Fix formatting issues

Author: Fengyu Zhang

docs/make.jl

@@ -13,7 +13,7 @@ makedocs(sitename = "SciMLBase.jl",
     format = Documenter.HTML(assets = ["assets/favicon.ico"],
         canonical = "https://docs.sciml.ai/SciMLBase/stable"),
     linkcheck_ignore = [
-    "https://www.sciencedirect.com/science/article/abs/pii/S0045782523007156"
+        "https://www.sciencedirect.com/science/article/abs/pii/S0045782523007156"
     ],
     pages = pages)
 

docs/src/interfaces/Ensembles.md

@@ -476,7 +476,7 @@ compute covariance matrices similarly:
 
 ```@example ensemble4
 timeseries_steps_meancov(sim) # Use the time steps, assume fixed dt
-timeseries_point_meancov(sim, 0:(1 // 2^(3)):1, 0:(1 // 2^(3)):1) # Use time points, interpolate
+timeseries_point_meancov(sim, 0:(1 // 2 ^ (3)):1, 0:(1 // 2 ^ (3)):1) # Use time points, interpolate
 ```
 
 For general analysis, we can build a `EnsembleSummary` type.

ext/SciMLBaseChainRulesCoreExt.jl

@@ -16,7 +16,8 @@ function ChainRulesCore.rrule(
         j::Integer)
     function ODESolution_getindex_pullback(Δ)
         i = symbolic_type(sym) != NotSymbolic() ? variable_index(VA, sym) : sym
-        du, dprob = if i === nothing
+        du,
+        dprob = if i === nothing
             getter = getobserved(VA)
             grz = rrule_via_ad(config, getter, sym, VA.u[j], VA.prob.p, VA.t[j])[2](Δ)
             du = [k == j ? grz[3] : zero(VA.u[1]) for k in 1:length(VA.u)]
@@ -83,7 +84,8 @@ function ChainRulesCore.rrule(
         (NoTangent(), ȳ, ntuple(_ -> NoTangent(), length(args))...)
     end
 
-    ODESolution{T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15, T16}(u, args...),
+    ODESolution{T1, T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12, T13, T14, T15, T16}(
+        u, args...),
     ODESolutionAdjoint
 end
 
@@ -99,7 +101,7 @@ function ChainRulesCore.rrule(
     end
 
     RODESolution{T1, T2, T3, T4, T5, T6, T7, T8, T9, T10,
-    T11, T12, T13, T14}(u, args...),
+        T11, T12, T13, T14}(u, args...),
     RODESolutionAdjoint
 end
 

ext/SciMLBaseMakieExt.jl

@@ -105,7 +105,8 @@ function Makie.convert_arguments(PT::Type{<:Plot},
     @assert tscale isa Symbol "`tscale` if passed in to `Makie.plot` must be a Symbol, got a $(typeof(tscale))"
 
     # Convert the solution to arrays - this is the hard part!
-    plot_vecs, labels = SciMLBase.diffeq_to_arrays(sol, plot_analytic, denseplot,
+    plot_vecs,
+    labels = SciMLBase.diffeq_to_arrays(sol, plot_analytic, denseplot,
         plotdensity, tspan, vars, tscale, plotat)
 
     # We must convert from plot Type to symbol here, for plotspec use

src/SciMLBase.jl

@@ -108,7 +108,8 @@ abstract type AbstractNonlinearProblem{uType, isinplace} <: AbstractDEProblem en
 abstract type AbstractIntervalNonlinearProblem{uType, isinplace} <:
               AbstractNonlinearProblem{uType,
     isinplace} end
-const AbstractSteadyStateProblem{uType, isinplace} = AbstractNonlinearProblem{uType,
+const AbstractSteadyStateProblem{
+    uType, isinplace} = AbstractNonlinearProblem{uType,
     isinplace}
 
 """
@@ -373,7 +374,6 @@ abstract type AbstractDiscretization <: AbstractSciMLAlgorithm end
 # Discretization metadata
 """
 $(TYPEDEF)
-
 """
 abstract type AbstractDiscretizationMetadata{hasTime} end
 
@@ -566,7 +566,10 @@ abstract type AbstractPDENoTimeSolution{T, N, S, D} <:
 """
 $(TYPEDEF)
 """
-const AbstractPDESolution{T, N, S, D} = Union{AbstractPDETimeSeriesSolution{T, N, S, D},
+const AbstractPDESolution{T,
+    N,
+    S,
+    D} = Union{AbstractPDETimeSeriesSolution{T, N, S, D},
     AbstractPDENoTimeSolution{T, N, S, D}}
 
 """
@@ -628,8 +631,8 @@ abstract type ADOriginator end
 """
 $(TYPEDEF)
 
-Used to specify which variables can be aliased in a solve. 
-Every concrete AbstractAliasSpecifier should have at least the fields `alias_p` and `alias_f`. 
+Used to specify which variables can be aliased in a solve.
+Every concrete AbstractAliasSpecifier should have at least the fields `alias_p` and `alias_f`.
 """
 abstract type AbstractAliasSpecifier end
 

src/callbacks.jl

@@ -378,16 +378,15 @@ is constructed by passing the constructor `ContinuousCallback`, `DiscreteCallbac
 You can pass as many callbacks as you like. When the solvers encounter multiple
 callbacks, the following rules apply:
 
-* `ContinuousCallback`s and `VectorContinuousCallback`s are applied before `DiscreteCallback`s. (This is because
-  they often implement event-finding that will backtrack the timestep to smaller
-  than `dt`).
-* For `ContinuousCallback`s and `VectorContinuousCallback`s, the event times are found by rootfinding and only
-  the first `ContinuousCallback` or `VectorContinuousCallback` affect is applied.
-* The `DiscreteCallback`s are then applied in order. Note that the ordering only
-  matters for the conditions: if a previous callback modifies `u` in such a way
-  that the next callback no longer evaluates condition to `true`, its `affect`
-  will not be applied.
-
+  - `ContinuousCallback`s and `VectorContinuousCallback`s are applied before `DiscreteCallback`s. (This is because
+    they often implement event-finding that will backtrack the timestep to smaller
+    than `dt`).
+  - For `ContinuousCallback`s and `VectorContinuousCallback`s, the event times are found by rootfinding and only
+    the first `ContinuousCallback` or `VectorContinuousCallback` affect is applied.
+  - The `DiscreteCallback`s are then applied in order. Note that the ordering only
+    matters for the conditions: if a previous callback modifies `u` in such a way
+    that the next callback no longer evaluates condition to `true`, its `affect`
+    will not be applied.
 """
 struct CallbackSet{T1 <: Tuple, T2 <: Tuple} <: DECallback
     continuous_callbacks::T1

src/ensemble/basic_ensemble_solve.jl

@@ -138,8 +138,10 @@ tighten_container_eltype(u) = u
 function __solve(prob::EnsembleProblem{<:AbstractVector{<:AbstractSciMLProblem}},
         alg::Union{AbstractDEAlgorithm, Nothing},
         ensemblealg::BasicEnsembleAlgorithm; kwargs...)
-    Base.depwarn("This dispatch is deprecated for the standard ensemble syntax. See the Parallel
-    Ensembles Simulations Interface page for more details", :EnsembleProblemSolve)
+    Base.depwarn(
+        "This dispatch is deprecated for the standard ensemble syntax. See the Parallel
+Ensembles Simulations Interface page for more details",
+        :EnsembleProblemSolve)
     invoke(__solve, Tuple{AbstractEnsembleProblem, typeof(alg), typeof(ensemblealg)},
         prob, alg, ensemblealg; trajectories = length(prob.prob), kwargs...)
 end

src/ensemble/ensemble_problems.jl

@@ -102,6 +102,7 @@ Defines a structure to manage an ensemble (batch) of problems.
 Each field controls how the ensemble behaves during simulation.
 
 ## Arguments
+
     - `prob`: The original base problem to replicate or modify.
     - `prob_func`: A function that defines how to generate each subproblem.
     - `output_func`: A function to post-process each individual simulation result.
@@ -144,11 +145,14 @@ $(TYPEDEF)
 Constructor for deprecated usage where a vector of problems is passed directly.
 
 !!! warning
+
     This constructor is deprecated. Use the standard ensemble syntax with `prob_func` instead.
 """
 function EnsembleProblem(prob::AbstractVector{<:AbstractSciMLProblem}; kwargs...)
-    Base.depwarn("This dispatch is deprecated for the standard ensemble syntax. See the Parallel \
-    Ensembles Simulations Interface page for more details", :EnsembleProblem)
+    Base.depwarn(
+        "This dispatch is deprecated for the standard ensemble syntax. See the Parallel \
+Ensembles Simulations Interface page for more details",
+        :EnsembleProblem)
     invoke(EnsembleProblem,
         Tuple{Any},
         prob;
@@ -163,12 +167,12 @@ Main constructor for `EnsembleProblem`.
 
 ## Keyword Arguments
 
-- `prob`: The base problem.
-- `prob_func`: Function to modify the base problem per trajectory.
-- `output_func`: Function to extract output from a solution.
-- `reduction`: Function to aggregate results.
-- `u_init`: Initial value for aggregation.
-- `safetycopy`: Whether to deepcopy the problem before modifying.
+  - `prob`: The base problem.
+  - `prob_func`: Function to modify the base problem per trajectory.
+  - `output_func`: Function to extract output from a solution.
+  - `reduction`: Function to aggregate results.
+  - `u_init`: Initial value for aggregation.
+  - `safetycopy`: Whether to deepcopy the problem before modifying.
 """
 function EnsembleProblem(prob;
         prob_func = DEFAULT_PROB_FUNC,
@@ -203,12 +207,15 @@ $(TYPEDEF)
 Constructor that is used for NOnlinearProblem.
 
 !!! warning
+
     This dispatch is deprecated. See the Parallel Ensembles Simulations Interface page.
 """
 function SciMLBase.EnsembleProblem(
         prob::AbstractSciMLProblem, u0s::Vector{Vector{T}}; kwargs...) where {T}
-    Base.depwarn("This dispatch is deprecated for the standard ensemble syntax. See the Parallel \
-    Ensembles Simulations Interface page for more details", :EnsembleProblem)
+    Base.depwarn(
+        "This dispatch is deprecated for the standard ensemble syntax. See the Parallel \
+Ensembles Simulations Interface page for more details",
+        :EnsembleProblem)
     prob_func = (prob, i, repeat = nothing) -> remake(prob, u0 = u0s[i])
     return SciMLBase.EnsembleProblem(prob; prob_func, kwargs...)
 end
@@ -220,8 +227,8 @@ Defines a weighted version of an `EnsembleProblem`, where different simulations
 
 ## Arguments
 
-- `ensembleprob`: The base ensemble problem.
-- `weights`: A vector of weights corresponding to each simulation.
+  - `ensembleprob`: The base ensemble problem.
+  - `weights`: A vector of weights corresponding to each simulation.
 """
 struct WeightedEnsembleProblem{T1 <: AbstractEnsembleProblem, T2 <: AbstractVector} <:
        AbstractEnsembleProblem
@@ -251,7 +258,6 @@ end
 $(TYPEDEF)
 
 Constructor for `WeightedEnsembleProblem`. Ensures weights sum to 1 and matches problem count.
-
 """
 function WeightedEnsembleProblem(args...; weights, kwargs...)
     # TODO: allow skipping checks?
@@ -260,4 +266,3 @@ function WeightedEnsembleProblem(args...; weights, kwargs...)
     @assert length(ep.prob) == length(weights)
     WeightedEnsembleProblem(ep, weights)
 end
-

src/initialization.jl

@@ -164,9 +164,10 @@ the `u0` and `p` as-is, and is always successful if it returns. Valid only for
 `AbstractDEProblem` and `AbstractDAEProblem`. Requires a `DEIntegrator` as its second argument.
 
 Keyword arguments:
-- `abstol`: The absolute value below which the norm of the residual of algebraic equations
-  should lie. The norm function used is `integrator.opts.internalnorm` if present, and
-  `LinearAlgebra.norm` if not.
+
+  - `abstol`: The absolute value below which the norm of the residual of algebraic equations
+    should lie. The norm function used is `integrator.opts.internalnorm` if present, and
+    `LinearAlgebra.norm` if not.
 """
 function get_initial_values(
         prob::AbstractDEProblem, integrator::DEIntegrator, f, alg::CheckInit,
@@ -219,12 +220,13 @@ If the field is absent or the value is `nothing`, return `u0` and `p` successful
 The success value returned depends on the success of the nonlinear solve.
 
 Keyword arguments:
-- `nlsolve_alg`: The NonlinearSolve.jl algorithm to use. If not provided, this function will
-  throw an error.
-- `abstol`, `reltol`: The `abstol` (`reltol`) to use for the nonlinear solve. The value
-  provided to the `OverrideInit` constructor takes priority over this keyword argument.
-  If the former is `nothing`, this keyword argument will be used. If it is also not provided,
-  an error will be thrown.
+
+  - `nlsolve_alg`: The NonlinearSolve.jl algorithm to use. If not provided, this function will
+    throw an error.
+  - `abstol`, `reltol`: The `abstol` (`reltol`) to use for the nonlinear solve. The value
+    provided to the `OverrideInit` constructor takes priority over this keyword argument.
+    If the former is `nothing`, this keyword argument will be used. If it is also not provided,
+    an error will be thrown.
 
 All additional keyword arguments are forwarded to `solve`.
 

src/remake.jl

@@ -1120,7 +1120,8 @@ function updated_u0_p(
         return (u0 === missing ? state_values(prob) : u0),
         (p === missing ? parameter_values(prob) : p)
     end
-    newu0, newp = _updated_u0_p_internal(
+    newu0,
+    newp = _updated_u0_p_internal(
         prob, u0, p, t0; interpret_symbolicmap, use_defaults)
     return late_binding_update_u0_p(prob, u0, p, t0, newu0, newp)
 end
@@ -1164,7 +1165,8 @@ function maybe_eager_initialize_problem(prob::AbstractSciMLProblem, initializati
     end
     if initialization_data !== nothing && !lazy_initialization &&
        (!is_time_dependent(prob) || current_time(prob) !== nothing)
-        u0, p, _ = get_initial_values(
+        u0, p,
+        _ = get_initial_values(
             prob, prob, prob.f, OverrideInit(), Val(isinplace(prob)))
         if u0 !== nothing && eltype(u0) == Any && isempty(u0)
             u0 = nothing