From 7d622c179284069a84eaf0367068ea6450a41457 Mon Sep 17 00:00:00 2001 From: vyudu Date: Wed, 20 Nov 2024 14:42:38 -0500 Subject: [PATCH 1/5] init --- Project.toml | 11 +++++------ .../component_based_model_creation.jl | 4 ++-- test/dsl/dsl_options.jl | 2 +- test/extensions/lattice_simulation_plotting.jl | 4 ++-- test/extensions/stability_computation.jl | 4 ++-- test/miscellaneous_tests/api.jl | 4 ++-- test/network_analysis/conservation_laws.jl | 8 ++++---- .../lattice_reaction_systems_ODE_performance.jl | 2 +- .../coupled_equation_crn_systems.jl | 2 +- test/reactionsystem_core/events.jl | 2 +- .../reactionsystem_core/parameter_type_designation.jl | 2 +- test/reactionsystem_core/reactionsystem.jl | 4 ++-- test/reactionsystem_core/symbolic_stoichiometry.jl | 4 ++-- test/simulation_and_solving/simulate_ODEs.jl | 4 ++-- test/simulation_and_solving/simulate_jumps.jl | 2 +- test/simulation_and_solving/solve_nonlinear.jl | 4 ++-- test/spatial_modelling/lattice_reaction_systems.jl | 4 ++-- .../lattice_reaction_systems_ODEs.jl | 4 ++-- .../lattice_reaction_systems_lattice_types.jl | 4 ++-- .../lattice_simulation_struct_interfacing.jl | 2 +- test/spatial_modelling/simulate_PDEs.jl | 2 +- test/upstream/mtk_problem_inputs.jl | 2 +- test/upstream/mtk_structure_indexing.jl | 2 +- 23 files changed, 41 insertions(+), 42 deletions(-) diff --git a/Project.toml b/Project.toml index cedb612e95..e617c673aa 100644 --- a/Project.toml +++ b/Project.toml @@ -64,7 +64,6 @@ Requires = "1.0" RuntimeGeneratedFunctions = "0.5.12" SciMLBase = "< 2.57.2" Setfield = "1" -# StructuralIdentifiability = "0.5.8" SymbolicUtils = "2.1.2, 3.3.0" Symbolics = "5.30.1, 6" Unitful = "1.12.4" @@ -77,7 +76,10 @@ Graphviz_jll = "3c863552-8265-54e4-a6dc-903eb78fde85" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" Logging = "56ddb016-857b-54e1-b83d-db4d58db5568" NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" +OrdinaryDiffEqBDF = "6ad6398a-0878-4a85-9266-38940aa047c8" +OrdinaryDiffEqRosenbrock = "43230ef6-c299-4910-a778-202eb28ce4ce" +OrdinaryDiffEqTsit5 = "b1df2697-797e-41e3-8120-5422d3b24e4a" +OrdinaryDiffEqVerner = "79d7bb75-1356-48c1-b8c0-6832512096c2" Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" @@ -93,7 +95,4 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [targets] -test = ["DiffEqCallbacks", "DomainSets", "Graphviz_jll", "Logging", "NonlinearSolve", - "OrdinaryDiffEq", "Pkg", "Plots", "Random", "SafeTestsets", "SciMLBase", "SciMLNLSolve", - "StableRNGs", "StaticArrays", "Statistics", "SteadyStateDiffEq", "StochasticDiffEq", - "Test", "Unitful"] +test = ["DiffEqCallbacks", "DomainSets", "Graphviz_jll", "Logging", "NonlinearSolve", "OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqTsit5", "OrdinaryDiffEqVerner", "Pkg", "Plots", "Random", "SafeTestsets", "SciMLBase", "SciMLNLSolve", "StableRNGs", "StaticArrays", "Statistics", "SteadyStateDiffEq", "StochasticDiffEq", "Test", "Unitful"] diff --git a/test/compositional_modelling/component_based_model_creation.jl b/test/compositional_modelling/component_based_model_creation.jl index 5efd20967f..bcbcf393db 100644 --- a/test/compositional_modelling/component_based_model_creation.jl +++ b/test/compositional_modelling/component_based_model_creation.jl @@ -3,7 +3,7 @@ ### Prepares Tests ### # Fetch packages. -using Catalyst, LinearAlgebra, OrdinaryDiffEq, SciMLNLSolve, Test +using Catalyst, LinearAlgebra, OrdinaryDiffEqTsit5, SciMLNLSolve, Test using ModelingToolkit: nameof # Sets the default `t` to use. @@ -543,4 +543,4 @@ let @test length(unknowns(sys3)) == 4 @test length(parameters(sys4)) == 5 @test any(isequal(p5), parameters(sys4)) -end \ No newline at end of file +end diff --git a/test/dsl/dsl_options.jl b/test/dsl/dsl_options.jl index 8174598fd4..939ad3e118 100644 --- a/test/dsl/dsl_options.jl +++ b/test/dsl/dsl_options.jl @@ -3,7 +3,7 @@ ### Prepares Tests ### # Fetch packages. -using Catalyst, ModelingToolkit, OrdinaryDiffEq, StochasticDiffEq, Plots, Test +using Catalyst, ModelingToolkit, OrdinaryDiffEqTsit5, OrdinaryDiffEqRosenbrock, StochasticDiffEq, Plots, Test using Symbolics: unwrap # Sets stable rng number. diff --git a/test/extensions/lattice_simulation_plotting.jl b/test/extensions/lattice_simulation_plotting.jl index 0092916748..f9cc29d179 100644 --- a/test/extensions/lattice_simulation_plotting.jl +++ b/test/extensions/lattice_simulation_plotting.jl @@ -91,7 +91,7 @@ let lattice = CartesianGrid((2,2,2)) lrs = LatticeReactionSystem(rs, [diffusion_rx], lattice) oprob = ODEProblem(lrs, [:X => 1.0], 1.0, [:d => 1.0, :D => 0.2]) - osol = solve(oprob) + osol = solve(oprob, Tsit5()) @test_throws ArgumentError lattice_plot(osol, :X, lrs) @test_throws ArgumentError lattice_animation(osol, :X, lrs, "animation_tmp.mp4") @@ -130,4 +130,4 @@ let @test isfile("animation_tmp.mp4") rm("animation_tmp.mp4") end -end \ No newline at end of file +end diff --git a/test/extensions/stability_computation.jl b/test/extensions/stability_computation.jl index 24ddfe7a29..eeeba72131 100644 --- a/test/extensions/stability_computation.jl +++ b/test/extensions/stability_computation.jl @@ -1,7 +1,7 @@ ### Fetch Packages ### # Fetch packages. -using Catalyst, OrdinaryDiffEq, SteadyStateDiffEq, Test +using Catalyst, OrdinaryDiffEqVerner, SteadyStateDiffEq, Test import HomotopyContinuation # Sets rnd number. @@ -105,4 +105,4 @@ let p = [:p => 1.0, :d => 1.0] u = [1.0] @test_throws Exception steady_state_stability(u, rn, p) -end \ No newline at end of file +end diff --git a/test/miscellaneous_tests/api.jl b/test/miscellaneous_tests/api.jl index 9f2cddbb20..85b51ff43b 100644 --- a/test/miscellaneous_tests/api.jl +++ b/test/miscellaneous_tests/api.jl @@ -3,7 +3,7 @@ ### Prepares Tests ### # Fetch packages. -using Catalyst, NonlinearSolve, OrdinaryDiffEq, SparseArrays, StochasticDiffEq, Test +using Catalyst, NonlinearSolve, OrdinaryDiffEqTsit5, SparseArrays, StochasticDiffEq, Test using LinearAlgebra: norm using ModelingToolkit: value @@ -505,4 +505,4 @@ let f(d,t), X --> 0 end @test !isautonomous(rn8) -end \ No newline at end of file +end diff --git a/test/network_analysis/conservation_laws.jl b/test/network_analysis/conservation_laws.jl index fe79920a02..5ae268a021 100644 --- a/test/network_analysis/conservation_laws.jl +++ b/test/network_analysis/conservation_laws.jl @@ -1,7 +1,7 @@ ### Prepares Tests ### # Fetch packages. -using Catalyst, JumpProcesses, LinearAlgebra, NonlinearSolve, OrdinaryDiffEq, SteadyStateDiffEq, StochasticDiffEq, Test +using Catalyst, JumpProcesses, LinearAlgebra, NonlinearSolve, OrdinaryDiffEqTsit5, SteadyStateDiffEq, StochasticDiffEq, Test # Sets stable rng number. using StableRNGs @@ -192,7 +192,7 @@ let oprob1 = ODEProblem(rn, u0_1, 10.0, ps; remove_conserved = true, remove_conserved_warn) oprob2 = ODEProblem(rn, u0_2, 10.0, ps; remove_conserved = true, remove_conserved_warn) oprob3 = ODEProblem(rn, u0_3, 10.0, ps; remove_conserved = true, remove_conserved_warn) - @test solve(oprob1)[sps] ≈ solve(oprob2)[sps] ≈ solve(oprob3)[sps] + @test solve(oprob1, Tsit5())[sps] ≈ solve(oprob2, Tsit5())[sps] ≈ solve(oprob3, Tsit5())[sps] end # Tests conservation laws in SDE simulation. @@ -224,8 +224,8 @@ let oprob2 = ODEProblem(osys, u0, 10.0, ps_2) # Checks that the solutions generates the correct conserved quantities. - sol1 = solve(oprob1; saveat = 1.0) - sol2 = solve(oprob2; saveat = 1.0) + sol1 = solve(oprob1, Tsit5(); saveat = 1.0) + sol2 = solve(oprob2, Tsit5(); saveat = 1.0) @test all(sol1[osys.X1 + osys.X2] .== 2.0) @test all(sol2[osys.X1 + osys.X2] .== 4.0) end diff --git a/test/performance_benchmarks/lattice_reaction_systems_ODE_performance.jl b/test/performance_benchmarks/lattice_reaction_systems_ODE_performance.jl index 804dc4bc05..ca044d87e1 100644 --- a/test/performance_benchmarks/lattice_reaction_systems_ODE_performance.jl +++ b/test/performance_benchmarks/lattice_reaction_systems_ODE_performance.jl @@ -3,7 +3,7 @@ ### Preparations ### # Fetch packages. -using OrdinaryDiffEq +using OrdinaryDiffEqTsit5 using Random, Statistics, SparseArrays, Test # Fetch test networks. diff --git a/test/reactionsystem_core/coupled_equation_crn_systems.jl b/test/reactionsystem_core/coupled_equation_crn_systems.jl index d6c8bd5dc6..9968eb05f3 100644 --- a/test/reactionsystem_core/coupled_equation_crn_systems.jl +++ b/test/reactionsystem_core/coupled_equation_crn_systems.jl @@ -1,5 +1,5 @@ # Fetch packages. -using Catalyst, NonlinearSolve, OrdinaryDiffEq, Statistics, SteadyStateDiffEq, StochasticDiffEq, Test +using Catalyst, NonlinearSolve, OrdinaryDiffEqVerner, OrdinaryDiffEqTsit5, OrdinaryDiffEqRosenbrock, Statistics, SteadyStateDiffEq, StochasticDiffEq, Test using ModelingToolkit: getdefault, getdescription, getdefault using Symbolics: BasicSymbolic, unwrap diff --git a/test/reactionsystem_core/events.jl b/test/reactionsystem_core/events.jl index 5264114d83..f98d77c6e9 100644 --- a/test/reactionsystem_core/events.jl +++ b/test/reactionsystem_core/events.jl @@ -1,7 +1,7 @@ ### Prepares Tests ### # Fetch packages. -using Catalyst, DiffEqCallbacks, JumpProcesses, OrdinaryDiffEq, StochasticDiffEq, Test +using Catalyst, DiffEqCallbacks, JumpProcesses, OrdinaryDiffEqTsit5, StochasticDiffEq, Test # Sets stable rng number. using StableRNGs diff --git a/test/reactionsystem_core/parameter_type_designation.jl b/test/reactionsystem_core/parameter_type_designation.jl index 2a95bfa312..9b535e352c 100644 --- a/test/reactionsystem_core/parameter_type_designation.jl +++ b/test/reactionsystem_core/parameter_type_designation.jl @@ -1,7 +1,7 @@ ### Fetch Packages and Set Global Variables ### # Fetch packages. -using Catalyst, JumpProcesses, NonlinearSolve, OrdinaryDiffEq, StochasticDiffEq, Test +using Catalyst, JumpProcesses, NonlinearSolve, OrdinaryDiffEqTsit5, StochasticDiffEq, Test using Symbolics: BasicSymbolic, unwrap # Sets stable rng number. diff --git a/test/reactionsystem_core/reactionsystem.jl b/test/reactionsystem_core/reactionsystem.jl index 3acdf008e3..505781305a 100644 --- a/test/reactionsystem_core/reactionsystem.jl +++ b/test/reactionsystem_core/reactionsystem.jl @@ -1,7 +1,7 @@ ### Fetch Packages and Set Global Variables ### # Fetch packages. -using Catalyst, LinearAlgebra, JumpProcesses, OrdinaryDiffEq, StochasticDiffEq, Test +using Catalyst, LinearAlgebra, JumpProcesses, OrdinaryDiffEqTsit5, OrdinaryDiffEqVerner, StochasticDiffEq, Test const MT = ModelingToolkit # Sets stable rng number. @@ -1021,4 +1021,4 @@ let jprob = JumpProblem(jinput; rng) sol = solve(jprob) @test sol(10.0; idxs = :A) > 0 -end \ No newline at end of file +end diff --git a/test/reactionsystem_core/symbolic_stoichiometry.jl b/test/reactionsystem_core/symbolic_stoichiometry.jl index c2ec784919..2b51bba630 100644 --- a/test/reactionsystem_core/symbolic_stoichiometry.jl +++ b/test/reactionsystem_core/symbolic_stoichiometry.jl @@ -1,7 +1,7 @@ ### Prepares Tests ### # Fetch packages. -using Catalyst, JumpProcesses, OrdinaryDiffEq, StochasticDiffEq, Statistics, Test +using Catalyst, JumpProcesses, OrdinaryDiffEqTsit5, StochasticDiffEq, Statistics, Test using Symbolics: BasicSymbolic, unwrap # Sets stable rng number. @@ -297,4 +297,4 @@ let end_vals_ref = [[sol[s][end] for sol in sols_ref.u] for s in species(sir_ref)] @test mean.(end_vals_ref) ≈ mean.(end_vals) atol=1e-2 rtol = 1e-2 @test var.(end_vals_ref) ≈ var.(end_vals) atol=1e-1 rtol = 1e-1 -end \ No newline at end of file +end diff --git a/test/simulation_and_solving/simulate_ODEs.jl b/test/simulation_and_solving/simulate_ODEs.jl index ecb2a468ce..3bff83eae5 100644 --- a/test/simulation_and_solving/simulate_ODEs.jl +++ b/test/simulation_and_solving/simulate_ODEs.jl @@ -1,7 +1,7 @@ ### Prepares Tests ### # Fetch packages. -using Catalyst, OrdinaryDiffEq, Test +using Catalyst, OrdinaryDiffEqVerner, OrdinaryDiffEqRosenbrock, Test # Sets stable rng number. using StableRNGs @@ -200,4 +200,4 @@ let oprob.f(du1, oprob.u0, oprob.p, 90.0) oderhs(du2, u_2, p_2, 0.0) @test du1 ≈ du2 -end \ No newline at end of file +end diff --git a/test/simulation_and_solving/simulate_jumps.jl b/test/simulation_and_solving/simulate_jumps.jl index a5d91d758b..c0b19a81da 100644 --- a/test/simulation_and_solving/simulate_jumps.jl +++ b/test/simulation_and_solving/simulate_jumps.jl @@ -1,7 +1,7 @@ ### Prepares Tests ### # Fetch packages. -using Catalyst, JumpProcesses, OrdinaryDiffEq, Statistics, Test +using Catalyst, JumpProcesses, OrdinaryDiffEqTsit5, Statistics, Test # Sets stable rng number. using StableRNGs diff --git a/test/simulation_and_solving/solve_nonlinear.jl b/test/simulation_and_solving/solve_nonlinear.jl index 0315a65ac5..4f5b19a8a6 100644 --- a/test/simulation_and_solving/solve_nonlinear.jl +++ b/test/simulation_and_solving/solve_nonlinear.jl @@ -1,7 +1,7 @@ ### Prepares Tests ### # Fetch packages. -using Catalyst, NonlinearSolve, OrdinaryDiffEq, SteadyStateDiffEq +using Catalyst, NonlinearSolve, OrdinaryDiffEqRosenbrock, SteadyStateDiffEq using Random, Test # Sets stable rng number. @@ -100,4 +100,4 @@ let # Checks output using the ODE's drift function @test f_eval(steady_state_network_3, [:X => sol1[X], :Y => sol1[Y], :Y2 => sol1[Y2], :XY2 => sol1[XY2]], p, 0.0) ≈ [0.0, 0.0, 0.0, 0.0] atol=1e-10 @test f_eval(steady_state_network_3, [:X => sol2[X], :Y => sol2[Y], :Y2 => sol2[Y2], :XY2 => sol2[XY2]], p, 0.0) ≈ [0.0, 0.0, 0.0, 0.0] atol=1e-10 -end \ No newline at end of file +end diff --git a/test/spatial_modelling/lattice_reaction_systems.jl b/test/spatial_modelling/lattice_reaction_systems.jl index 875f9a45ee..b7fcb607bb 100644 --- a/test/spatial_modelling/lattice_reaction_systems.jl +++ b/test/spatial_modelling/lattice_reaction_systems.jl @@ -1,7 +1,7 @@ ### Preparations ### # Fetch packages. -using Catalyst, Graphs, OrdinaryDiffEq, Test +using Catalyst, Graphs, OrdinaryDiffEqTsit5, Test # Fetch test networks. include("../spatial_test_networks.jl") @@ -392,4 +392,4 @@ let @test_throws Exception make_directed_edge_values(lrs_2d, (1.0, 0.0), (1.0, 0.0), (1.0, 0.0)) @test_throws Exception make_directed_edge_values(lrs_3d, (1.0, 0.0)) @test_throws Exception make_directed_edge_values(lrs_3d, (1.0, 0.0), (1.0, 0.0)) -end \ No newline at end of file +end diff --git a/test/spatial_modelling/lattice_reaction_systems_ODEs.jl b/test/spatial_modelling/lattice_reaction_systems_ODEs.jl index f2a247a6b6..3bce253820 100644 --- a/test/spatial_modelling/lattice_reaction_systems_ODEs.jl +++ b/test/spatial_modelling/lattice_reaction_systems_ODEs.jl @@ -1,7 +1,7 @@ ### Preparations ### # Fetch packages. -using OrdinaryDiffEq +using OrdinaryDiffEqTsit5, OrdinaryDiffEqRosenbrock, OrdinaryDiffEqBDF using Random, Statistics, SparseArrays, Test # Fetch test networks. @@ -665,4 +665,4 @@ let @test_throws ArgumentError ODEProblem(lrs, u0, tspan, [d1 => 1.0]) @test_throws ArgumentError ODEProblem(lrs, [X1 => [1.0, 2.0, 3.0]], tspan, ps) @test_throws ArgumentError ODEProblem(lrs, [X1 => ones(3,1)], tspan, ps) -end \ No newline at end of file +end diff --git a/test/spatial_modelling/lattice_reaction_systems_lattice_types.jl b/test/spatial_modelling/lattice_reaction_systems_lattice_types.jl index dbdc233b89..bf37344d30 100644 --- a/test/spatial_modelling/lattice_reaction_systems_lattice_types.jl +++ b/test/spatial_modelling/lattice_reaction_systems_lattice_types.jl @@ -1,7 +1,7 @@ ### Preparations ### # Fetch packages. -using Catalyst, Graphs, OrdinaryDiffEq, Test +using Catalyst, Graphs, OrdinaryDiffEqTsit5, OrdinaryDiffEqBDF, Test # Fetch test networks. include("../spatial_test_networks.jl") @@ -257,4 +257,4 @@ let sol = solve(oprob, Tsit5(); saveat = 1.0, abstol = 1e-9, reltol = 1e-9) @test hcat(sol.u...) ≈ sol_base[13:end,:] end -end \ No newline at end of file +end diff --git a/test/spatial_modelling/lattice_simulation_struct_interfacing.jl b/test/spatial_modelling/lattice_simulation_struct_interfacing.jl index df49fe0743..6a31d21030 100644 --- a/test/spatial_modelling/lattice_simulation_struct_interfacing.jl +++ b/test/spatial_modelling/lattice_simulation_struct_interfacing.jl @@ -1,7 +1,7 @@ ### Preparations ### # Fetch packages. -using Catalyst, Graphs, JumpProcesses, OrdinaryDiffEq, SparseArrays, Test +using Catalyst, Graphs, JumpProcesses, OrdinaryDiffEqVerner, OrdinaryDiffEqTsit5, OrdinaryDiffEqRosenbrock, SparseArrays, Test # Fetch test networks. include("../spatial_test_networks.jl") diff --git a/test/spatial_modelling/simulate_PDEs.jl b/test/spatial_modelling/simulate_PDEs.jl index f0051e69fd..3ccf17f0e9 100644 --- a/test/spatial_modelling/simulate_PDEs.jl +++ b/test/spatial_modelling/simulate_PDEs.jl @@ -1,7 +1,7 @@ ### Fetch Packages and Set Global Variables ### # Fetch packages. -using Catalyst, OrdinaryDiffEq, Test +using Catalyst, Test using ModelingToolkit, DomainSets const MT = ModelingToolkit diff --git a/test/upstream/mtk_problem_inputs.jl b/test/upstream/mtk_problem_inputs.jl index c973596f03..4997a36dfc 100644 --- a/test/upstream/mtk_problem_inputs.jl +++ b/test/upstream/mtk_problem_inputs.jl @@ -3,7 +3,7 @@ ### Prepares Tests ### # Fetch packages -using Catalyst, JumpProcesses, NonlinearSolve, OrdinaryDiffEq, StaticArrays, SteadyStateDiffEq, +using Catalyst, JumpProcesses, NonlinearSolve, OrdinaryDiffEqTsit5, StaticArrays, SteadyStateDiffEq, StochasticDiffEq, Test # Sets rnd number. diff --git a/test/upstream/mtk_structure_indexing.jl b/test/upstream/mtk_structure_indexing.jl index f8768b8ed0..ab2b369bba 100644 --- a/test/upstream/mtk_structure_indexing.jl +++ b/test/upstream/mtk_structure_indexing.jl @@ -1,7 +1,7 @@ ### Prepares Tests ### # Fetch packages -using Catalyst, JumpProcesses, NonlinearSolve, OrdinaryDiffEq, Plots, SteadyStateDiffEq, StochasticDiffEq, Test +using Catalyst, JumpProcesses, NonlinearSolve, OrdinaryDiffEqTsit5, Plots, SteadyStateDiffEq, StochasticDiffEq, Test import ModelingToolkit: getp, getu, setp, setu # Sets rnd number. From caaea721c03fc69efc7c54d463c6aa07c7ae4bdb Mon Sep 17 00:00:00 2001 From: vyudu Date: Wed, 20 Nov 2024 15:16:51 -0500 Subject: [PATCH 2/5] bump project --- Project.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/Project.toml b/Project.toml index e617c673aa..80d6627337 100644 --- a/Project.toml +++ b/Project.toml @@ -64,6 +64,7 @@ Requires = "1.0" RuntimeGeneratedFunctions = "0.5.12" SciMLBase = "< 2.57.2" Setfield = "1" +# StructuralIdentifiability = "0.5.8" SymbolicUtils = "2.1.2, 3.3.0" Symbolics = "5.30.1, 6" Unitful = "1.12.4" From f6f19c5aa90785ff143f83bd94b8f30ececeaa96 Mon Sep 17 00:00:00 2001 From: vyudu Date: Wed, 20 Nov 2024 15:38:40 -0500 Subject: [PATCH 3/5] up --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 80d6627337..8b357fd258 100644 --- a/Project.toml +++ b/Project.toml @@ -96,4 +96,4 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [targets] -test = ["DiffEqCallbacks", "DomainSets", "Graphviz_jll", "Logging", "NonlinearSolve", "OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqTsit5", "OrdinaryDiffEqVerner", "Pkg", "Plots", "Random", "SafeTestsets", "SciMLBase", "SciMLNLSolve", "StableRNGs", "StaticArrays", "Statistics", "SteadyStateDiffEq", "StochasticDiffEq", "Test", "Unitful"] +test = ["DiffEqCallbacks", "DomainSets", "Graphviz_jll", "Logging", "NonlinearSolve", "OrdinaryDiffEqBDF", "OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqTsit5", "OrdinaryDiffEqVerner", "Pkg", "Plots", "Random", "SafeTestsets", "SciMLBase", "SciMLNLSolve", "StableRNGs", "StaticArrays", "Statistics", "SteadyStateDiffEq", "StochasticDiffEq", "Test", "Unitful"] From 926626cb892bcc150a6c57d08908ce2b9170d7f4 Mon Sep 17 00:00:00 2001 From: vyudu Date: Wed, 20 Nov 2024 17:11:19 -0500 Subject: [PATCH 4/5] add default --- test/extensions/lattice_simulation_plotting.jl | 4 ++-- test/network_analysis/conservation_laws.jl | 8 ++++---- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/test/extensions/lattice_simulation_plotting.jl b/test/extensions/lattice_simulation_plotting.jl index f9cc29d179..808acc877f 100644 --- a/test/extensions/lattice_simulation_plotting.jl +++ b/test/extensions/lattice_simulation_plotting.jl @@ -1,7 +1,7 @@ ### Preparations ### # Fetch packages. -using Catalyst, CairoMakie, GraphMakie, Graphs, JumpProcesses, OrdinaryDiffEq, Test +using Catalyst, CairoMakie, GraphMakie, Graphs, JumpProcesses, OrdinaryDiffEqDefault, OrdinaryDiffEq, Test ### Checks Basic Plot Cases ### @@ -91,7 +91,7 @@ let lattice = CartesianGrid((2,2,2)) lrs = LatticeReactionSystem(rs, [diffusion_rx], lattice) oprob = ODEProblem(lrs, [:X => 1.0], 1.0, [:d => 1.0, :D => 0.2]) - osol = solve(oprob, Tsit5()) + osol = solve(oprob) @test_throws ArgumentError lattice_plot(osol, :X, lrs) @test_throws ArgumentError lattice_animation(osol, :X, lrs, "animation_tmp.mp4") diff --git a/test/network_analysis/conservation_laws.jl b/test/network_analysis/conservation_laws.jl index 5ae268a021..31736d8fa2 100644 --- a/test/network_analysis/conservation_laws.jl +++ b/test/network_analysis/conservation_laws.jl @@ -1,7 +1,7 @@ ### Prepares Tests ### # Fetch packages. -using Catalyst, JumpProcesses, LinearAlgebra, NonlinearSolve, OrdinaryDiffEqTsit5, SteadyStateDiffEq, StochasticDiffEq, Test +using Catalyst, JumpProcesses, LinearAlgebra, NonlinearSolve, OrdinaryDiffEqTsit5, OrdinaryDiffEqDefault, OrdinaryDiffEqVerner, SteadyStateDiffEq, StochasticDiffEq, Test # Sets stable rng number. using StableRNGs @@ -192,7 +192,7 @@ let oprob1 = ODEProblem(rn, u0_1, 10.0, ps; remove_conserved = true, remove_conserved_warn) oprob2 = ODEProblem(rn, u0_2, 10.0, ps; remove_conserved = true, remove_conserved_warn) oprob3 = ODEProblem(rn, u0_3, 10.0, ps; remove_conserved = true, remove_conserved_warn) - @test solve(oprob1, Tsit5())[sps] ≈ solve(oprob2, Tsit5())[sps] ≈ solve(oprob3, Tsit5())[sps] + @test solve(oprob1)[sps] ≈ solve(oprob2)[sps] ≈ solve(oprob3)[sps] end # Tests conservation laws in SDE simulation. @@ -224,8 +224,8 @@ let oprob2 = ODEProblem(osys, u0, 10.0, ps_2) # Checks that the solutions generates the correct conserved quantities. - sol1 = solve(oprob1, Tsit5(); saveat = 1.0) - sol2 = solve(oprob2, Tsit5(); saveat = 1.0) + sol1 = solve(oprob1; saveat = 1.0) + sol2 = solve(oprob2; saveat = 1.0) @test all(sol1[osys.X1 + osys.X2] .== 2.0) @test all(sol2[osys.X1 + osys.X2] .== 4.0) end From 68c368f1fe745c97a23d22e629ecc3bdcd7b7f15 Mon Sep 17 00:00:00 2001 From: vyudu Date: Wed, 20 Nov 2024 17:13:20 -0500 Subject: [PATCH 5/5] up --- Project.toml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 8b357fd258..57ef384930 100644 --- a/Project.toml +++ b/Project.toml @@ -78,6 +78,7 @@ LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" Logging = "56ddb016-857b-54e1-b83d-db4d58db5568" NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" OrdinaryDiffEqBDF = "6ad6398a-0878-4a85-9266-38940aa047c8" +OrdinaryDiffEqDefault = "50262376-6c5a-4cf5-baba-aaf4f84d72d7" OrdinaryDiffEqRosenbrock = "43230ef6-c299-4910-a778-202eb28ce4ce" OrdinaryDiffEqTsit5 = "b1df2697-797e-41e3-8120-5422d3b24e4a" OrdinaryDiffEqVerner = "79d7bb75-1356-48c1-b8c0-6832512096c2" @@ -96,4 +97,4 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [targets] -test = ["DiffEqCallbacks", "DomainSets", "Graphviz_jll", "Logging", "NonlinearSolve", "OrdinaryDiffEqBDF", "OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqTsit5", "OrdinaryDiffEqVerner", "Pkg", "Plots", "Random", "SafeTestsets", "SciMLBase", "SciMLNLSolve", "StableRNGs", "StaticArrays", "Statistics", "SteadyStateDiffEq", "StochasticDiffEq", "Test", "Unitful"] +test = ["DiffEqCallbacks", "DomainSets", "Graphviz_jll", "Logging", "NonlinearSolve", "OrdinaryDiffEqBDF", "OrdinaryDiffEqDefault", "OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqTsit5", "OrdinaryDiffEqVerner", "Pkg", "Plots", "Random", "SafeTestsets", "SciMLBase", "SciMLNLSolve", "StableRNGs", "StaticArrays", "Statistics", "SteadyStateDiffEq", "StochasticDiffEq", "Test", "Unitful"]