Merge pull request #755 from AayushSabharwal/as/format

refactor: format

ext/SciMLBaseZygoteExt.jl

@@ -174,15 +174,16 @@ end
     VA[sym], ODESolution_getindex_pullback
 end
 
-@adjoint function ODESolution{T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13
-, T14, T15}(u,
+@adjoint function ODESolution{
+        T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15}(u,
         args...) where {T1, T2, T3, T4, T5, T6, T7, T8,
         T9, T10, T11, T12, T13, T14, T15}
     function ODESolutionAdjoint(ȳ)
         (ȳ, ntuple(_ -> nothing, length(args))...)
     end
 
-    ODESolution{T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15}(u, args...),
+    ODESolution{T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15}(
+        u, args...),
     ODESolutionAdjoint
 end
 

src/clock.jl

@@ -88,7 +88,7 @@ Base.getindex(c::TimeDomain, idx) = IndexedClock(c, idx)
 
 function canonicalize_indexed_clock(ic::IndexedClock, sol::AbstractTimeseriesSolution)
     c = ic.clock
-    
+
     return @match c begin
         PeriodicClock(dt, _...) => ceil(sol.prob.tspan[1] / dt) * dt .+ (ic.idx .- 1) .* dt
         &SolverStepClock => begin

src/ensemble/ensemble_solutions.jl

@@ -211,11 +211,13 @@ end
     end
 end
 
-Base.@propagate_inbounds function Base.getindex(x::AbstractEnsembleSolution, s::Integer, i::Integer)
+Base.@propagate_inbounds function Base.getindex(
+        x::AbstractEnsembleSolution, s::Integer, i::Integer)
     return x.u[s].u[i]
 end
 
-Base.@propagate_inbounds function Base.getindex(x::AbstractEnsembleSolution, s::Integer, i2::Integer, i3::Integer, idxs::Integer...)
+Base.@propagate_inbounds function Base.getindex(
+        x::AbstractEnsembleSolution, s::Integer, i2::Integer, i3::Integer, idxs::Integer...)
     return x.u[s][i2, i3, idxs...]
 end
 

src/problems/linear_problems.jl

@@ -75,4 +75,4 @@ function LinearProblem(A, b, args...; kwargs...)
     else
         LinearProblem{isinplace(A, 4)}(A, b, args...; kwargs...)
     end
-end
+end

src/remake.jl

@@ -476,7 +476,7 @@ anydict(d) = Dict{Any, Any}(d)
 anydict() = Dict{Any, Any}()
 
 function _updated_u0_p_internal(
-    prob, ::Missing, ::Missing; interpret_symbolicmap = true, use_defaults = false)
+        prob, ::Missing, ::Missing; interpret_symbolicmap = true, use_defaults = false)
     return state_values(prob), parameter_values(prob)
 end
 function _updated_u0_p_internal(

src/scimlfunctions.jl

@@ -2615,7 +2615,8 @@ end
         typeof(cache), typeof(analytic), typeof(tgrad), typeof(jac), typeof(jvp),
         typeof(vjp), typeof(jac_prototype), typeof(sparsity),
         typeof(Wfact), typeof(Wfact_t), typeof(paramjac), typeof(observed), typeof(colorvec),
-        typeof(sys), typeof(initializeprob), typeof(initializeprobmap)}(f1, f2, mass_matrix, 
+        typeof(sys), typeof(initializeprob), typeof(initializeprobmap)}(
+        f1, f2, mass_matrix,
         cache, analytic, tgrad, jac, jvp, vjp,
         jac_prototype, sparsity, Wfact, Wfact_t, paramjac, observed, colorvec, sys,
         initializeprob, initializeprobmap)
@@ -2649,7 +2650,7 @@ function SplitFunction{iip, specialize}(f1, f2;
         sys = __has_sys(f1) ? f1.sys : nothing,
         initializeprob = __has_initializeprob(f1) ? f1.initializeprob : nothing,
         initializeprobmap = __has_initializeprobmap(f1) ? f1.initializeprobmap : nothing
-        ) where {iip,
+) where {iip,
         specialize
 }
     sys = sys_or_symbolcache(sys, syms, paramsyms, indepsym)

src/solutions/ode_solutions.jl

@@ -275,7 +275,8 @@ function (sol::AbstractODESolution)(t::Number, ::Type{deriv}, idxs,
         ps = parameter_values(discs)
         for ts_idx in eachindex(discs)
             partition = discs[ts_idx]
-            interp_val = ConstantInterpolation(partition.t, partition.u)(t, nothing, deriv, nothing, continuity)
+            interp_val = ConstantInterpolation(partition.t, partition.u)(
+                t, nothing, deriv, nothing, continuity)
             ps = with_updated_parameter_timeseries_values(sol, ps, ts_idx => interp_val)
         end
     end
@@ -296,7 +297,8 @@ function (sol::AbstractODESolution)(t::Number, ::Type{deriv}, idxs::AbstractVect
         ps = parameter_values(discs)
         for ts_idx in eachindex(discs)
             partition = discs[ts_idx]
-            interp_val = ConstantInterpolation(partition.t, partition.u)(t, nothing, deriv, nothing, continuity)
+            interp_val = ConstantInterpolation(partition.t, partition.u)(
+                t, nothing, deriv, nothing, continuity)
             ps = with_updated_parameter_timeseries_values(sol, ps, ts_idx => interp_val)
         end
     end
@@ -374,7 +376,9 @@ function get_saveable_values(sys, ps, timeseries_idx)
 end
 
 function save_discretes!(integ::DEIntegrator, timeseries_idx)
-    save_discretes!(integ.sol, current_time(integ), get_saveable_values(integ, parameter_values(integ), timeseries_idx), timeseries_idx)
+    save_discretes!(integ.sol, current_time(integ),
+        get_saveable_values(integ, parameter_values(integ), timeseries_idx),
+        timeseries_idx)
 end
 
 save_discretes!(args...) = nothing
@@ -555,7 +559,8 @@ end
 
 mask_discretes(::Nothing, _, _...) = nothing
 
-function mask_discretes(discretes::ParameterTimeseriesCollection, new_t, ::Union{Int, CartesianIndex})
+function mask_discretes(
+        discretes::ParameterTimeseriesCollection, new_t, ::Union{Int, CartesianIndex})
     masked_discretes = map(discretes) do disc
         i = searchsortedlast(disc.t, new_t)
         disc[i:i]

src/solutions/solution_interface.jl

@@ -149,9 +149,9 @@ DEFAULT_PLOT_FUNC(x, y, z) = (x, y, z) # For v0.5.2 bug
 
 function isdenseplot(sol)
     (sol.dense || sol.prob isa AbstractDiscreteProblem) &&
-    !(sol isa AbstractRODESolution) &&
-    !(hasfield(typeof(sol), :interp) &&
-    sol.interp isa SensitivityInterpolation)
+        !(sol isa AbstractRODESolution) &&
+        !(hasfield(typeof(sol), :interp) &&
+          sol.interp isa SensitivityInterpolation)
 end
 
 @recipe function f(sol::AbstractTimeseriesSolution;
@@ -187,7 +187,8 @@ end
     disc_vars = Tuple[]
     cont_vars = Tuple[]
     for var in vars
-        tsidxs = union(get_all_timeseries_indexes(sol, var[2]), get_all_timeseries_indexes(sol, var[3]))
+        tsidxs = union(get_all_timeseries_indexes(sol, var[2]),
+            get_all_timeseries_indexes(sol, var[3]))
         if ContinuousTimeseries() in tsidxs
             push!(cont_vars, var)
         else
@@ -209,7 +210,6 @@ end
             plot_vecs, labels = diffeq_to_arrays(sol, plot_analytic, denseplot,
                 plotdensity, tspan, vars, tscale, plotat)
 
-
             # Special case labels when idxs = (:x,:y,:z) or (:x) or [:x,:y] ...
             if idxs isa Tuple && vars[1][1] === DEFAULT_PLOT_FUNC
                 val = hasname(vars[1][2]) ? String(getname(vars[1][2])) : vars[1][2]
@@ -311,12 +311,12 @@ end
             seriestype := :line
             linestyle --> :dash
             markershape --> :o
-            markersize --> repeat([2, 0], length(ts)-1)
-            markeralpha --> repeat([1, 0], length(ts)-1)
+            markersize --> repeat([2, 0], length(ts) - 1)
+            markeralpha --> repeat([1, 0], length(ts) - 1)
             label --> string(hasname(yvar) ? getname(yvar) : yvar)
 
-            x = vec([xvals[1:end-1]'; xvals[2:end]'])
-            y = repeat(yvals, inner=2)[1:end-1]
+            x = vec([xvals[1:(end - 1)]'; xvals[2:end]'])
+            y = repeat(yvals, inner = 2)[1:(end - 1)]
             x, y
         end
     end

test/downstream/comprehensive_indexing.jl

@@ -556,7 +556,8 @@ end
             newx = []
             for i in eachindex(x)
                 if x[i] isa Symbol
-                    push!(newx, allsyms[findfirst(y -> hasname(y) && x[i] == getname(y), allsyms)])
+                    push!(newx,
+                        allsyms[findfirst(y -> hasname(y) && x[i] == getname(y), allsyms)])
                 else
                     push!(newx, x[i])
                 end
@@ -590,7 +591,8 @@ end
             newx = []
             for i in eachindex(x)
                 if x[i] isa Symbol
-                    push!(newx, allsyms[findfirst(y -> hasname(y) && x[i] == getname(y), allsyms)])
+                    push!(newx,
+                        allsyms[findfirst(y -> hasname(y) && x[i] == getname(y), allsyms)])
                 else
                     push!(newx, x[i])
                 end
@@ -896,9 +898,11 @@ end
             @test_nowarn plot(sol; idxs = idx)
             @test_nowarn plot(sol; idxs = [idx])
         end
-        for idx in Iterators.flatten((Iterators.product(all_idxs, all_idxs), Iterators.product(sym_idxs, sym_idxs)))
+        for idx in Iterators.flatten((
+            Iterators.product(all_idxs, all_idxs), Iterators.product(sym_idxs, sym_idxs)))
             @test_nowarn plot(sol; idxs = collect(idx))
-            if !(idx[1] isa Tuple || idx[2] isa Tuple || length(get_all_timeseries_indexes(sol, collect(idx))) > 1)
+            if !(idx[1] isa Tuple || idx[2] isa Tuple ||
+                 length(get_all_timeseries_indexes(sol, collect(idx))) > 1)
                 @test_nowarn plot(sol; idxs = idx)
             end
         end

test/downstream/solution_interface.jl

@@ -156,14 +156,15 @@ sol10 = sol(0.1, idxs = 2)
 
     plotfn(t, u) = (t, 2u)
     all_idxs = [x, x + p * y, t, (plotfn, 0, 1), (plotfn, t, 1), (plotfn, 0, x),
-                (plotfn, t, x), (plotfn, t, p * y)]
+        (plotfn, t, x), (plotfn, t, p * y)]
     sym_idxs = [:x, :t, (plotfn, :t, 1), (plotfn, 0, :x),
-                (plotfn, :t, :x)]
+        (plotfn, :t, :x)]
     for idx in Iterators.flatten((all_idxs, sym_idxs))
         @test_nowarn plot(sol; idxs = idx)
         @test_nowarn plot(sol; idxs = [idx])
     end
-    for idx in Iterators.flatten((Iterators.product(all_idxs, all_idxs), Iterators.product(sym_idxs, sym_idxs)))
+    for idx in Iterators.flatten((
+        Iterators.product(all_idxs, all_idxs), Iterators.product(sym_idxs, sym_idxs)))
         @test_nowarn plot(sol; idxs = collect(idx))
         if !(idx[1] isa Tuple || idx[2] isa Tuple)
             @test_nowarn plot(sol; idxs = idx)

test/serialization_tests.jl

@@ -3,11 +3,11 @@ using Serialization
 using Test
 
 for clock in [
-        SciMLBase.Clock(0.5),
-        SciMLBase.Clock(0.5; phase = 0.1),
-        SciMLBase.SolverStepClock,
-        SciMLBase.Continuous,
-    ]
+    SciMLBase.Clock(0.5),
+    SciMLBase.Clock(0.5; phase = 0.1),
+    SciMLBase.SolverStepClock,
+    SciMLBase.Continuous
+]
     serialize("_tmp.jls", clock)
     newclock = deserialize("_tmp.jls")
     @test newclock == clock