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Bump compat for OrdinaryDiffEq v7 / SciMLBase v3 ecosystem #1466

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Merged
TorkelE merged 1 commit into from
Jun 2, 2026
Merged

Bump compat for OrdinaryDiffEq v7 / SciMLBase v3 ecosystem #1466

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13 changes: 9 additions & 4 deletions Project.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,7 @@ BifurcationKit = "0.4.4, 0.5"
CairoMakie = "0.12, 0.13, 0.14, 0.15"
Combinatorics = "1.0.2"
DataStructures = "0.18, 0.19"
DiffEqBase = "6.165.0"
DiffEqBase = "6.165.0, 7"
DocStringExtensions = "0.8, 0.9"
DynamicPolynomials = "0.6"
DynamicQuantities = "1"
Expand All @@ -65,14 +65,19 @@ MacroTools = "0.5.5"
Makie = "0.22.1, 0.23, 0.24"
ModelingToolkitBase = "1.17"
NetworkLayout = "0.4.7"
OrdinaryDiffEqCore = "3.22"
OrdinaryDiffEqBDF = "1, 2"
OrdinaryDiffEqCore = "3.22, 4"
OrdinaryDiffEqDefault = "1, 2"
OrdinaryDiffEqRosenbrock = "1, 2"
OrdinaryDiffEqTsit5 = "1, 2"
OrdinaryDiffEqVerner = "1, 2"
Parameters = "0.12"
Reexport = "1.0"
RuntimeGeneratedFunctions = "0.5.12"
SciMLBase = "2.84"
SciMLBase = "2.84, 3"
SciMLPublic = "1"
Setfield = "1"
StochasticDiffEq = "6.101"
StochasticDiffEq = "6.101, 7"
StructuralIdentifiability = "0.5.11"
SymbolicIndexingInterface = "0.3"
SymbolicUtils = "4.9.1"
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20 changes: 10 additions & 10 deletions docs/Project.toml
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Expand Up @@ -63,7 +63,7 @@ CairoMakie = "0.15"
Catalyst = "16"
DataFrames = "1.6"
DataInterpolations = "7.2, 8"
DiffEqBase = "6.159.0"
DiffEqBase = "6.159.0, 7"
DiffEqNoiseProcess = "5.31.1"
Distributions = "0.25"
Documenter = "1.11.1"
Expand All @@ -88,25 +88,25 @@ OptimizationLBFGSB = "1"
OptimizationNLopt = "0.3"
OptimizationOptimJL = "0.4"
OptimizationOptimisers = "0.3"
OrdinaryDiffEqBDF = "1"
OrdinaryDiffEqDefault = "1"
OrdinaryDiffEqNonlinearSolve = "1"
OrdinaryDiffEqRosenbrock = "1"
OrdinaryDiffEqSDIRK = "1"
OrdinaryDiffEqTsit5 = "1"
OrdinaryDiffEqVerner = "1"
OrdinaryDiffEqBDF = "1, 2"
OrdinaryDiffEqDefault = "1, 2"
OrdinaryDiffEqNonlinearSolve = "1, 2"
OrdinaryDiffEqRosenbrock = "1, 2"
OrdinaryDiffEqSDIRK = "1, 2"
OrdinaryDiffEqTsit5 = "1, 2"
OrdinaryDiffEqVerner = "1, 2"
PEtab = "5"
Plots = "1.40"
QuasiMonteCarlo = "0.3"
ReactionNetworkImporters = "1.1.0"
SBMLImporter = "4.0.0"
SciMLBase = "2.46"
SciMLBase = "2.46, 3"
SciMLSensitivity = "7.60"
SpecialFunctions = "2.4"
StaticArrays = "1.9"
StatsPlots = "0.15.8"
SteadyStateDiffEq = "2.2"
StochasticDiffEq = "6.65"
StochasticDiffEq = "6.65, 7"
StructuralIdentifiability = "0.5.11"
SymbolicIndexingInterface = "0.3"
Symbolics = "7.13"
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6 changes: 4 additions & 2 deletions src/spatial_reaction_systems/discrete_space_sim_struct_interfacing.jl
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Expand Up @@ -412,12 +412,14 @@ rebuild_spat_internals!(oprob)
```
"""
function rebuild_spat_internals!(oprob::ODEProblem)
rebuild_spat_internals!(oprob.f.f, oprob.p, oprob.f.f.dsrs)
lt_ofun = SciMLBase.unwrapped_f(oprob.f.f)
rebuild_spat_internals!(lt_ofun, oprob.p, lt_ofun.dsrs)
end

# Function for rebuilding a `DiscreteSpaceReactionSystem` integrator after it has been updated.
function rebuild_spat_internals!(integrator::SciMLBase.AbstractODEIntegrator)
rebuild_spat_internals!(integrator.f.f, integrator.p, integrator.f.f.dsrs)
lt_ofun = SciMLBase.unwrapped_f(integrator.f.f)
rebuild_spat_internals!(lt_ofun, integrator.p, lt_ofun.dsrs)
end

# Function which rebuilds a `LatticeTransportODEFunction` functor for a new parameter set.
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4 changes: 2 additions & 2 deletions test/simulation_and_solving/hybrid_models.jl
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Expand Up @@ -188,7 +188,7 @@ let

# Solves and checks values of solution (do this before integrator mutation test
# since integrator mutation affects shared parameter state).
sol = solve(prob, Tsit5(); maxiters = 10, verbose = false)

@TorkelE TorkelE Apr 29, 2026

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Is verobes = false now the default for solve?

@ChrisRackauckas ChrisRackauckas May 10, 2026

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No, it doesn't use booleans at all.

sol = solve(prob, Tsit5(); maxiters = 10)

@TorkelE TorkelE Jun 1, 2026

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I am still confussed here, verbose = false (or whatever is the new syntax) is not the default, right? I.e. we would need to put whatever is the new thing here?

@ChrisRackauckas ChrisRackauckas Jun 1, 2026

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verbose = DEVerbosity(SciMLLogging.None())

@ChrisRackauckas ChrisRackauckas Jun 1, 2026

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That's if you want literally everything off, though it's probably not a good idea to always do that 😅

@TorkelE TorkelE Jun 1, 2026

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To be honest, not sure what the intention is for these tests, I didn't write them

@ChrisRackauckas ChrisRackauckas Jun 1, 2026

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I don't think it needs verbosity turned off.

@test sol[:X][1] == 1.0
@test sol[:X2][1] == 0.0
@test sol[:Y][1] == 0.0
Expand All @@ -215,7 +215,7 @@ let
@test prob2.ps[:d] == 0.5 # not changed

# Test that we can solve the remade problem and verify solution values.
sol2 = solve(prob2, Tsit5(); maxiters = 10, verbose = false)
sol2 = solve(prob2, Tsit5(); maxiters = 10)
@test sol2[:X][1] == 3.0
@test sol2[:X2][1] == 2.0
@test sol2[:Y][1] == 1.0
Expand Down
4 changes: 2 additions & 2 deletions test/simulation_and_solving/simulate_SDEs.jl
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Expand Up @@ -618,8 +618,8 @@ let
cat_sol = solve(cat_ensemble, EM(); dt = 0.001, trajectories = N, saveat = 20.0)
hand_sol = solve(hand_ensemble, EM(); dt = 0.001, trajectories = N, saveat = 20.0)

cat_endpoints = [sol[1, end] for sol in cat_sol]
hand_endpoints = [sol[1, end] for sol in hand_sol]
cat_endpoints = [sol[1, end] for sol in cat_sol.u]
hand_endpoints = [sol[1, end] for sol in hand_sol.u]

cat_mean = mean(cat_endpoints)
hand_mean = mean(hand_endpoints)
Expand Down
14 changes: 10 additions & 4 deletions test/simulation_and_solving/simulate_jumps.jl
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Expand Up @@ -2,6 +2,7 @@

# Fetch packages.
using Catalyst, JumpProcesses, ModelingToolkitBase, OrdinaryDiffEqTsit5, Statistics, Test
using SymbolicIndexingInterface: setp

# Sets stable rng number.
using StableRNGs
Expand Down Expand Up @@ -447,8 +448,9 @@ end
jprob_cb = JumpProblem(rn, u0, (0.0, 200.0), ps;
aggregator = Direct(), save_positions = (false, false))
condit(u, t, integrator) = t == 100.0
setk! = setp(jprob_cb, :k)
function affect_cb!(integrator)
integrator.ps[:k] = 24.0
setk!(integrator, 24.0)
reset_aggregated_jumps!(integrator)
end
cb = DiscreteCallback(condit, affect_cb!)
Expand Down Expand Up @@ -496,8 +498,9 @@ end
jprob_cb = JumpProblem(rn, u0, (0.0, 200.0), ps;
aggregator = Direct(), save_positions = (false, false))
condit(u, t, integrator) = t == 100.0
setk! = setp(jprob_cb, :k)
function affect_cb!(integrator)
integrator.ps[:k] = 24.0
setk!(integrator, 24.0)
reset_aggregated_jumps!(integrator)
end
cb = DiscreteCallback(condit, affect_cb!)
Expand Down Expand Up @@ -541,8 +544,9 @@ end
jprob_cb = JumpProblem(rn, u0, (0.0, 200.0), ps;
aggregator = Direct(), save_positions = (false, false))
condit(u, t, integrator) = t == 100.0
setk1! = setp(jprob_cb, :k1)
function affect_cb!(integrator)
integrator.ps[:k1] = 24.0
setk1!(integrator, 24.0)
reset_aggregated_jumps!(integrator)
end
cb = DiscreteCallback(condit, affect_cb!)
Expand Down Expand Up @@ -641,8 +645,10 @@ end
aggregator = Direct(), save_positions = (false, false))
condit(u, t, integrator) = t == 100.0
new_k_true = 24.0
new_k_val = rn === rn_true ? new_k_true : new_k_true / factorial(3)
setk! = setp(jp, :k)
function affect_equiv!(integrator)
integrator.ps[:k] = rn === rn_true ? new_k_true : new_k_true / factorial(3)
setk!(integrator, new_k_val)
reset_aggregated_jumps!(integrator)
end
cb = DiscreteCallback(condit, affect_equiv!)
Expand Down
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