Merge pull request #1226 from SciML/project.toml_housekeeping

Project.toml housekeeping

Author: TorkelE

Project.toml

@@ -91,15 +91,12 @@ Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
-SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
-SciMLNLSolve = "e9a6253c-8580-4d32-9898-8661bb511710"
 StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 SteadyStateDiffEq = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f"
 StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
 [targets]
-test = ["DataInterpolations", "DiffEqCallbacks", "DomainSets", "Logging", "NonlinearSolve", "OrdinaryDiffEqBDF", "OrdinaryDiffEqDefault", "OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqTsit5", "OrdinaryDiffEqVerner", "Pkg", "Plots", "Random", "SafeTestsets", "SciMLBase", "SciMLNLSolve", "StableRNGs", "StaticArrays", "Statistics", "SteadyStateDiffEq", "StochasticDiffEq", "Test", "Unitful"]
+test = ["DataInterpolations", "DiffEqCallbacks", "DomainSets", "Logging", "NonlinearSolve", "OrdinaryDiffEqBDF", "OrdinaryDiffEqDefault", "OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqTsit5", "OrdinaryDiffEqVerner", "Pkg", "Plots", "Random", "SafeTestsets", "StableRNGs", "StaticArrays", "Statistics", "SteadyStateDiffEq", "StochasticDiffEq", "Test"]

test/compositional_modelling/component_based_model_creation.jl

@@ -3,7 +3,7 @@
 ### Prepares Tests ###
 
 # Fetch packages.
-using Catalyst, LinearAlgebra, OrdinaryDiffEqTsit5, SciMLNLSolve, Test
+using Catalyst, LinearAlgebra, OrdinaryDiffEqTsit5, NonlinearSolve, Test
 using ModelingToolkit: nameof, getname
 
 # Sets the default `t` to use.
@@ -103,7 +103,7 @@ let
     sys2 = structural_simplify(nlrepressilator)
     @test length(equations(sys2)) <= 6
     nlprob = NonlinearProblem(sys2, u₀_nl, pvals)
-    sol = solve(nlprob, NLSolveJL(), abstol = 1e-9)
+    sol = solve(nlprob; abstol = 1e-9)
     @test sol[sys₁.P] ≈ sol[sys₂.P] ≈ sol[sys₃.P]
     @test sol[sys₁.m] ≈ sol[sys₂.m] atol=1e-7
     @test sol[sys₁.m] ≈ sol[sys₃.m] atol=1e-7
@@ -116,7 +116,7 @@ let
     sys2 = structural_simplify(nlrepressilator)
     @test length(equations(sys2)) <= 6
     nlprob = NonlinearProblem(sys2, u₀_nl, pvals)
-    sol = solve(nlprob, NLSolveJL(), abstol = 1e-9)
+    sol = solve(nlprob; abstol = 1e-9)
     @test sol[sys₁.P] ≈ sol[sys₂.P] ≈ sol[sys₃.P]
     @test sol[sys₁.m] ≈ sol[sys₂.m] atol=1e-7
     @test sol[sys₁.m] ≈ sol[sys₃.m] atol=1e-7
@@ -134,7 +134,7 @@ let
     sys2 = structural_simplify(nlrepressilator)
     @test length(equations(sys2)) <= 6
     nlprob = NonlinearProblem(sys2, u₀_nl, pvals)
-    sol = solve(nlprob, NLSolveJL(), abstol = 1e-9)
+    sol = solve(nlprob; abstol = 1e-9)
     @test sol[sys₁.P] ≈ sol[sys₂.P] ≈ sol[sys₃.P]
     @test sol[sys₁.m] ≈ sol[sys₂.m] atol=1e-7
     @test sol[sys₁.m] ≈ sol[sys₃.m] atol=1e-7
@@ -253,7 +253,7 @@ let
     sys2 = structural_simplify(nlrepressilator)
     @test length(equations(sys2)) <= 6
     nlprob = NonlinearProblem(sys2, u₀_nl, pvals)
-    sol = solve(nlprob, NLSolveJL(), abstol = 1e-9)
+    sol = solve(nlprob; abstol = 1e-9)
     @test sol[sys₁.P] ≈ sol[sys₂.P] ≈ sol[sys₃.P]
     @test sol[sys₁.m] ≈ sol[sys₂.m] atol=1e-7
     @test sol[sys₁.m] ≈ sol[sys₃.m] atol=1e-7
@@ -503,7 +503,7 @@ end
 let
     t = default_t()
     D = default_time_deriv()
-    @species x1(t) x2(t) 
+    @species x1(t) x2(t)
     @variables x3(t) x4(t) x5(t)
     x2 = ParentScope(x2)
     x3 = ParentScope(ParentScope(x3))
@@ -514,7 +514,7 @@ let
     p3 = ParentScope(ParentScope(p3))
     p4 = DelayParentScope(p4)
     p5 = GlobalScope(p5)
-    rxs = [Reaction(p1, nothing, [x1]), Reaction(p2, [x2], nothing), 
+    rxs = [Reaction(p1, nothing, [x1]), Reaction(p2, [x2], nothing),
            D(x3) ~ p3, D(x4) ~ p4, D(x5) ~ p5]
     @named sys1 = ReactionSystem(rxs, t)
     @test isequal(x1, only(unknowns(sys1)))