Merge branch 'master' into fix_deprecation

Author: ChrisRackauckas

Project.toml

@@ -32,13 +32,11 @@ JumpProcessesOrdinaryDiffEqCoreExt = "OrdinaryDiffEqCore"
 [compat]
 ADTypes = "1.22.0"
 Adapt = "4.6.0"
-Aqua = "0.8.16"
 ArrayInterface = "7.25.0"
 DataStructures = "0.19.5, 0.19"
 DiffEqBase = "7.5.5, 7"
 DiffEqCallbacks = "4.17.0"
 DocStringExtensions = "0.9.5"
-ExplicitImports = "1"
 FastBroadcast = "1.3.2, 1"
 FunctionWrappers = "1.1.3"
 Graphs = "1.14.0"
@@ -55,6 +53,7 @@ RecursiveArrayTools = "4.3.0, 4"
 Reexport = "1.2.2"
 SafeTestsets = "0.1"
 SciMLBase = "3.18.0, 3.1"
+SciMLTesting = "1.6"
 StableRNGs = "1"
 StaticArrays = "1.9.18"
 Statistics = "1"
@@ -65,19 +64,18 @@ julia = "1.10"
 
 [extras]
 ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
-Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
-ExplicitImports = "7d51a73a-1435-4ff3-83d9-f097790105c7"
 FastBroadcast = "7034ab61-46d4-4ed7-9d0f-46aef9175898"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 LinearSolve = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 OrdinaryDiffEqFunctionMap = "d3585ca7-f5d3-4ba6-8057-292ed1abd90f"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
+SciMLTesting = "09d9d899-5365-40a9-917a-5f67fddea283"
 StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["ADTypes", "Aqua", "ExplicitImports", "FastBroadcast", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEq", "OrdinaryDiffEqFunctionMap", "Pkg", "SafeTestsets", "StableRNGs", "Statistics", "StochasticDiffEq", "Test"]
+test = ["ADTypes", "FastBroadcast", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEq", "OrdinaryDiffEqFunctionMap", "Pkg", "SafeTestsets", "SciMLTesting", "StableRNGs", "Statistics", "StochasticDiffEq", "Test"]

ext/JumpProcessesOrdinaryDiffEqCoreExt.jl

@@ -2,6 +2,7 @@ module JumpProcessesOrdinaryDiffEqCoreExt
 
 using JumpProcesses
 import DiffEqBase
+import SciMLBase
 import OrdinaryDiffEqCore: OrdinaryDiffEqAlgorithm, DAEAlgorithm,
     StochasticDiffEqAlgorithm, StochasticDiffEqRODEAlgorithm
 
@@ -14,8 +15,8 @@ import OrdinaryDiffEqCore: OrdinaryDiffEqAlgorithm, DAEAlgorithm,
 # This method resolves the ambiguity by being more specific in the problem type
 # (AbstractJumpProblem vs Union{..., AbstractJumpProblem, ...}) while matching
 # the exact algorithm union from OrdinaryDiffEqCore.
-function DiffEqBase.__init(
-        _jump_prob::DiffEqBase.AbstractJumpProblem{P},
+function SciMLBase.__init(
+        _jump_prob::SciMLBase.AbstractJumpProblem{P},
         alg::Union{OrdinaryDiffEqAlgorithm, DAEAlgorithm,
             StochasticDiffEqAlgorithm, StochasticDiffEqRODEAlgorithm};
         merge_callbacks = true, kwargs...) where {P}

src/SSA_stepper.jl

@@ -56,7 +56,7 @@ see the
 [tutorial](https://docs.sciml.ai/JumpProcesses/stable/tutorials/discrete_stochastic_example/)
 for details.
 """
-struct SSAStepper <: DiffEqBase.AbstractDEAlgorithm end
+struct SSAStepper <: SciMLBase.AbstractDEAlgorithm end
 SciMLBase.allows_late_binding_tstops(::SSAStepper) = true
 
 """
@@ -140,14 +140,20 @@ function SciMLBase.derivative_discontinuity!(integrator::SSAIntegrator, bool::Bo
     integrator.u_modified = bool
 end
 
-function DiffEqBase.__solve(jump_prob::JumpProblem, alg::SSAStepper; kwargs...)
+@static if isdefined(SciMLBase, :derivative_discontinuity!)
+    function SciMLBase.derivative_discontinuity!(integrator::SSAIntegrator, bool::Bool)
+        integrator.u_modified = bool
+    end
+end
+
+function SciMLBase.__solve(jump_prob::JumpProblem, alg::SSAStepper; kwargs...)
     # init will handle kwargs merging via init_call
     integrator = init(jump_prob, alg; kwargs...)
     solve!(integrator)
     integrator.sol
 end
 
-function DiffEqBase.solve!(integrator::SSAIntegrator)
+function SciMLBase.solve!(integrator::SSAIntegrator)
     end_time = integrator.sol.prob.tspan[2]
     while should_continue_solve(integrator) # It stops before adding a tstop over
         step!(integrator)
@@ -185,7 +191,7 @@ function DiffEqBase.solve!(integrator::SSAIntegrator)
     end
 
     if integrator.sol.retcode === ReturnCode.Default
-        integrator.sol = DiffEqBase.solution_new_retcode(integrator.sol, ReturnCode.Success)
+        integrator.sol = SciMLBase.solution_new_retcode(integrator.sol, ReturnCode.Success)
     end
 end
 
@@ -216,7 +222,7 @@ function check_continuous_callback_error(callback)
     return nothing
 end
 
-function DiffEqBase.__init(jump_prob::JumpProblem,
+function SciMLBase.__init(jump_prob::JumpProblem,
         alg::SSAStepper;
         save_start = true,
         save_end = true,
@@ -267,10 +273,10 @@ function DiffEqBase.__init(jump_prob::JumpProblem,
     end
     save_everystep = any(cb.save_positions)
 
-    sol = DiffEqBase.build_solution(prob, alg, t, u, dense = save_everystep,
+    sol = SciMLBase.build_solution(prob, alg, t, u, dense = save_everystep,
         calculate_error = false,
         stats = DiffEqBase.Stats(0),
-        interp = DiffEqBase.ConstantInterpolation(t, u))
+        interp = SciMLBase.ConstantInterpolation(t, u))
 
     _saveat = (saveat isa Number) ? (prob.tspan[1]:saveat:prob.tspan[2]) : saveat
     if _saveat !== nothing && !isempty(_saveat) && _saveat[1] == prob.tspan[1]
@@ -456,7 +462,7 @@ end
 
 function DiffEqBase.terminate!(integrator::SSAIntegrator, retcode = ReturnCode.Terminated)
     integrator.keep_stepping = false
-    integrator.sol = DiffEqBase.solution_new_retcode(integrator.sol, retcode)
+    integrator.sol = SciMLBase.solution_new_retcode(integrator.sol, retcode)
     nothing
 end
 

src/coupling.jl

@@ -3,8 +3,8 @@ David F. Anderson, Masanori Koyama; An asymptotic relationship between coupling
 methods for stochastically modeled population processes. IMA J Numer Anal 2015;
 35 (4): 1757-1778. doi: 10.1093/imanum/dru044
 """
-function SplitCoupledJumpProblem(prob::DiffEqBase.AbstractJumpProblem,
-        prob_control::DiffEqBase.AbstractJumpProblem,
+function SplitCoupledJumpProblem(prob::SciMLBase.AbstractJumpProblem,
+        prob_control::SciMLBase.AbstractJumpProblem,
         aggregator::AbstractAggregatorAlgorithm,
         coupling_map::Vector{Tuple{Int, Int}}; kwargs...)
     JumpProblem(cat_problems(prob.prob, prob_control.prob), aggregator,
@@ -17,8 +17,8 @@ function cat_problems(prob::DiscreteProblem, prob_control::DiscreteProblem)
     DiscreteProblem(u0_coupled, prob.tspan, prob.p)
 end
 
-function cat_problems(prob::DiffEqBase.AbstractODEProblem,
-        prob_control::DiffEqBase.AbstractODEProblem)
+function cat_problems(prob::SciMLBase.AbstractODEProblem,
+        prob_control::SciMLBase.AbstractODEProblem)
     l = length(prob.u0) # add l_c = length(prob_control.u0)
 
     _f = SciMLBase.unwrapped_f(prob.f)
@@ -32,9 +32,9 @@ function cat_problems(prob::DiffEqBase.AbstractODEProblem,
     ODEProblem(new_f, u0_coupled, prob.tspan, prob.p)
 end
 
-function cat_problems(prob::DiscreteProblem, prob_control::DiffEqBase.AbstractODEProblem)
+function cat_problems(prob::DiscreteProblem, prob_control::SciMLBase.AbstractODEProblem)
     l = length(prob.u0) # add l_c = length(prob_control.u0)
-    if !(prob.f isa typeof(DiffEqBase.DISCRETE_INPLACE_DEFAULT))
+    if !(prob.f isa typeof(SciMLBase.DISCRETE_INPLACE_DEFAULT))
         @warn("Coupling to DiscreteProblem with nontrivial f. Note that, unless scale_by_time=true, the meaning of f will change when using an ODE/SDE/DDE/DAE solver.")
     end
 
@@ -49,8 +49,8 @@ function cat_problems(prob::DiscreteProblem, prob_control::DiffEqBase.AbstractOD
     ODEProblem(new_f, u0_coupled, prob.tspan, prob.p)
 end
 
-function cat_problems(prob::DiffEqBase.AbstractSDEProblem,
-        prob_control::DiffEqBase.AbstractSDEProblem)
+function cat_problems(prob::SciMLBase.AbstractSDEProblem,
+        prob_control::SciMLBase.AbstractSDEProblem)
     l = length(prob.u0)
     new_f = function (du, u, p, t)
         prob.f(@view(du[1:l]), u.u, p, t)
@@ -64,8 +64,8 @@ function cat_problems(prob::DiffEqBase.AbstractSDEProblem,
     SDEProblem(new_f, new_g, u0_coupled, prob.tspan, prob.p)
 end
 
-function cat_problems(prob::DiffEqBase.AbstractSDEProblem,
-        prob_control::DiffEqBase.AbstractODEProblem)
+function cat_problems(prob::SciMLBase.AbstractSDEProblem,
+        prob_control::SciMLBase.AbstractODEProblem)
     l = length(prob.u0)
 
     _f = SciMLBase.unwrapped_f(prob.f)
@@ -85,9 +85,9 @@ function cat_problems(prob::DiffEqBase.AbstractSDEProblem,
     SDEProblem(new_f, new_g, u0_coupled, prob.tspan, prob.p)
 end
 
-function cat_problems(prob::DiffEqBase.AbstractSDEProblem, prob_control::DiscreteProblem)
+function cat_problems(prob::SciMLBase.AbstractSDEProblem, prob_control::DiscreteProblem)
     l = length(prob.u0)
-    if !(prob_control.f isa typeof(DiffEqBase.DISCRETE_INPLACE_DEFAULT))
+    if !(prob_control.f isa typeof(SciMLBase.DISCRETE_INPLACE_DEFAULT))
         @warn("Coupling to DiscreteProblem with nontrivial f. Note that, unless scale_by_time=true, the meaning of f will change when using an ODE/SDE/DDE/DAE solver.")
     end
     new_f = function (du, u, p, t)
@@ -104,20 +104,20 @@ function cat_problems(prob::DiffEqBase.AbstractSDEProblem, prob_control::Discret
     SDEProblem(new_f, new_g, u0_coupled, prob.tspan)
 end
 
-function cat_problems(prob_control::DiffEqBase.AbstractODEProblem, prob::DiscreteProblem)
+function cat_problems(prob_control::SciMLBase.AbstractODEProblem, prob::DiscreteProblem)
     cat_problems(prob, prob_control)
 end
-function cat_problems(prob_control::DiscreteProblem, prob::DiffEqBase.AbstractSDEProblem)
+function cat_problems(prob_control::DiscreteProblem, prob::SciMLBase.AbstractSDEProblem)
     cat_problems(prob, prob_control)
 end
-function cat_problems(prob_control::DiffEqBase.AbstractODEProblem,
-        prob::DiffEqBase.AbstractSDEProblem)
+function cat_problems(prob_control::SciMLBase.AbstractODEProblem,
+        prob::SciMLBase.AbstractSDEProblem)
     cat_problems(prob, prob_control)
 end
 
 # this only depends on the jumps in prob, not prob.prob
-function build_split_jumps(prob::DiffEqBase.AbstractJumpProblem,
-        prob_control::DiffEqBase.AbstractJumpProblem,
+function build_split_jumps(prob::SciMLBase.AbstractJumpProblem,
+        prob_control::SciMLBase.AbstractJumpProblem,
         coupling_map::Vector{Tuple{Int, Int}})
     num_jumps = length(prob.discrete_jump_aggregation.rates)
     num_jumps_control = length(prob_control.discrete_jump_aggregation.rates)

src/problem.jl

@@ -1,5 +1,5 @@
 function isinplace_jump(p, rj)
-    if p isa DiscreteProblem && p.f === DiffEqBase.DISCRETE_INPLACE_DEFAULT &&
+    if p isa DiscreteProblem && p.f === SciMLBase.DISCRETE_INPLACE_DEFAULT &&
        rj !== nothing
         # Just a default discrete problem f, so don't use it for iip
         DiffEqBase.isinplace(rj)
@@ -71,7 +71,7 @@ the DifferentialEquations.jl [docs](https://docs.sciml.ai/JumpProcesses/stable/)
 examples and commonly asked questions.
 """
 mutable struct JumpProblem{iip, P, A, C, J <: Union{Nothing, AbstractJumpAggregator}, J1, 
-        J2, J3, J4, R, K} <: DiffEqBase.AbstractJumpProblem{P, J}
+        J2, J3, J4, R, K} <: SciMLBase.AbstractJumpProblem{P, J}
     """The type of problem to couple the jumps to. For a pure jump process use `DiscreteProblem`, to couple to ODEs, `ODEProblem`, etc."""
     prob::P
     """The aggregator algorithm that determines the next jump times and types for `ConstantRateJump`s and `MassActionJump`s. Examples include `Direct`."""
@@ -111,7 +111,7 @@ function remake_extended_u0(prob, newu0, rng)
     ExtendedJumpArray(newu0, jump_u)
 end
 
-Base.@pure remaker_of(prob::T) where {T <: JumpProblem} = DiffEqBase.parameterless_type(T)
+Base.@pure remaker_of(prob::T) where {T <: JumpProblem} = SciMLBase.parameterless_type(T)
 function DiffEqBase.remake(jprob::JumpProblem; u0 = missing, p = missing,
         interpret_symbolicmap = true, use_defaults = false, kwargs...)
     T = remaker_of(jprob)
@@ -240,7 +240,7 @@ make_kwarg(; kwargs...) = kwargs
 
 function JumpProblem(prob, aggregator::AbstractAggregatorAlgorithm, jumps::JumpSet;
         vr_aggregator::VariableRateAggregator = VR_FRM(),
-        save_positions = prob isa DiffEqBase.AbstractDiscreteProblem ?
+        save_positions = prob isa SciMLBase.AbstractDiscreteProblem ?
                          (false, true) : (true, true),
         rng = DEFAULT_RNG, scale_rates = true, useiszero = true,
         spatial_system = nothing, hopping_constants = nothing,
@@ -319,7 +319,7 @@ end
 
 # Special dispatch for PureLeaping aggregator - bypasses all aggregation
 function JumpProblem(prob, aggregator::PureLeaping, jumps::JumpSet;
-        save_positions = prob isa DiffEqBase.AbstractDiscreteProblem ?
+        save_positions = prob isa SciMLBase.AbstractDiscreteProblem ?
                          (false, true) : (true, true),
         rng = DEFAULT_RNG, scale_rates = true, useiszero = true,
         spatial_system = nothing, hopping_constants = nothing,

src/simple_regular_solve.jl

@@ -1,6 +1,6 @@
-struct SimpleTauLeaping <: DiffEqBase.AbstractDEAlgorithm end
+struct SimpleTauLeaping <: SciMLBase.AbstractDEAlgorithm end
 
-struct SimpleExplicitTauLeaping{T <: AbstractFloat} <: DiffEqBase.AbstractDEAlgorithm
+struct SimpleExplicitTauLeaping{T <: AbstractFloat} <: SciMLBase.AbstractDEAlgorithm
     epsilon::T  # Error control parameter
 end
 
@@ -142,9 +142,9 @@ function DiffEqBase.solve(jump_prob::JumpProblem, alg::SimpleTauLeaping;
         push!(tsave, tspan[2])
     end
 
-    sol = DiffEqBase.build_solution(prob, alg, tsave, usave,
+    sol = SciMLBase.build_solution(prob, alg, tsave, usave,
         calculate_error = false,
-        interp = DiffEqBase.ConstantInterpolation(tsave, usave))
+        interp = SciMLBase.ConstantInterpolation(tsave, usave))
 end
 
 # Compute the highest order of reaction (HOR) for each reaction j, as per Cao et al. (2006), Section IV.
@@ -399,9 +399,9 @@ function DiffEqBase.solve(jump_prob::JumpProblem, alg::SimpleExplicitTauLeaping;
         dtmin, saveat_times, usave, tsave, du, counts, rate_cache, rate_effective, maj,
         save_end)
 
-    sol = DiffEqBase.build_solution(prob, alg, tsave, usave,
+    sol = SciMLBase.build_solution(prob, alg, tsave, usave,
         calculate_error = false,
-        interp = DiffEqBase.ConstantInterpolation(tsave, usave))
+        interp = SciMLBase.ConstantInterpolation(tsave, usave))
     return sol
 end
 

src/solve.jl

@@ -1,5 +1,5 @@
-function DiffEqBase.__solve(jump_prob::DiffEqBase.AbstractJumpProblem{P},
-        alg::DiffEqBase.AbstractDEAlgorithm;
+function SciMLBase.__solve(jump_prob::SciMLBase.AbstractJumpProblem{P},
+        alg::SciMLBase.AbstractDEAlgorithm;
         merge_callbacks = true, kwargs...) where {P}
     # Merge jump_prob.kwargs with passed kwargs
     kwargs = DiffEqBase.merge_problem_kwargs(jump_prob; merge_callbacks, kwargs...)
@@ -10,7 +10,7 @@ function DiffEqBase.__solve(jump_prob::DiffEqBase.AbstractJumpProblem{P},
 end
 
 #Ambiguity Fix
-function DiffEqBase.__solve(jump_prob::DiffEqBase.AbstractJumpProblem{P},
+function SciMLBase.__solve(jump_prob::SciMLBase.AbstractJumpProblem{P},
         alg::Union{SciMLBase.AbstractRODEAlgorithm, SciMLBase.AbstractSDEAlgorithm};
         merge_callbacks = true, kwargs...) where {P}
     # Merge jump_prob.kwargs with passed kwargs
@@ -23,24 +23,24 @@ end
 
 # if passed a JumpProblem over a DiscreteProblem, and no aggregator is selected use
 # SSAStepper
-function DiffEqBase.__solve(jump_prob::DiffEqBase.AbstractJumpProblem{P};
+function SciMLBase.__solve(jump_prob::SciMLBase.AbstractJumpProblem{P};
         kwargs...) where {P <: DiscreteProblem}
-    DiffEqBase.__solve(jump_prob, SSAStepper(); kwargs...)
+    SciMLBase.__solve(jump_prob, SSAStepper(); kwargs...)
 end
 
-function DiffEqBase.__solve(jump_prob::DiffEqBase.AbstractJumpProblem; kwargs...)
+function SciMLBase.__solve(jump_prob::SciMLBase.AbstractJumpProblem; kwargs...)
     error("Auto-solver selection is currently only implemented for JumpProblems defined over DiscreteProblems. Please explicitly specify a solver algorithm in calling solve.")
 end
 
-function DiffEqBase.__init(_jump_prob::DiffEqBase.AbstractJumpProblem{P},
-        alg::DiffEqBase.AbstractDEAlgorithm; merge_callbacks = true, kwargs...) where {P}
+function SciMLBase.__init(_jump_prob::SciMLBase.AbstractJumpProblem{P},
+        alg::SciMLBase.AbstractDEAlgorithm; merge_callbacks = true, kwargs...) where {P}
     # Merge jump_prob.kwargs with passed kwargs
     kwargs = DiffEqBase.merge_problem_kwargs(_jump_prob; merge_callbacks, kwargs...)
 
     __jump_init(_jump_prob, alg; kwargs...)
 end 
 
-function __jump_init(_jump_prob::DiffEqBase.AbstractJumpProblem{P}, alg;
+function __jump_init(_jump_prob::SciMLBase.AbstractJumpProblem{P}, alg;
         callback = nothing, seed = nothing,
         alias_jump = Threads.threadid() == 1,
         kwargs...) where {P}
@@ -52,7 +52,7 @@ function __jump_init(_jump_prob::DiffEqBase.AbstractJumpProblem{P}, alg;
     end
 
     # DDEProblems do not have a recompile_flag argument
-    if jump_prob.prob isa DiffEqBase.AbstractDDEProblem
+    if jump_prob.prob isa SciMLBase.AbstractDDEProblem
         # callback comes after jump consistent with SSAStepper
         integrator = init(jump_prob.prob, alg;
             callback = CallbackSet(jump_prob.jump_callback, callback),