various doc and style improvements

.JuliaFormatter.toml

@@ -1 +1,2 @@
 style = "sciml"
+format_markdown = true

.github/workflows/FormatCheck.yml

@@ -0,0 +1,42 @@
+name: format-check
+
+on:
+  push:
+    branches:
+      - 'master'
+      - 'release-'
+    tags: '*'
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version: [1]
+        julia-arch: [x86]
+        os: [ubuntu-latest]
+    steps:
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia-version }}
+
+      - uses: actions/checkout@v1
+      - name: Install JuliaFormatter and format
+        # This will use the latest version by default but you can set the version like so:
+        #
+        # julia  -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter", version="0.13.0"))'
+        run: |
+          julia  -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter"))'
+          julia  -e 'using JuliaFormatter; format(".", verbose=true)'
+      - name: Format check
+        run: |
+          julia -e '
+          out = Cmd(`git diff --name-only`) |> read |> String
+          if out == ""
+              exit(0)
+          else
+              @error "Some files have not been formatted !!!"
+              write(stdout, out)
+              exit(1)
+          end'

LICENSE.md

@@ -19,13 +19,10 @@ The RecursiveArrayTools.jl package is licensed under the MIT "Expat" License:
 > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 > SOFTWARE.
-> 
 
 The chain function is from Iterators.jl and is licensed under the MIT License:
 
->Copyright (c) 2012-2016: Daniel Jones, Stefan Karpinski, Simon Kornblith, Kevin Squire, Jeff Bezanson, Tim Holy, Jonathan Malmaud, Eric Davies, and other contributors.
+> Copyright (c) 2012-2016: Daniel Jones, Stefan Karpinski, Simon Kornblith, Kevin Squire, Jeff Bezanson, Tim Holy, Jonathan Malmaud, Eric Davies, and other contributors.
 
 The above copyright notice and this permission notice shall be included in all
 copies or substantial portions of the Software.
-
-

README.md

@@ -7,7 +7,7 @@
 [![Build Status](https://github.com/SciML/RecursiveArrayTools.jl/workflows/CI/badge.svg)](https://github.com/SciML/RecursiveArrayTools.jl/actions?query=workflow%3ACI)
 [![build status](https://badge.buildkite.com/9eab94781cf0af9a3566e9b9f16abe5aea167b640b88065285.svg?branch=master)](https://buildkite.com/julialang/recursivearraytools-dot-jl)
 
-[![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)
 
 RecursiveArrayTools.jl is a set of tools for dealing with recursive arrays like
@@ -31,8 +31,8 @@ vB = VectorOfArray(b)
 
 vA .* vB # Now all standard array stuff works!
 
-a = (rand(5),rand(5))
-b = (rand(5),rand(5))
+a = (rand(5), rand(5))
+b = (rand(5), rand(5))
 pA = ArrayPartition(a)
 pB = ArrayPartition(b)
 

docs/make.jl

@@ -5,18 +5,22 @@ cp("./docs/Project.toml", "./docs/src/assets/Project.toml", force = true)
 
 include("pages.jl")
 
-makedocs(
-    sitename="RecursiveArrayTools.jl",
-    authors="Chris Rackauckas",
-    modules=[RecursiveArrayTools],
-    clean=true,doctest=false,
-    format = Documenter.HTML(analytics = "UA-90474609-3",
-                             assets = ["assets/favicon.ico"],
-                             canonical="https://docs.sciml.ai/RecursiveArrayTools/stable/"),
-    pages=pages
-)
+makedocs(sitename = "RecursiveArrayTools.jl",
+         authors = "Chris Rackauckas",
+         modules = [RecursiveArrayTools],
+         clean = true, doctest = false, linkcheck = true,
+         strict = [
+             :doctest,
+             :linkcheck,
+             :parse_error,
+             :example_block,
+             # Other available options are
+             # :autodocs_block, :cross_references, :docs_block, :eval_block, :example_block, :footnote, :meta_block, :missing_docs, :setup_block
+         ],
+         format = Documenter.HTML(analytics = "UA-90474609-3",
+                                  assets = ["assets/favicon.ico"],
+                                  canonical = "https://docs.sciml.ai/RecursiveArrayTools/stable/"),
+         pages = pages)
 
-deploydocs(
-   repo = "github.com/SciML/RecursiveArrayTools.jl.git";
-   push_preview = true
-)
+deploydocs(repo = "github.com/SciML/RecursiveArrayTools.jl.git";
+           push_preview = true)

docs/pages.jl

@@ -1,7 +1,7 @@
 # Put in a separate page so it can be used by SciMLDocs.jl
 
-pages=[
+pages = [
     "Home" => "index.md",
     "array_types.md",
-    "recursive_array_functions.md"
-]
+    "recursive_array_functions.md",
+]

docs/src/array_types.md

@@ -13,4 +13,4 @@ mapping and iteration functions, and more.
 VectorOfArray
 DiffEqArray
 ArrayPartition
-```
+```

docs/src/index.md

@@ -1,6 +1,6 @@
 # RecursiveArrayTools.jl: Arrays of Arrays and Even Deeper
 
-RecursiveArrayTools.jl is a set of tools for dealing with recursive arrays like
+RecursiveArrayTools.jl is a set of tools for dealing with recursive arrays, like
 arrays of arrays. It contains type wrappers for making recursive arrays act more
 like normal arrays (for example, automating the recursion of broadcast, maps,
 iteration, and more), and utility functions which make it easier to work with
@@ -17,66 +17,87 @@ Pkg.add("RecursiveArrayTools")
 
 ## Contributing
 
-- Please refer to the
-  [SciML ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://github.com/SciML/ColPrac/blob/master/README.md)
-  for guidance on PRs, issues, and other matters relating to contributing to SciML.
-- There are a few community forums:
-    - the #diffeq-bridged channel in the [Julia Slack](https://julialang.org/slack/)
-    - [JuliaDiffEq](https://gitter.im/JuliaDiffEq/Lobby) on Gitter
-    - on the [Julia Discourse forums](https://discourse.julialang.org)
-    - see also [SciML Community page](https://sciml.ai/community/)
+  - Please refer to the
+    [SciML ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://github.com/SciML/ColPrac/blob/master/README.md)
+    for guidance on PRs, issues, and other matters relating to contributing to SciML.
+
+  - See the [SciML Style Guide](https://github.com/SciML/SciMLStyle) for common coding practices and other style decisions.
+  - There are a few community forums:
+
+      + The #diffeq-bridged and #sciml-bridged channels in the
+        [Julia Slack](https://julialang.org/slack/)
+      + The #diffeq-bridged and #sciml-bridged channels in the
+        [Julia Zulip](https://julialang.zulipchat.com/#narrow/stream/279055-sciml-bridged)
+      + On the [Julia Discourse forums](https://discourse.julialang.org)
+      + See also [SciML Community page](https://sciml.ai/community/)
 
 ## Reproducibility
+
 ```@raw html
 <details><summary>The documentation of this SciML package was built using these direct dependencies,</summary>
 ```
+
 ```@example
 using Pkg # hide
 Pkg.status() # hide
 ```
+
 ```@raw html
 </details>
 ```
+
 ```@raw html
 <details><summary>and using this machine and Julia version.</summary>
 ```
+
 ```@example
 using InteractiveUtils # hide
 versioninfo() # hide
 ```
+
 ```@raw html
 </details>
 ```
+
 ```@raw html
 <details><summary>A more complete overview of all dependencies and their versions is also provided.</summary>
 ```
+
 ```@example
 using Pkg # hide
-Pkg.status(;mode = PKGMODE_MANIFEST) # hide
+Pkg.status(; mode = PKGMODE_MANIFEST) # hide
 ```
+
 ```@raw html
 </details>
 ```
+
 ```@raw html
 You can also download the 
 <a href="
 ```
+
 ```@eval
 using TOML
-version = TOML.parse(read("../../Project.toml",String))["version"]
-name = TOML.parse(read("../../Project.toml",String))["name"]
-link = "https://github.com/SciML/"*name*".jl/tree/gh-pages/v"*version*"/assets/Manifest.toml"
+version = TOML.parse(read("../../Project.toml", String))["version"]
+name = TOML.parse(read("../../Project.toml", String))["name"]
+link = "https://github.com/SciML/" * name * ".jl/tree/gh-pages/v" * version *
+       "/assets/Manifest.toml"
 ```
+
 ```@raw html
 ">manifest</a> file and the
 <a href="
 ```
+
 ```@eval
 using TOML
-version = TOML.parse(read("../../Project.toml",String))["version"]
-name = TOML.parse(read("../../Project.toml",String))["name"]
-link = "https://github.com/SciML/"*name*".jl/tree/gh-pages/v"*version*"/assets/Project.toml"
+version = TOML.parse(read("../../Project.toml", String))["version"]
+name = TOML.parse(read("../../Project.toml", String))["name"]
+link = "https://github.com/SciML/" * name * ".jl/tree/gh-pages/v" * version *
+       "/assets/Project.toml"
 ```
+
 ```@raw html
 ">project</a> file.
-```
+```

docs/src/recursive_array_functions.md

@@ -10,4 +10,4 @@ recursivecopy
 recursivecopy!
 vecvecapply
 copyat_or_push!
-```
+```

ext/RecursiveArrayToolsTrackerExt.jl

@@ -15,4 +15,4 @@ function RecursiveArrayTools.recursivecopy!(b::AbstractArray{T, N},
     end
 end
 
-end
+end

src/RecursiveArrayTools.jl

@@ -45,7 +45,7 @@ end
 import Requires
 @static if !isdefined(Base, :get_extension)
     function __init__()
-            Requires.@require Tracker="9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" begin include("../ext/RecursiveArrayToolsTrackerExt.jl") end
+        Requires.@require Tracker="9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" begin include("../ext/RecursiveArrayToolsTrackerExt.jl") end
     end
 end
 

src/array_partition.jl

@@ -18,7 +18,7 @@ Thus, for:
 
 ```julia
 using RecursiveArrayTools
-A = ArrayPartition(y,z)
+A = ArrayPartition(y, z)
 ```
 
 we would have `A.x[1]==y` and `A.x[2]==z`. Broadcasting like `f.(A)` is efficient.

src/tabletraits.jl

@@ -7,12 +7,17 @@ function Tables.rows(A::AbstractDiffEqArray)
         N = length(A.u[1])
         names = [
             :timestamp,
-            (!(A.sc isa  SymbolicIndexingInterface.SymbolCache{Nothing, Nothing, Nothing}) ? (states(A.sc)[i] for i in 1:N) :
+            (!(A.sc isa SymbolicIndexingInterface.SymbolCache{Nothing, Nothing, Nothing}) ?
+             (states(A.sc)[i] for i in 1:N) :
              (Symbol("value", i) for i in 1:N))...,
         ]
         types = Type[eltype(A.t), (eltype(A.u[1]) for _ in 1:N)...]
     else
-        names = [:timestamp, !(A.sc isa  SymbolicIndexingInterface.SymbolCache{Nothing, Nothing, Nothing}) ? states(A.sc)[1] : :value]
+        names = [
+            :timestamp,
+            !(A.sc isa SymbolicIndexingInterface.SymbolCache{Nothing, Nothing, Nothing}) ?
+            states(A.sc)[1] : :value,
+        ]
         types = Type[eltype(A.t), VT]
     end
     return AbstractDiffEqArrayRows(names, types, A.t, A.u)
@@ -32,14 +37,15 @@ struct AbstractDiffEqArrayRows{T, U}
 end
 function AbstractDiffEqArrayRows(names, types, t, u)
     AbstractDiffEqArrayRows(Symbol.(names), types,
-                                   Dict(Symbol(nm) => i for (i, nm) in enumerate(names)), t, u)
+                            Dict(Symbol(nm) => i for (i, nm) in enumerate(names)), t, u)
 end
 
 Base.length(x::AbstractDiffEqArrayRows) = length(x.u)
 function Base.eltype(::Type{AbstractDiffEqArrayRows{T, U}}) where {T, U}
     AbstractDiffEqArrayRow{eltype(T), eltype(U)}
 end
-function Base.iterate(x::AbstractDiffEqArrayRows, (t_state, u_state)=(iterate(x.t), iterate(x.u)))
+function Base.iterate(x::AbstractDiffEqArrayRows,
+                      (t_state, u_state) = (iterate(x.t), iterate(x.u)))
     t_state === nothing && return nothing
     u_state === nothing && return nothing
     t, _t_state = t_state