Merge pull request #632 from ArnoStrouwen/formatter

reapply formatting

Author: ChrisRackauckas

.JuliaFormatter.toml

@@ -1 +1,3 @@
-style = "sciml"
+style = "sciml"
+format_markdown = true
+format_docstrings = true

README.md

@@ -6,7 +6,7 @@
 [![codecov](https://codecov.io/gh/SciML/SciMLBase.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/SciML/SciMLBase.jl)
 [![Build Status](https://github.com/SciML/SciMLBase.jl/workflows/CI/badge.svg)](https://github.com/SciML/SciMLBase.jl/actions?query=workflow%3ACI)
 
-[![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor's%20Guide-blueviolet)](https://github.com/SciML/ColPrac)
+[![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor%27s%20Guide-blueviolet)](https://github.com/SciML/ColPrac)
 [![SciML Code Style](https://img.shields.io/static/v1?label=code%20style&message=SciML&color=9558b2&labelColor=389826)](https://github.com/SciML/SciMLStyle)
 
 SciMLBase.jl is the core interface definition of the SciML ecosystem. It is a
@@ -17,11 +17,11 @@ supply the common interface and allow for interexchange of mathematical problems
 
 The breaking changes in v2.0 are:
 
-* `IntegralProblem` has moved to an interface with `IntegralFunction` and `BatchedIntegralFunction` which requires specifying `prototype`s for the values to be modified
-  instead of `nout` and `batch`. https://github.com/SciML/SciMLBase.jl/pull/497
-* `ODEProblem` was made temporarily into a `mutable struct` to allow for EnzymeRules support. Using the mutation throws a warning that this is only experimental and should not be relied on.
-  https://github.com/SciML/SciMLBase.jl/pull/501
-* `BVProblem` now has a new interface for `TwoPointBVProblem` which splits the bc terms for the two sides, forcing a true two-point BVProblem to allow for further specializations and to allow
-  for wrapping Fortran solvers in the interface. https://github.com/SciML/SciMLBase.jl/pull/477
-* `SDEProblem` constructor was changed to remove an anti-pattern which required passing the diffusion function `g` twice, i.e. `SDEProblem(SDEFunction(f,g),g, ...)`.
-  Now this is simply `SDEProblem(SDEFunction(f,g),...)`. https://github.com/SciML/SciMLBase.jl/pull/489
+  - `IntegralProblem` has moved to an interface with `IntegralFunction` and `BatchedIntegralFunction` which requires specifying `prototype`s for the values to be modified
+    instead of `nout` and `batch`. https://github.com/SciML/SciMLBase.jl/pull/497
+  - `ODEProblem` was made temporarily into a `mutable struct` to allow for EnzymeRules support. Using the mutation throws a warning that this is only experimental and should not be relied on.
+    https://github.com/SciML/SciMLBase.jl/pull/501
+  - `BVProblem` now has a new interface for `TwoPointBVProblem` which splits the bc terms for the two sides, forcing a true two-point BVProblem to allow for further specializations and to allow
+    for wrapping Fortran solvers in the interface. https://github.com/SciML/SciMLBase.jl/pull/477
+  - `SDEProblem` constructor was changed to remove an anti-pattern which required passing the diffusion function `g` twice, i.e. `SDEProblem(SDEFunction(f,g),g, ...)`.
+    Now this is simply `SDEProblem(SDEFunction(f,g),...)`. https://github.com/SciML/SciMLBase.jl/pull/489

docs/pages.jl

@@ -12,5 +12,5 @@ pages = [
         "interfaces/Common_Keywords.md",
         "interfaces/Differentiation.md",
         "interfaces/PDE.md"],
-    "Fundamentals" => Any["fundamentals/FAQ.md"],
+    "Fundamentals" => Any["fundamentals/FAQ.md"]
 ]

docs/src/fundamentals/FAQ.md

@@ -16,4 +16,4 @@ See [ColPrac: Contributor's Guide on Collaborative Practices for Community Packa
 
 ## Are there developer programs to help fund parties interested in helping develop SciML?
 
-Yes! See [the SciML Developer Programs](https://sciml.ai/dev/) webpage.
+Yes! See [the SciML Developer Programs](https://sciml.ai/dev/) webpage.

docs/src/index.md

@@ -5,7 +5,7 @@
 `SciMLAlgorithms` are defined as types which have dispatches to the function signature:
 
 ```julia
-CommonSolve.solve(prob::AbstractSciMLProblem,alg::AbstractSciMLAlgorithm;kwargs...)
+CommonSolve.solve(prob::AbstractSciMLProblem, alg::AbstractSciMLAlgorithm; kwargs...)
 ```
 
 ### Algorithm-Specific Arguments

docs/src/interfaces/Algorithms.md

@@ -5,12 +5,12 @@ the rules which are required on container and number types which are allowable
 in SciML tools.
 
 !!! warn
-
+    
     In general as of 2023, strict adherence to this interface is an early work-in-progress.
     If anything does not conform to the documented interface, please open an issue.
 
 !!! note
-
+    
     There are many types which can work with a specific solver that do satisfy this
     interface. Many times as part of prototyping you may want to side-step the
     high level interface checks in order to simply test whether a new type is working.
@@ -35,45 +35,45 @@ independent variables (`t` or `tspan`). These two types can be different, and ca
 different restrictions depending on the type of solver which is employed. The following
 rules for a Number type are held in general:
 
-* Number types can be used in SciML directly or in containers. If a problem defines a value like `u0`
-  using a Number type, the out-of-place form must be used for the problem definition.
-* `x::T + y::T = z::T`
-* `x::T * y::T = z::T`
-* `oneunit(x::T)::T`
-* `one(x::T) * oneunit(x::T) = z::T`
-* `t::T2 * x::T + y::T = z::T` for `T2` a time type and `T` the dependent variable type (this includes the
-  `muladd` equivalent form).
+  - Number types can be used in SciML directly or in containers. If a problem defines a value like `u0`
+    using a Number type, the out-of-place form must be used for the problem definition.
+  - `x::T + y::T = z::T`
+  - `x::T * y::T = z::T`
+  - `oneunit(x::T)::T`
+  - `one(x::T) * oneunit(x::T) = z::T`
+  - `t::T2 * x::T + y::T = z::T` for `T2` a time type and `T` the dependent variable type (this includes the
+    `muladd` equivalent form).
 
 Additionally, the following rules apply to subsets of uses:
 
 ### Adaptive Number Types
 
-* `x::T / y::T = z::T`
-* Default choices of norms can assume `sqrt(x::T)::T` exists. If `internalnorm` is overridden then this
-  may not be required (for example, changing the norm to inf-norm).
-* `x::T ^ y::T = z::T`
+  - `x::T / y::T = z::T`
+  - Default choices of norms can assume `sqrt(x::T)::T` exists. If `internalnorm` is overridden then this
+    may not be required (for example, changing the norm to inf-norm).
+  - `x::T ^ y::T = z::T`
 
 ### Time Types (Independent Variables)
 
-* If a solver is time adaptive, the time type must be a floating point number. `Rational` is only allowed
-  for non-adaptive solves.
+  - If a solver is time adaptive, the time type must be a floating point number. `Rational` is only allowed
+    for non-adaptive solves.
 
 ## SciML Container (Array) Types
 
-Container types are types which hold number types. They can be used to define objects like the state vector 
+Container types are types which hold number types. They can be used to define objects like the state vector
 (`u0`) of a problem. The following operations are required in a container type to be used with SciML
 solvers:
 
-* Broadcast is defined [according to the Julia broadcast interface](https://docs.julialang.org/en/v1/manual/interfaces/#man-interfaces-broadcasting).
-* The container type correctly defines [interface overloads to satisfy the ArrayInterface.jl specification](https://docs.sciml.ai/ArrayInterface/stable/).
-* `ArrayInterface.zeromatrix(x::T)::T2` defines a compatible matrix type (see below)
-* `eltype(x::T)::T2` is a compatible Number type.
-* `x::T .+ y::T = z::T` (i.e. broadcast similar is defined to be type-presurving)
-* Indexing is only required if `ArrayInterface.fast_scalar_indexing(x::T)==true`. If true,
-  scalar indexing `x[i]` is assumed to be defined and run through all variables.
+  - Broadcast is defined [according to the Julia broadcast interface](https://docs.julialang.org/en/v1/manual/interfaces/#man-interfaces-broadcasting).
+  - The container type correctly defines [interface overloads to satisfy the ArrayInterface.jl specification](https://docs.sciml.ai/ArrayInterface/stable/).
+  - `ArrayInterface.zeromatrix(x::T)::T2` defines a compatible matrix type (see below)
+  - `eltype(x::T)::T2` is a compatible Number type.
+  - `x::T .+ y::T = z::T` (i.e. broadcast similar is defined to be type-presurving)
+  - Indexing is only required if `ArrayInterface.fast_scalar_indexing(x::T)==true`. If true,
+    scalar indexing `x[i]` is assumed to be defined and run through all variables.
 
 !!! note
-
+    
     "`eltype(x::T)::T2` is a compatible Number type" excludes `Array{Array{T}}` types of types. However, recursive
     vectors can conformed to the interface with zero overhead using tools from RecursiveArrayTools.jl such as
     `VectorOfArray(x)`. Since this greatly simplifies the interfaces and the ability to check for correctness,
@@ -83,21 +83,21 @@ Additionally, the following rules apply to subsets of uses:
 
 ### SciML Mutable Array Types
 
-* `similar(x::T)::T`
-* `zero(x::T)::T`
-* `z::T .= x::T .+ y::T` is defined
-* `z::T .= x::T .* y::T` is defined
-* `z::T .= t::T2 .* x::T` where `T2` is the time type (a Number) and `T` is the container type.
-* (Optional) `Base.resize!(x,i)` is required for `resize!(integrator,i)` to be supported.
+  - `similar(x::T)::T`
+  - `zero(x::T)::T`
+  - `z::T .= x::T .+ y::T` is defined
+  - `z::T .= x::T .* y::T` is defined
+  - `z::T .= t::T2 .* x::T` where `T2` is the time type (a Number) and `T` is the container type.
+  - (Optional) `Base.resize!(x,i)` is required for `resize!(integrator,i)` to be supported.
 
 ### SciML Matrix (Operator) Type
 
 Note that the matrix type may not match the type of the initial container `u0`. An example is `ComponentMatrix`
 as the matrix structure corresponding to a `ComponentArray`. However, the following actions are assumed
 to hold on the resulting matrix type:
 
-* `solve(LinearProblem(A::T,b::T2),linsolve)` must be defined for a solver to work on a given SciML matrix
-  type `T2`.
-* If the matrix is an operator, i.e. a lazy construct, it should conform to the 
-  [SciMLOperators](https://docs.sciml.ai/SciMLOperators/stable/) interface.
-* If not a SciMLOperator, `diagind(W::T)` should be defined and `@view(A[idxs])=@view(A[idxs]) + λ::T`
+  - `solve(LinearProblem(A::T,b::T2),linsolve)` must be defined for a solver to work on a given SciML matrix
+    type `T2`.
+  - If the matrix is an operator, i.e. a lazy construct, it should conform to the
+    [SciMLOperators](https://docs.sciml.ai/SciMLOperators/stable/) interface.
+  - If not a SciMLOperator, `diagind(W::T)` should be defined and `@view(A[idxs])=@view(A[idxs]) + λ::T`