop)
+sol = solve(prob, Rosenbrock23(autodiff = AutoFiniteDiff()), callback = growing_cb, tstops = tstop)
+sol = solve(
+    prob, Rosenbrock23(autodiff = AutoForwardDiff(chunksize = 1)), callback = growing_cb,
+    tstops = tstop
+)
 
 affect_del! = function (integrator)
     return remove_node!(integrator, 1, 1, 1)
@@ -76,9 +80,12 @@ shrinking_cb = DiscreteCallback(condition, affect_del!)
 
 sol = solve(prob, Tsit5(), callback = shrinking_cb, tstops = tstop)
 
-sol = solve(prob, Rosenbrock23(autodiff = false), callback = shrinking_cb, tstops = tstop)
+sol = solve(prob, Rosenbrock23(autodiff = AutoFiniteDiff()), callback = shrinking_cb, tstops = tstop)
 
-sol = solve(prob, Rosenbrock23(chunk_size = 1), callback = shrinking_cb, tstops = tstop)
+sol = solve(
+    prob, Rosenbrock23(autodiff = AutoForwardDiff(chunksize = 1)), callback = shrinking_cb,
+    tstops = tstop
+)
 
 @test length(sol[end]) == 17
 

test/single_layer_diffeq.jl

@@ -1,5 +1,6 @@
 using MultiScaleArrays
 using OrdinaryDiffEq, DiffEqBase, Test, StochasticDiffEq, Statistics
+using ADTypes
 
 struct Cell2{B} <: AbstractMultiScaleArrayLeaf{B}
     values::Vector{B}
@@ -50,7 +51,7 @@ add_node!(pop, pop.nodes[1])
 
 sol = solve(prob, Tsit5(), callback = growing_cb, tstops = tstop)
 
-sol = solve(prob, Rosenbrock23(chunk_size = 1), callback = growing_cb, tstops = tstop)
+sol = solve(prob, Rosenbrock23(autodiff = AutoForwardDiff(chunksize = 1)), callback = growing_cb, tstops = tstop)
 
 @test length(sol[end]) == 13
 
@@ -64,7 +65,7 @@ prob = ODEProblem(f4, deepcopy(pop), (0.0, 1.0))
 sol = solve(prob, Tsit5(), callback = shrinking_cb, tstops = tstop)
 
 prob = ODEProblem(f4, deepcopy(pop), (0.0, 1.0))
-sol = solve(prob, Rosenbrock23(chunk_size = 1), callback = shrinking_cb, tstops = tstop)
+sol = solve(prob, Rosenbrock23(autodiff = AutoForwardDiff(chunksize = 1)), callback = shrinking_cb, tstops = tstop)
 @test length(sol[end]) == 10
 
 println("Do the SDE Part")