Merge branch 'master' into dsl-no-infer-docs

vyudu · vyudu · commit 625a2d5f5ac8 · 2024-11-21T14:21:38.000-05:00
diff --git a/Project.toml b/Project.toml
@@ -77,7 +77,11 @@ 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"
+OrdinaryDiffEqDefault = "50262376-6c5a-4cf5-baba-aaf4f84d72d7"
+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 +97,4 @@ 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", "OrdinaryDiffEqBDF", "OrdinaryDiffEqDefault", "OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqTsit5", "OrdinaryDiffEqVerner", "Pkg", "Plots", "Random", "SafeTestsets", "SciMLBase", "SciMLNLSolve", "StableRNGs", "StaticArrays", "Statistics", "SteadyStateDiffEq", "StochasticDiffEq", "Test", "Unitful"]
diff --git a/docs/src/model_creation/dsl_advanced.md b/docs/src/model_creation/dsl_advanced.md
@@ -273,7 +273,7 @@ plot(sol)
 ```
 
 ### [Turning off species, parameter, and variable inferring](@id dsl_advanced_options_require_dec)
-In some cases it may be desirable for Catalyst to not infer species and parameters from the DSL, as in the case of reaction networks with very many variables, or as a sanity check that variable names are written correctly. To turn off inferring, simply add the `@require_declaration` macro to one of the lines of the `@reaction_network` declaration. Having this macro means that every single variable, species, or parameter will have to be explicitly declared using the `@variable`, `@species`, or `@parameter` macro. In the case that the DSL parser encounters an undeclared symbolic in this case, it will error with an `UndeclaredSymbolicError` and print the reaction or equation that the undeclared symbolic was found in. 
+In some cases it may be desirable for Catalyst to not infer species and parameters from the DSL, as in the case of reaction networks with very many variables, or as a sanity check that variable names are written correctly. To turn off inferring, simply add the `@require_declaration` macro to one of the lines of the `@reaction_network` declaration. Having this macro means that every single variable, species, or parameter will have to be explicitly declared using the `@variable`, `@species`, or `@parameter` macro. In the case that the DSL parser encounters an undeclared symbolic, it will error with an `UndeclaredSymbolicError` and print the reaction or equation that the undeclared symbolic was found in. 
 
 ```@example dsl_advanced_no_infer
 using Catalyst
diff --git 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
+end
diff --git 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
@@ -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 ###
@@ -130,4 +130,4 @@ let
         @test isfile("animation_tmp.mp4")
         rm("animation_tmp.mp4")
     end
-end
+end
diff --git 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
+end
diff --git 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
+end
diff --git 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, OrdinaryDiffEqDefault, OrdinaryDiffEqVerner, SteadyStateDiffEq, StochasticDiffEq, Test
 
 # Sets stable rng number.
 using StableRNGs
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
+end
diff --git 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
+end
diff --git 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
+end
diff --git 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
@@ -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
+end
diff --git 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
+end
diff --git 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
+end
diff --git 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
+end
diff --git 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
@@ -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
@@ -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
@@ -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.
