Merge pull request #167 from LilithHafner/lh/format

Run JuliaFormatter.format()

benchmark/simple_pendulum.jl

@@ -43,32 +43,42 @@ function create_simple_pendulum_benchmark()
     suite["OOP"] = oop_suite
 
     if @isdefined(MultipleShooting)
-        iip_suite["MultipleShooting(100, Tsit5; grid_coarsening = true)"] = @benchmarkable solve($SimplePendulumBenchmark.prob_iip,
+        iip_suite["MultipleShooting(100, Tsit5; grid_coarsening = true)"] = @benchmarkable solve(
+            $SimplePendulumBenchmark.prob_iip,
             $MultipleShooting(100, Tsit5()))
-        iip_suite["MultipleShooting(100, Tsit5; grid_coarsening = false)"] = @benchmarkable solve($SimplePendulumBenchmark.prob_iip,
+        iip_suite["MultipleShooting(100, Tsit5; grid_coarsening = false)"] = @benchmarkable solve(
+            $SimplePendulumBenchmark.prob_iip,
             $MultipleShooting(100, Tsit5(); grid_coarsening = false))
-        iip_suite["MultipleShooting(10, Tsit5; grid_coarsening = true)"] = @benchmarkable solve($SimplePendulumBenchmark.prob_iip,
+        iip_suite["MultipleShooting(10, Tsit5; grid_coarsening = true)"] = @benchmarkable solve(
+            $SimplePendulumBenchmark.prob_iip,
             $MultipleShooting(10, Tsit5()))
-        iip_suite["MultipleShooting(10, Tsit5; grid_coarsening = false)"] = @benchmarkable solve($SimplePendulumBenchmark.prob_iip,
+        iip_suite["MultipleShooting(10, Tsit5; grid_coarsening = false)"] = @benchmarkable solve(
+            $SimplePendulumBenchmark.prob_iip,
             $MultipleShooting(10, Tsit5(); grid_coarsening = false))
     end
     if @isdefined(Shooting)
-        iip_suite["Shooting(Tsit5())"] = @benchmarkable solve($SimplePendulumBenchmark.prob_iip,
+        iip_suite["Shooting(Tsit5())"] = @benchmarkable solve(
+            $SimplePendulumBenchmark.prob_iip,
             $Shooting(Tsit5()))
     end
 
     if @isdefined(MultipleShooting)
-        oop_suite["MultipleShooting(100, Tsit5; grid_coarsening = true)"] = @benchmarkable solve($SimplePendulumBenchmark.prob_oop,
+        oop_suite["MultipleShooting(100, Tsit5; grid_coarsening = true)"] = @benchmarkable solve(
+            $SimplePendulumBenchmark.prob_oop,
             $MultipleShooting(100, Tsit5()))
-        oop_suite["MultipleShooting(100, Tsit5; grid_coarsening = false)"] = @benchmarkable solve($SimplePendulumBenchmark.prob_oop,
+        oop_suite["MultipleShooting(100, Tsit5; grid_coarsening = false)"] = @benchmarkable solve(
+            $SimplePendulumBenchmark.prob_oop,
             $MultipleShooting(100, Tsit5(); grid_coarsening = false))
-        oop_suite["MultipleShooting(10, Tsit5; grid_coarsening = true)"] = @benchmarkable solve($SimplePendulumBenchmark.prob_oop,
+        oop_suite["MultipleShooting(10, Tsit5; grid_coarsening = true)"] = @benchmarkable solve(
+            $SimplePendulumBenchmark.prob_oop,
             $MultipleShooting(10, Tsit5()))
-        oop_suite["MultipleShooting(10, Tsit5; grid_coarsening = false)"] = @benchmarkable solve($SimplePendulumBenchmark.prob_oop,
+        oop_suite["MultipleShooting(10, Tsit5; grid_coarsening = false)"] = @benchmarkable solve(
+            $SimplePendulumBenchmark.prob_oop,
             $MultipleShooting(10, Tsit5(); grid_coarsening = false))
     end
     if @isdefined(Shooting)
-        oop_suite["Shooting(Tsit5())"] = @benchmarkable solve($SimplePendulumBenchmark.prob_oop,
+        oop_suite["Shooting(Tsit5())"] = @benchmarkable solve(
+            $SimplePendulumBenchmark.prob_oop,
             $Shooting(Tsit5()))
     end
 

ext/BoundaryValueDiffEqODEInterfaceExt.jl

@@ -3,15 +3,18 @@ module BoundaryValueDiffEqODEInterfaceExt
 using SciMLBase, BoundaryValueDiffEq, ODEInterface
 import SciMLBase: __solve
 import ODEInterface: OptionsODE, OPT_ATOL, OPT_RTOL, OPT_METHODCHOICE, OPT_DIAGNOSTICOUTPUT,
-    OPT_ERRORCONTROL, OPT_SINGULARTERM, OPT_MAXSTEPS, OPT_BVPCLASS, OPT_SOLMETHOD,
-    OPT_RHS_CALLMODE, OPT_COLLOCATIONPTS, OPT_MAXSUBINTERVALS, RHS_CALL_INSITU, evalSolution
+                     OPT_ERRORCONTROL, OPT_SINGULARTERM, OPT_MAXSTEPS, OPT_BVPCLASS,
+                     OPT_SOLMETHOD,
+                     OPT_RHS_CALLMODE, OPT_COLLOCATIONPTS, OPT_MAXSUBINTERVALS,
+                     RHS_CALL_INSITU, evalSolution
 import ODEInterface: Bvpm2, bvpm2_init, bvpm2_solve, bvpm2_destroy, bvpm2_get_x
 import ODEInterface: bvpsol
 import ODEInterface: colnew
 
 import ForwardDiff
 
-function _test_bvpm2_bvpsol_colnew_problem_criteria(_, ::SciMLBase.StandardBVProblem, alg::Symbol)
+function _test_bvpm2_bvpsol_colnew_problem_criteria(
+        _, ::SciMLBase.StandardBVProblem, alg::Symbol)
     throw(ArgumentError("$(alg) does not support standard BVProblem. Only TwoPointBVProblem is supported."))
 end
 function _test_bvpm2_bvpsol_colnew_problem_criteria(prob, ::TwoPointBVProblem, alg::Symbol)
@@ -54,7 +57,8 @@ function SciMLBase.__solve(prob::BVProblem, alg::BVPM2; dt = 0.0, reltol = 1e-3,
 
     sol, retcode, stats = bvpm2_solve(initial_guess, bvp2m_f, bvp2m_bc, opt)
     retcode = retcode ≥ 0 ? ReturnCode.Success : ReturnCode.Failure
-    destats = SciMLBase.DEStats(stats["no_rhs_calls"], 0, 0, 0, stats["no_jac_calls"], 0, 0, 0, 0, 0, 0)
+    destats = SciMLBase.DEStats(
+        stats["no_rhs_calls"], 0, 0, 0, stats["no_jac_calls"], 0, 0, 0, 0, 0, 0)
 
     x_mesh = bvpm2_get_x(sol)
     evalsol = evalSolution(sol, x_mesh)
@@ -72,7 +76,7 @@ end
 #-------
 function SciMLBase.__solve(prob::BVProblem, alg::BVPSOL; maxiters = 1000, reltol = 1e-3,
         dt = 0.0, verbose = true, kwargs...)
-        _test_bvpm2_bvpsol_colnew_problem_criteria(prob, prob.problem_type, :BVPSOL)
+    _test_bvpm2_bvpsol_colnew_problem_criteria(prob, prob.problem_type, :BVPSOL)
     @assert isa(prob.p, SciMLBase.NullParameters) "BVPSOL only supports NullParameters!"
     @assert isa(prob.u0, AbstractVector{<:AbstractArray}) "BVPSOL requires a vector of initial guesses!"
     n, u0 = (length(prob.u0) - 1), reduce(hcat, prob.u0)
@@ -125,7 +129,8 @@ end
 #-------
 # COLNEW
 #-------
-function SciMLBase.__solve(prob::BVProblem, alg::COLNEW; maxiters = 1000, reltol=1e-4, dt = 0.0, verbose = true, kwargs...)
+function SciMLBase.__solve(prob::BVProblem, alg::COLNEW; maxiters = 1000,
+        reltol = 1e-4, dt = 0.0, verbose = true, kwargs...)
     _test_bvpm2_bvpsol_colnew_problem_criteria(prob, prob.problem_type, :COLNEW)
     has_initial_guess = prob.u0 isa AbstractVector{<:AbstractArray}
     dt ≤ 0 && throw(ArgumentError("dt must be positive"))
@@ -136,18 +141,20 @@ function SciMLBase.__solve(prob::BVProblem, alg::COLNEW; maxiters = 1000, reltol
     end
     T = eltype(u0)
     mesh = collect(range(prob.tspan[1], stop = prob.tspan[2], length = n + 1))
-    opt = OptionsODE(OPT_BVPCLASS => alg.bvpclass, OPT_COLLOCATIONPTS => alg.collocationpts,
+    opt = OptionsODE(
+        OPT_BVPCLASS => alg.bvpclass, OPT_COLLOCATIONPTS => alg.collocationpts,
         OPT_MAXSTEPS => maxiters, OPT_DIAGNOSTICOUTPUT => alg.diagnostic_output,
-        OPT_MAXSUBINTERVALS => alg.max_num_subintervals,  OPT_RTOL => reltol)
+        OPT_MAXSUBINTERVALS => alg.max_num_subintervals, OPT_RTOL => reltol)
     orders = ones(Int, no_odes)
     _tspan = [prob.tspan[1], prob.tspan[2]]
     iip = SciMLBase.isinplace(prob)
 
-    rhs(t, u, du) = if iip
-        prob.f(du, u, prob.p, t)
-    else
-        (du .= prob.f(u, prob.p, t))
-    end
+    rhs(t, u, du) =
+        if iip
+            prob.f(du, u, prob.p, t)
+        else
+            (du .= prob.f(u, prob.p, t))
+        end
 
     if prob.f.jac === nothing
         if iip
@@ -169,38 +176,38 @@ function SciMLBase.__solve(prob::BVProblem, alg::COLNEW; maxiters = 1000, reltol
     end
     Drhs(t, u, df) = jac(df, u, prob.p, t)
 
-
     #TODO: Fix bc and bcjac for multi-points BVP
 
     n_bc_a = length(first(prob.f.bcresid_prototype.x))
     n_bc_b = length(last(prob.f.bcresid_prototype.x))
     zeta = vcat(fill(first(prob.tspan), n_bc_a), fill(last(prob.tspan), n_bc_b))
     bc = function (i, z, resid)
-        tmpa = copy(z); tmpb = copy(z)
+        tmpa = copy(z)
+        tmpb = copy(z)
         tmp_resid_a = zeros(T, n_bc_a)
         tmp_resid_b = zeros(T, n_bc_b)
         prob.f.bc[1](tmp_resid_a, tmpa, prob.p)
         prob.f.bc[2](tmp_resid_b, tmpb, prob.p)
 
-        for j=1:n_bc_a
+        for j in 1:n_bc_a
             if i == j
                 resid[1] = tmp_resid_a[j]
             end
         end
-        for j=1:n_bc_b
+        for j in 1:n_bc_b
             if i == (j + n_bc_a)
                 resid[1] = tmp_resid_b[j]
             end
         end
     end
 
     Dbc = function (i, z, dbc)
-        for j=1:n_bc_a
+        for j in 1:n_bc_a
             if i == j
                 dbc[i] = 1.0
             end
         end
-        for j=1:n_bc_b
+        for j in 1:n_bc_b
             if i == (j + n_bc_a)
                 dbc[i] = 1.0
             end
@@ -222,7 +229,8 @@ function SciMLBase.__solve(prob::BVProblem, alg::COLNEW; maxiters = 1000, reltol
     end
 
     evalsol = evalSolution(sol, mesh)
-    destats = SciMLBase.DEStats(stats["no_rhs_calls"], 0, 0, 0, stats["no_jac_calls"], 0, 0, 0, 0, 0, 0)
+    destats = SciMLBase.DEStats(
+        stats["no_rhs_calls"], 0, 0, 0, stats["no_jac_calls"], 0, 0, 0, 0, 0, 0)
 
     return DiffEqBase.build_solution(prob, alg, mesh,
         collect(Vector{eltype(evalsol)}, eachrow(evalsol));

ext/BoundaryValueDiffEqOrdinaryDiffEqExt.jl

@@ -38,7 +38,7 @@ end
         BVProblem(f1!, bc1!, u0, tspan),
         BVProblem(f1, bc1, u0, tspan),
         TwoPointBVProblem(f1!, (bc1_a!, bc1_b!), u0, tspan; bcresid_prototype),
-        TwoPointBVProblem(f1, (bc1_a, bc1_b), u0, tspan; bcresid_prototype),
+        TwoPointBVProblem(f1, (bc1_a, bc1_b), u0, tspan; bcresid_prototype)
     ]
 
     algs = []
@@ -101,7 +101,7 @@ end
         TwoPointBVProblem(f1_nlls!, (bc1_nlls_a!, bc1_nlls_b!), u0, tspan;
             bcresid_prototype = bcresid_prototype2),
         TwoPointBVProblem(f1_nlls, (bc1_nlls_a, bc1_nlls_b), u0, tspan;
-            bcresid_prototype = bcresid_prototype2),
+            bcresid_prototype = bcresid_prototype2)
     ]
 
     algs = []
@@ -112,7 +112,7 @@ end
                 Shooting(Tsit5(); nlsolve = LevenbergMarquardt(),
                     jac_alg = BVPJacobianAlgorithm(AutoForwardDiff(; chunksize = 2))),
                 Shooting(Tsit5(); nlsolve = GaussNewton(),
-                    jac_alg = BVPJacobianAlgorithm(AutoForwardDiff(; chunksize = 2))),
+                    jac_alg = BVPJacobianAlgorithm(AutoForwardDiff(; chunksize = 2)))
             ])
     end
 
@@ -129,7 +129,7 @@ end
                     nlsolve = GaussNewton(; autodiff = AutoForwardDiff(chunksize = 2)),
                     jac_alg = BVPJacobianAlgorithm(;
                         bc_diffmode = AutoForwardDiff(; chunksize = 2),
-                        nonbc_diffmode = AutoSparseForwardDiff(; chunksize = 2))),
+                        nonbc_diffmode = AutoSparseForwardDiff(; chunksize = 2)))
             ])
     end
 

src/BoundaryValueDiffEq.jl

@@ -4,15 +4,16 @@ import PrecompileTools: @compile_workload, @setup_workload, @recompile_invalidat
 
 @recompile_invalidations begin
     using ADTypes, Adapt, DiffEqBase, ForwardDiff, LinearAlgebra, NonlinearSolve,
-        PreallocationTools, Preferences, RecursiveArrayTools, Reexport, SciMLBase, Setfield,
-        SparseDiffTools, Tricks
+          PreallocationTools, Preferences, RecursiveArrayTools, Reexport, SciMLBase,
+          Setfield,
+          SparseDiffTools, Tricks
 
     # Special Matrix Types
     using BandedMatrices, FastAlmostBandedMatrices, SparseArrays
 
     import ADTypes: AbstractADType
     import ArrayInterface: matrix_colors,
-        parameterless_type, undefmatrix, fast_scalar_indexing
+                           parameterless_type, undefmatrix, fast_scalar_indexing
     import ConcreteStructs: @concrete
     import DiffEqBase: solve
     import ForwardDiff: pickchunksize
@@ -74,7 +75,7 @@ end
         BVProblem(f1!, bc1!, u0, tspan),
         BVProblem(f1, bc1, u0, tspan),
         TwoPointBVProblem(f1!, (bc1_a!, bc1_b!), u0, tspan; bcresid_prototype),
-        TwoPointBVProblem(f1, (bc1_a, bc1_b), u0, tspan; bcresid_prototype),
+        TwoPointBVProblem(f1, (bc1_a, bc1_b), u0, tspan; bcresid_prototype)
     ]
 
     algs = []
@@ -129,7 +130,7 @@ end
         TwoPointBVProblem(f1_nlls!, (bc1_nlls_a!, bc1_nlls_b!), u0, tspan;
             bcresid_prototype = bcresid_prototype2),
         TwoPointBVProblem(f1_nlls, (bc1_nlls_a, bc1_nlls_b), u0, tspan;
-            bcresid_prototype = bcresid_prototype2),
+            bcresid_prototype = bcresid_prototype2)
     ]
 
     jac_alg = BVPJacobianAlgorithm(AutoForwardDiff(; chunksize = 2))
@@ -144,7 +145,7 @@ end
                 [
                     MIRK2(; jac_alg, nlsolve), MIRK3(; jac_alg, nlsolve),
                     MIRK4(; jac_alg, nlsolve), MIRK5(; jac_alg, nlsolve),
-                    MIRK6(; jac_alg, nlsolve),
+                    MIRK6(; jac_alg, nlsolve)
                 ])
         end
     end

src/algorithms.jl

@@ -55,9 +55,11 @@ function __propagate_nlsolve_ad_to_jac_alg(nlsolve::N) where {N}
     ad = hasfield(N, :ad) ? nlsolve.ad : nothing
     ad === nothing && return BVPJacobianAlgorithm()
 
-    Base.depwarn("Setting autodiff to the nonlinear solver in Shooting has been deprecated \
-                  and will have no effect from the next major release. Update to use \
-                  `BVPJacobianAlgorithm` directly", :Shooting)
+    Base.depwarn(
+        "Setting autodiff to the nonlinear solver in Shooting has been deprecated \
+         and will have no effect from the next major release. Update to use \
+         `BVPJacobianAlgorithm` directly",
+        :Shooting)
     return BVPJacobianAlgorithm(ad)
 end
 

src/mirk_tableaus.jl

@@ -31,7 +31,7 @@ function constructMIRK3(::Type{T}) where {T}
     v = [0, 4 // 9]
     b = [1 // 4, 3 // 4]
     x = [0 0
-        2//9 0]
+         2//9 0]
 
     # Interpolant tableau
     s_star = 3
@@ -52,8 +52,8 @@ function constructMIRK4(::Type{T}) where {T}
     v = [0, 1, 1 // 2, 27 // 32]
     b = [1 // 6, 1 // 6, 2 // 3, 0]
     x = [0 0 0 0
-        0 0 0 0
-        1//8 -1//8 0 0]
+         0 0 0 0
+         1//8 -1//8 0 0]
 
     # Interpolant tableau
     s_star = 4
@@ -74,16 +74,16 @@ function constructMIRK5(::Type{T}) where {T}
     v = [0, 1, 27 // 32, 837 // 1250]
     b = [5 // 54, 1 // 14, 32 // 81, 250 // 567]
     x = [0 0 0 0
-        0 0 0 0
-        3//64 -9//64 0 0
-        21//1000 63//5000 -252//625 0]
+         0 0 0 0
+         3//64 -9//64 0 0
+         21//1000 63//5000 -252//625 0]
 
     # Interpolant tableau
     s_star = 6
     c_star = [4 // 5, 13 // 23]
     v_star = [4 // 5, 13 // 23]
     x_star = [14//1125 -74//875 -128//3375 104//945 0 0
-        1//2 4508233//1958887 48720832//2518569 -27646420//17629983 -11517095//559682 0]
+              1//2 4508233//1958887 48720832//2518569 -27646420//17629983 -11517095//559682 0]
     τ_star = 0.3
 
     TU = MIRKTableau(s, T.(c), T.(v), T.(b), T.(x))
@@ -98,19 +98,19 @@ function constructMIRK6(::Type{T}) where {T}
     v = [0, 1, 5 // 32, 27 // 32, 1 // 2]
     b = [7 // 90, 7 // 90, 16 // 45, 16 // 45, 2 // 15, 0, 0, 0, 0]
     x = [0 0 0 0 0
-        0 0 0 0 0
-        9//64 -3//64 0 0 0
-        3//64 -9//64 0 0 0
-        -5//24 5//24 2//3 -2//3 0]
+         0 0 0 0 0
+         9//64 -3//64 0 0 0
+         3//64 -9//64 0 0 0
+         -5//24 5//24 2//3 -2//3 0]
 
     # Interpolant tableau
     s_star = 9
     c_star = [7 // 16, 3 // 8, 9 // 16, 1 // 8]
     v_star = [7 // 16, 3 // 8, 9 // 16, 1 // 8]
     x_star = [1547//32768 -1225//32768 749//4096 -287//2048 -861//16384 0 0 0 0
-        83//1536 -13//384 283//1536 -167//1536 -49//512 0 0 0 0
-        1225//32768 -1547//32768 287//2048 -749//4096 861//16384 0 0 0 0
-        233//3456 -19//1152 0 0 0 -5//72 7//72 -17//216 0]
+              83//1536 -13//384 283//1536 -167//1536 -49//512 0 0 0 0
+              1225//32768 -1547//32768 287//2048 -749//4096 861//16384 0 0 0 0
+              233//3456 -19//1152 0 0 0 -5//72 7//72 -17//216 0]
     τ_star = 0.7156
 
     TU = MIRKTableau(s, T.(c), T.(v), T.(b), T.(x))

src/solve/mirk.jl

@@ -224,7 +224,8 @@ function __mirk_loss!(resid, u, p, y, pt::StandardBVProblem, bc!::BC, residual,
     return nothing
 end
 
-function __mirk_loss!(resid, u, p, y, pt::TwoPointBVProblem, bc!::Tuple{BC1, BC2}, residual,
+function __mirk_loss!(
+        resid, u, p, y, pt::TwoPointBVProblem, bc!::Tuple{BC1, BC2}, residual,
         mesh, cache) where {BC1, BC2}
     y_ = recursive_unflatten!(y, u)
     resids = [get_tmp(r, u) for r in residual]
@@ -347,7 +348,8 @@ function __mirk_mpoint_jacobian!(J, _, x, bc_diffmode, nonbc_diffmode, bc_diffca
     return nothing
 end
 
-function __mirk_mpoint_jacobian!(J::AlmostBandedMatrix, J_c, x, bc_diffmode, nonbc_diffmode,
+function __mirk_mpoint_jacobian!(
+        J::AlmostBandedMatrix, J_c, x, bc_diffmode, nonbc_diffmode,
         bc_diffcache, nonbc_diffcache, loss_bc::BC, loss_collocation::C, resid_bc,
         resid_collocation, L::Int) where {BC, C}
     J_bc = fillpart(J)