Skip to content

Commit

Permalink
Merge pull request #1128 from vyudu/drop-ordinarydiffeq
Browse files Browse the repository at this point in the history
Drop OrdinaryDiffEq from tests
  • Loading branch information
isaacsas authored Nov 20, 2024
2 parents ef6ef28 + 68c368f commit 28d1cc7
Show file tree
Hide file tree
Showing 23 changed files with 39 additions and 38 deletions.
11 changes: 6 additions & 5 deletions Project.toml
Original file line number Diff line number Diff line change
Expand Up @@ -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"
Expand All @@ -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"]
Original file line number Diff line number Diff line change
Expand Up @@ -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.
Expand Down Expand Up @@ -543,4 +543,4 @@ let
@test length(unknowns(sys3)) == 4
@test length(parameters(sys4)) == 5
@test any(isequal(p5), parameters(sys4))
end
end
2 changes: 1 addition & 1 deletion test/dsl/dsl_options.jl
Original file line number Diff line number Diff line change
Expand Up @@ -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.
Expand Down
4 changes: 2 additions & 2 deletions test/extensions/lattice_simulation_plotting.jl
Original file line number Diff line number Diff line change
@@ -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 ###
Expand Down Expand Up @@ -130,4 +130,4 @@ let
@test isfile("animation_tmp.mp4")
rm("animation_tmp.mp4")
end
end
end
4 changes: 2 additions & 2 deletions test/extensions/stability_computation.jl
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
### Fetch Packages ###

# Fetch packages.
using Catalyst, OrdinaryDiffEq, SteadyStateDiffEq, Test
using Catalyst, OrdinaryDiffEqVerner, SteadyStateDiffEq, Test
import HomotopyContinuation

# Sets rnd number.
Expand Down Expand Up @@ -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
4 changes: 2 additions & 2 deletions test/miscellaneous_tests/api.jl
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down Expand Up @@ -505,4 +505,4 @@ let
f(d,t), X --> 0
end
@test !isautonomous(rn8)
end
end
2 changes: 1 addition & 1 deletion test/network_analysis/conservation_laws.jl
Original file line number Diff line number Diff line change
@@ -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
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
### Preparations ###

# Fetch packages.
using OrdinaryDiffEq
using OrdinaryDiffEqTsit5
using Random, Statistics, SparseArrays, Test

# Fetch test networks.
Expand Down
2 changes: 1 addition & 1 deletion test/reactionsystem_core/coupled_equation_crn_systems.jl
Original file line number Diff line number Diff line change
@@ -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

Expand Down
2 changes: 1 addition & 1 deletion test/reactionsystem_core/events.jl
Original file line number Diff line number Diff line change
@@ -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
Expand Down
2 changes: 1 addition & 1 deletion test/reactionsystem_core/parameter_type_designation.jl
Original file line number Diff line number Diff line change
@@ -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.
Expand Down
4 changes: 2 additions & 2 deletions test/reactionsystem_core/reactionsystem.jl
Original file line number Diff line number Diff line change
@@ -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.
Expand Down Expand Up @@ -1021,4 +1021,4 @@ let
jprob = JumpProblem(jinput; rng)
sol = solve(jprob)
@test sol(10.0; idxs = :A) > 0
end
end
4 changes: 2 additions & 2 deletions test/reactionsystem_core/symbolic_stoichiometry.jl
Original file line number Diff line number Diff line change
@@ -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.
Expand Down Expand Up @@ -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
4 changes: 2 additions & 2 deletions test/simulation_and_solving/simulate_ODEs.jl
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
### Prepares Tests ###

# Fetch packages.
using Catalyst, OrdinaryDiffEq, Test
using Catalyst, OrdinaryDiffEqVerner, OrdinaryDiffEqRosenbrock, Test

# Sets stable rng number.
using StableRNGs
Expand Down Expand Up @@ -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
2 changes: 1 addition & 1 deletion test/simulation_and_solving/simulate_jumps.jl
Original file line number Diff line number Diff line change
@@ -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
Expand Down
4 changes: 2 additions & 2 deletions test/simulation_and_solving/solve_nonlinear.jl
Original file line number Diff line number Diff line change
@@ -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.
Expand Down Expand Up @@ -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
4 changes: 2 additions & 2 deletions test/spatial_modelling/lattice_reaction_systems.jl
Original file line number Diff line number Diff line change
@@ -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")
Expand Down Expand Up @@ -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
4 changes: 2 additions & 2 deletions test/spatial_modelling/lattice_reaction_systems_ODEs.jl
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
### Preparations ###

# Fetch packages.
using OrdinaryDiffEq
using OrdinaryDiffEqTsit5, OrdinaryDiffEqRosenbrock, OrdinaryDiffEqBDF
using Random, Statistics, SparseArrays, Test

# Fetch test networks.
Expand Down Expand Up @@ -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
Original file line number Diff line number Diff line change
@@ -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")
Expand Down Expand Up @@ -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
Original file line number Diff line number Diff line change
@@ -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")
Expand Down
2 changes: 1 addition & 1 deletion test/spatial_modelling/simulate_PDEs.jl
Original file line number Diff line number Diff line change
@@ -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

Expand Down
2 changes: 1 addition & 1 deletion test/upstream/mtk_problem_inputs.jl
Original file line number Diff line number Diff line change
Expand Up @@ -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.
Expand Down
2 changes: 1 addition & 1 deletion test/upstream/mtk_structure_indexing.jl
Original file line number Diff line number Diff line change
@@ -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.
Expand Down

0 comments on commit 28d1cc7

Please sign in to comment.