Merge #536

536: apply JuliaFormatter.jl r=simonbyrne a=simonbyrne

This applies [JuliaFormatter.jl](https://github.com/domluna/JuliaFormatter.jl) to the whole repository.

Any thoughts/comments?

- [ ] Testing?

Co-authored-by: Simon Byrne <simonbyrne@gmail.com>

.github/pull_request_template.md

@@ -7,7 +7,7 @@ A clear and concise description of the code with usage.
 I have
 
 - [ ] Written and run all necessary tests with CLIMA by including `tests/runtests.jl`
-- [ ] Followed all necessary [style guidelines](https://climate-machine.github.io/CLIMA/latest/CodingConventions.html) and run `julia .dev/format.jl`
+- [ ] Followed all necessary [style guidelines](https://climate-machine.github.io/CLIMA/latest/CodingConventions.html) and run `julia .dev/climaformat.jl .`
 
 <!--- Please leave the following section --->
 

.github/workflows/JuliaFormatter.yml

@@ -15,7 +15,7 @@ jobs:
         version: 1.3
     - name: Apply JuliaFormatter
       run: |
-        julia --project=.dev .dev/format.jl origin/master
+        julia --project=.dev .dev/climaformat.jl .
     - name: Check formatting diff
       run: |
         git diff --color=always --exit-code

CONTRIBUTING.md

@@ -68,15 +68,6 @@ This will help us keep the commit history clean on the master branch of CLIMA.
 
 For the most part, we follow the [YASGuide](https://github.com/jrevels/YASGuide) for Julia formatting, with small exceptions covered in the [Coding Conventions](https://climate-machine.github.io/CLIMA/latest/CodingConventions.html) section of the documentation.
 
-In addition to this, once you are happy with your PR, please apply [JuliaFormatter.jl](https://github.com/domluna/JuliaFormatter.jl) to all changed files in the repository.
-
-To apply our formatter settings to all changed files, run:
-```
-julia .dev/format.jl
-```
-
-Formatting changes should be done as a separate commit, ideally the last commit of the pull request (you may want to leave it until all other changes have been approved).
-
 ### Formatting utility
 
 A convenience utility is located at `.dev/climaformat.jl` that will format the julia files in the given path. For example, from the top-level CLIMA directory

docs/generate.jl

@@ -2,7 +2,8 @@
 import Literate
 
 EXAMPLE_BL_DIR = joinpath(@__DIR__, "..", "examples", "DGmethods_old")
-GENERATED_BL_DIR = joinpath(@__DIR__, "src", "examples", "DGmethods_old", "generated")
+GENERATED_BL_DIR =
+    joinpath(@__DIR__, "src", "examples", "DGmethods_old", "generated")
 for example in readdir(EXAMPLE_BL_DIR)
     endswith(example, ".jl") || continue
     input = abspath(joinpath(EXAMPLE_BL_DIR, example))

docs/make.jl

@@ -5,78 +5,74 @@ using CLIMA, Documenter
 # TODO: Add generated examples back
 # include("generate.jl")
 
-GENERATED_BL_EXAMPLES =
-[joinpath("examples", "DGmethods_old", "generated", f) for f in
- (
-  "ex_001_periodic_advection.md",
-  "ex_002_solid_body_rotation.md",
- )]
-GENERATED_BL_EXAMPLES = filter!(x->isfile(x), GENERATED_BL_EXAMPLES)
+GENERATED_BL_EXAMPLES = [
+    joinpath("examples", "DGmethods_old", "generated", f)
+    for
+    f in ("ex_001_periodic_advection.md", "ex_002_solid_body_rotation.md")
+]
+GENERATED_BL_EXAMPLES = filter!(x -> isfile(x), GENERATED_BL_EXAMPLES)
 
 pages = Any[
-  "Home" => "index.md",
-  "Common" => Any[
-    "MoistThermodynamics" => "Common/MoistThermodynamics.md",
-  ],
-  "Utilites" => Any[
-    "RootSolvers" => "Utilities/RootSolvers.md",
-  ],
-  "Atmos" => Any[
-    "Atmos/SurfaceFluxes.md",
-    "Atmos/TurbulenceConvection.md",
-    "Atmos/EDMFEquations.md",
-    "Microphysics" => "Atmos/Microphysics.md",
-  ],
-  "ODESolvers" => "ODESolvers.md",
-  "LinearSolvers" => "LinearSolvers.md",
-  "Mesh" => "Mesh.md",
-  "Arrays" => "Arrays.md",
-  "DGmethods_old" => "DGmethods_old.md",
-  "InputOutput.md",
-  "Developer docs" => Any[
-    "CodingConventions.md",
-    "AcceptableUnicode.md",
-    "VariableList.md",
-  ],
+    "Home" => "index.md",
+    "Common" => Any["MoistThermodynamics" => "Common/MoistThermodynamics.md",],
+    "Utilites" => Any["RootSolvers" => "Utilities/RootSolvers.md",],
+    "Atmos" => Any[
+        "Atmos/SurfaceFluxes.md",
+        "Atmos/TurbulenceConvection.md",
+        "Atmos/EDMFEquations.md",
+        "Microphysics" => "Atmos/Microphysics.md",
+    ],
+    "ODESolvers" => "ODESolvers.md",
+    "LinearSolvers" => "LinearSolvers.md",
+    "Mesh" => "Mesh.md",
+    "Arrays" => "Arrays.md",
+    "DGmethods_old" => "DGmethods_old.md",
+    "InputOutput.md",
+    "Developer docs" => Any[
+        "CodingConventions.md",
+        "AcceptableUnicode.md",
+        "VariableList.md",
+    ],
 ]
 
 if !isempty(GENERATED_BL_EXAMPLES)
-  push!(pages,"Balance Law Examples" => ["BalanceLawOverview.md", GENERATED_BL_EXAMPLES...])
+    push!(
+        pages,
+        "Balance Law Examples" =>
+            ["BalanceLawOverview.md", GENERATED_BL_EXAMPLES...],
+    )
 end
 
 
 makedocs(
-  sitename = "CLIMA",
-  doctest = false,
-  strict = false,
-  linkcheck = false,
-  checkdocs = :exports,
-  # checkdocs = :all,
-  format = Documenter.HTML(
-    prettyurls = get(ENV, "CI", nothing) == "true",
+    sitename = "CLIMA",
+    doctest = false,
+    strict = false,
+    linkcheck = false,
+    checkdocs = :exports,
+    # checkdocs = :all,
+    format = Documenter.HTML(
+        prettyurls = get(ENV, "CI", nothing) == "true",
         mathengine = MathJax(Dict(
             :TeX => Dict(
                 :equationNumbers => Dict(:autoNumber => "AMS"),
-                :Macros => Dict()
-            )
-        ))
-    # prettyurls = !("local" in ARGS),
-    # canonical = "https://climate-machine.github.io/CLIMA/stable/",
-  ),
-  clean = true,
-  modules = [Documenter, CLIMA],
-  pages = pages,
+                :Macros => Dict(),
+            ),
+        )),
+        # prettyurls = !("local" in ARGS),
+        # canonical = "https://climate-machine.github.io/CLIMA/stable/",
+    ),
+    clean = true,
+    modules = [Documenter, CLIMA],
+    pages = pages,
 )
 
 # make sure there are no *.vtu files left around from the build
 p = joinpath(@__DIR__, "build", "examples", "DGmethods_old", "generated")
 if ispath(p)
-  cd(p) do
-    foreach(file -> endswith(file, ".vtu") && rm(file), readdir())
-  end
+    cd(p) do
+        foreach(file -> endswith(file, ".vtu") && rm(file), readdir())
+    end
 end
 
-deploydocs(
-  repo = "github.com/climate-machine/CLIMA.git",
-  target = "build",
-)
+deploydocs(repo = "github.com/climate-machine/CLIMA.git", target = "build")