Merge pull request #375 from SciML/ap/format

Run Formatter

Author: avik-pal

docs/make.jl

@@ -1,6 +1,6 @@
 using Documenter, DocumenterCitations
 using NonlinearSolve,
-    SimpleNonlinearSolve, Sundials, SteadyStateDiffEq, SciMLBase, DiffEqBase
+      SimpleNonlinearSolve, Sundials, SteadyStateDiffEq, SciMLBase, DiffEqBase
 
 cp(joinpath(@__DIR__, "Manifest.toml"), joinpath(@__DIR__, "src/assets/Manifest.toml"),
     force = true)

docs/pages.jl

@@ -43,5 +43,5 @@ pages = [
         "devdocs/operators.md",
         "devdocs/algorithm_helpers.md"],
     "Release Notes" => "release_notes.md",
-    "References" => "references.md",
+    "References" => "references.md"
 ]

docs/src/basics/faq.md

@@ -15,15 +15,19 @@ myfun(x, lv) = x * sin(x) - lv
 
 function f(out, levels, u0)
     for i in 1:N
-        out[i] = solve(IntervalNonlinearProblem{false}(IntervalNonlinearFunction{false}(myfun),
-                u0, levels[i]), Falsi()).u
+        out[i] = solve(
+            IntervalNonlinearProblem{false}(IntervalNonlinearFunction{false}(myfun),
+                u0, levels[i]),
+            Falsi()).u
     end
 end
 
 function f2(out, levels, u0)
     for i in 1:N
-        out[i] = solve(NonlinearProblem{false}(NonlinearFunction{false}(myfun),
-                u0, levels[i]), SimpleNewtonRaphson()).u
+        out[i] = solve(
+            NonlinearProblem{false}(NonlinearFunction{false}(myfun),
+                u0, levels[i]),
+            SimpleNewtonRaphson()).u
     end
 end
 

docs/src/basics/sparsity_detection.md

@@ -22,10 +22,12 @@ NonlinearSolve will automatically perform matrix coloring and use sparse differe
 Now you can help the solver further by providing the color vector. This can be done by
 
 ```julia
-prob = NonlinearProblem(NonlinearFunction(nlfunc; sparsity = jac_prototype,
+prob = NonlinearProblem(
+    NonlinearFunction(nlfunc; sparsity = jac_prototype,
         colorvec = colorvec), x0)
 # OR
-prob = NonlinearProblem(NonlinearFunction(nlfunc; jac_prototype = jac_prototype,
+prob = NonlinearProblem(
+    NonlinearFunction(nlfunc; jac_prototype = jac_prototype,
         colorvec = colorvec), x0)
 ```
 
@@ -47,7 +49,8 @@ algorithm you want to use, then you can create your problem as follows:
 prob = NonlinearProblem(NonlinearFunction(nlfunc; sparsity = SymbolicsSparsityDetection()),
     x0)  # Remember to have Symbolics.jl loaded
 # OR
-prob = NonlinearProblem(NonlinearFunction(nlfunc; sparsity = ApproximateJacobianSparsity()),
+prob = NonlinearProblem(
+    NonlinearFunction(nlfunc; sparsity = ApproximateJacobianSparsity()),
     x0)
 ```
 

docs/src/tutorials/large_systems.md

@@ -308,10 +308,14 @@ for the exact sparsity detection case, we left out the time it takes to perform
 sparsity detection. Let's compare the two by setting the sparsity detection algorithms.
 
 ```@example ill_conditioned_nlprob
-prob_brusselator_2d_exact = NonlinearProblem(NonlinearFunction(brusselator_2d_loop;
-        sparsity = SymbolicsSparsityDetection()), u0, p; abstol = 1e-10, reltol = 1e-10)
-prob_brusselator_2d_approx = NonlinearProblem(NonlinearFunction(brusselator_2d_loop;
-        sparsity = ApproximateJacobianSparsity()), u0, p; abstol = 1e-10, reltol = 1e-10)
+prob_brusselator_2d_exact = NonlinearProblem(
+    NonlinearFunction(brusselator_2d_loop;
+        sparsity = SymbolicsSparsityDetection()),
+    u0, p; abstol = 1e-10, reltol = 1e-10)
+prob_brusselator_2d_approx = NonlinearProblem(
+    NonlinearFunction(brusselator_2d_loop;
+        sparsity = ApproximateJacobianSparsity()),
+    u0, p; abstol = 1e-10, reltol = 1e-10)
 
 @btime solve(prob_brusselator_2d_exact, NewtonRaphson());
 @btime solve(prob_brusselator_2d_approx, NewtonRaphson());

docs/src/tutorials/modelingtoolkit.md

@@ -22,8 +22,8 @@ u0 = [x => 1.0,
     z => 0.0]
 
 ps = [σ => 10.0
-    ρ => 26.0
-    β => 8 / 3]
+      ρ => 26.0
+      β => 8 / 3]
 
 prob = NonlinearProblem(ns, u0, ps)
 sol = solve(prob, NewtonRaphson())
@@ -65,7 +65,7 @@ eqs = [
     0 ~ u2 - cos(u1),
     0 ~ u3 - hypot(u1, u2),
     0 ~ u4 - hypot(u2, u3),
-    0 ~ u5 - hypot(u4, u1),
+    0 ~ u5 - hypot(u4, u1)
 ]
 @named sys = NonlinearSystem(eqs, [u1, u2, u3, u4, u5], [])
 ```

ext/NonlinearSolveMINPACKExt.jl

@@ -4,7 +4,8 @@ using MINPACK, NonlinearSolve, SciMLBase
 import FastClosures: @closure
 
 function SciMLBase.__solve(prob::Union{NonlinearLeastSquaresProblem,
-            NonlinearProblem}, alg::CMINPACK, args...; abstol = nothing, maxiters = 1000,
+            NonlinearProblem},
+        alg::CMINPACK, args...; abstol = nothing, maxiters = 1000,
         alias_u0::Bool = false, show_trace::Val{ShT} = Val(false),
         store_trace::Val{StT} = Val(false), termination_condition = nothing,
         kwargs...) where {ShT, StT}

src/NonlinearSolve.jl

@@ -9,21 +9,22 @@ import PrecompileTools: @recompile_invalidations, @compile_workload, @setup_work
 
 @recompile_invalidations begin
     using ADTypes, ConcreteStructs, DiffEqBase, FastBroadcast, FastClosures, LazyArrays,
-        LineSearches, LinearAlgebra, LinearSolve, MaybeInplace, Preferences, Printf,
-        SciMLBase, SimpleNonlinearSolve, SparseArrays, SparseDiffTools
+          LineSearches, LinearAlgebra, LinearSolve, MaybeInplace, Preferences, Printf,
+          SciMLBase, SimpleNonlinearSolve, SparseArrays, SparseDiffTools
 
     import ArrayInterface: undefmatrix, can_setindex, restructure, fast_scalar_indexing
     import DiffEqBase: AbstractNonlinearTerminationMode,
-        AbstractSafeNonlinearTerminationMode, AbstractSafeBestNonlinearTerminationMode,
-        NonlinearSafeTerminationReturnCode, get_termination_mode
+                       AbstractSafeNonlinearTerminationMode,
+                       AbstractSafeBestNonlinearTerminationMode,
+                       NonlinearSafeTerminationReturnCode, get_termination_mode
     import FiniteDiff
     import ForwardDiff
     import ForwardDiff: Dual
     import LinearSolve: ComposePreconditioner, InvPreconditioner, needs_concrete_A
     import RecursiveArrayTools: recursivecopy!, recursivefill!
 
     import SciMLBase: AbstractNonlinearAlgorithm, JacobianWrapper, AbstractNonlinearProblem,
-        AbstractSciMLOperator, NLStats, _unwrap_val, has_jac, isinplace
+                      AbstractSciMLOperator, NLStats, _unwrap_val, has_jac, isinplace
     import SparseDiffTools: AbstractSparsityDetection, AutoSparseEnzyme
     import StaticArraysCore: StaticArray, SVector, SArray, MArray, Size, SMatrix, MMatrix
 end
@@ -95,20 +96,28 @@ include("default.jl")
     probs_nlls = NonlinearLeastSquaresProblem[]
     nlfuncs = ((NonlinearFunction{false}((u, p) -> (u .^ 2 .- p)[1:1]), [0.1, 0.0]),
         (NonlinearFunction{false}((u, p) -> vcat(u .* u .- p, u .* u .- p)), [0.1, 0.1]),
-        (NonlinearFunction{true}((du, u, p) -> du[1] = u[1] * u[1] - p,
-                resid_prototype = zeros(1)), [0.1, 0.0]),
-        (NonlinearFunction{true}((du, u, p) -> du .= vcat(u .* u .- p, u .* u .- p),
-                resid_prototype = zeros(4)), [0.1, 0.1]))
+        (
+            NonlinearFunction{true}((du, u, p) -> du[1] = u[1] * u[1] - p,
+                resid_prototype = zeros(1)),
+            [0.1, 0.0]),
+        (
+            NonlinearFunction{true}((du, u, p) -> du .= vcat(u .* u .- p, u .* u .- p),
+                resid_prototype = zeros(4)),
+            [0.1, 0.1]))
     for (fn, u0) in nlfuncs
         push!(probs_nlls, NonlinearLeastSquaresProblem(fn, u0, 2.0))
     end
     nlfuncs = ((NonlinearFunction{false}((u, p) -> (u .^ 2 .- p)[1:1]), Float32[0.1, 0.0]),
         (NonlinearFunction{false}((u, p) -> vcat(u .* u .- p, u .* u .- p)),
             Float32[0.1, 0.1]),
-        (NonlinearFunction{true}((du, u, p) -> du[1] = u[1] * u[1] - p,
-                resid_prototype = zeros(Float32, 1)), Float32[0.1, 0.0]),
-        (NonlinearFunction{true}((du, u, p) -> du .= vcat(u .* u .- p, u .* u .- p),
-                resid_prototype = zeros(Float32, 4)), Float32[0.1, 0.1]))
+        (
+            NonlinearFunction{true}((du, u, p) -> du[1] = u[1] * u[1] - p,
+                resid_prototype = zeros(Float32, 1)),
+            Float32[0.1, 0.0]),
+        (
+            NonlinearFunction{true}((du, u, p) -> du .= vcat(u .* u .- p, u .* u .- p),
+                resid_prototype = zeros(Float32, 4)),
+            Float32[0.1, 0.1]))
     for (fn, u0) in nlfuncs
         push!(probs_nlls, NonlinearLeastSquaresProblem(fn, u0, 2.0f0))
     end
@@ -132,18 +141,18 @@ end
 export NewtonRaphson, PseudoTransient, Klement, Broyden, LimitedMemoryBroyden, DFSane
 export GaussNewton, LevenbergMarquardt, TrustRegion
 export NonlinearSolvePolyAlgorithm,
-    RobustMultiNewton, FastShortcutNonlinearPolyalg, FastShortcutNLLSPolyalg
+       RobustMultiNewton, FastShortcutNonlinearPolyalg, FastShortcutNLLSPolyalg
 
 # Extension Algorithms
 export LeastSquaresOptimJL, FastLevenbergMarquardtJL, CMINPACK, NLsolveJL,
-    FixedPointAccelerationJL, SpeedMappingJL, SIAMFANLEquationsJL
+       FixedPointAccelerationJL, SpeedMappingJL, SIAMFANLEquationsJL
 
 # Advanced Algorithms -- Without Bells and Whistles
 export GeneralizedFirstOrderAlgorithm, ApproximateJacobianSolveAlgorithm, GeneralizedDFSane
 
 # Descent Algorithms
 export NewtonDescent, SteepestDescent, Dogleg, DampedNewtonDescent,
-    GeodesicAcceleration
+       GeodesicAcceleration
 
 # Globalization
 ## Line Search Algorithms
@@ -153,9 +162,9 @@ export RadiusUpdateSchemes
 
 # Export the termination conditions from DiffEqBase
 export SteadyStateDiffEqTerminationMode, SimpleNonlinearSolveTerminationMode,
-    NormTerminationMode, RelTerminationMode, RelNormTerminationMode, AbsTerminationMode,
-    AbsNormTerminationMode, RelSafeTerminationMode, AbsSafeTerminationMode,
-    RelSafeBestTerminationMode, AbsSafeBestTerminationMode
+       NormTerminationMode, RelTerminationMode, RelNormTerminationMode, AbsTerminationMode,
+       AbsNormTerminationMode, RelSafeTerminationMode, AbsSafeTerminationMode,
+       RelSafeBestTerminationMode, AbsSafeBestTerminationMode
 
 # Tracing Functionality
 export TraceAll, TraceMinimal, TraceWithJacobianConditionNumber

src/abstract_types.jl

@@ -16,7 +16,8 @@ squares solver.
 ### `__internal_init` specification
 
 ```julia
-__internal_init(prob::NonlinearProblem{uType, iip}, alg::AbstractDescentAlgorithm, J, fu, u;
+__internal_init(
+    prob::NonlinearProblem{uType, iip}, alg::AbstractDescentAlgorithm, J, fu, u;
     pre_inverted::Val{INV} = Val(false), linsolve_kwargs = (;), abstol = nothing,
     reltol = nothing, alias_J::Bool = true, shared::Val{N} = Val(1),
     kwargs...) where {INV, N, uType, iip} --> AbstractDescentCache
@@ -232,7 +233,8 @@ Abstract Type for Damping Functions in DampedNewton.
 ### `__internal_init` specification
 
 ```julia
-__internal_init(prob::AbstractNonlinearProblem, f::AbstractDampingFunction, initial_damping,
+__internal_init(
+    prob::AbstractNonlinearProblem, f::AbstractDampingFunction, initial_damping,
     J, fu, u, args...; internal_norm = DEFAULT_NORM,
     kwargs...) --> AbstractDampingFunctionCache
 ```

src/algorithms/broyden.jl

@@ -28,7 +28,8 @@ search.
         useful for specific problems, but whether it will work may depend strongly on the
         problem
 """
-function Broyden(; max_resets = 100, linesearch = NoLineSearch(), reset_tolerance = nothing,
+function Broyden(;
+        max_resets = 100, linesearch = NoLineSearch(), reset_tolerance = nothing,
         init_jacobian::Val{IJ} = Val(:identity), autodiff = nothing, alpha = nothing,
         update_rule::Val{UR} = Val(:good_broyden)) where {IJ, UR}
     if IJ === :identity