apply JuliaFormatter.jl

.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://CliMA.github.io/CLIMA/latest/CodingConventions.html) and run `julia .dev/format.jl`
+- [ ] Followed all necessary [style guidelines](https://CliMA.github.io/CLIMA/latest/CodingConventions.html) and run `julia .dev/climaformat.jl .`
 - [ ] Updated the documentation to reflect changes from this PR.
 
 <!--- 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

docs/src/HowToGuides/Contributing/CONTRIBUTING.md

@@ -70,13 +70,6 @@ For the most part, we follow the [YASGuide](https://github.com/jrevels/YASGuide)
 
 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 ClimateMachine directory

src/InputOutput/VTK/writemesh.jl

@@ -3,85 +3,124 @@ using WriteVTK
 #=
 This is the 1D WriteMesh routine
 =#
-function writemesh(base_name, x1; fields=(), realelems=1:size(x1)[end])
-  (Nqr, _) = size(x1)
-  Nsubcells = (Nqr-1)
+function writemesh(base_name, x1; fields = (), realelems = 1:size(x1)[end])
+    (Nqr, _) = size(x1)
+    Nsubcells = (Nqr - 1)
 
-  cells = Array{MeshCell{Array{Int,1}}, 1}(undef, Nsubcells * length(realelems))
-  for e ∈ realelems
-    offset = (e-1) * Nqr
-    for i = 1:Nqr-1
-        cells[i + (e-1)*Nsubcells] =
-          MeshCell(VTKCellTypes.VTK_LINE, offset .+ [i, i+1])
+    cells =
+        Array{MeshCell{Array{Int, 1}}, 1}(undef, Nsubcells * length(realelems))
+    for e in realelems
+        offset = (e - 1) * Nqr
+        for i in 1:(Nqr - 1)
+            cells[i + (e - 1) * Nsubcells] =
+                MeshCell(VTKCellTypes.VTK_LINE, offset .+ [i, i + 1])
+        end
     end
-  end
 
-  vtkfile = vtk_grid("$(base_name)", @view(x1[:]), cells; compress=false)
-  for (name, v) ∈ fields
-    vtk_point_data(vtkfile, v, name)
-  end
-  outfiles = vtk_save(vtkfile)
+    vtkfile = vtk_grid("$(base_name)", @view(x1[:]), cells; compress = false)
+    for (name, v) in fields
+        vtk_point_data(vtkfile, v, name)
+    end
+    outfiles = vtk_save(vtkfile)
 end
 
 #=
 This is the 2D WriteMesh routine
 =#
-function writemesh(base_name, x1, x2; x3=nothing, fields=(), realelems=1:size(x1)[end])
-  @assert size(x1) == size(x2)
-  (Nqr, Nqs, _) = size(x1)
-  Nsubcells = (Nqr-1) * (Nqs-1)
+function writemesh(
+    base_name,
+    x1,
+    x2;
+    x3 = nothing,
+    fields = (),
+    realelems = 1:size(x1)[end],
+)
+    @assert size(x1) == size(x2)
+    (Nqr, Nqs, _) = size(x1)
+    Nsubcells = (Nqr - 1) * (Nqs - 1)
 
-  cells = Array{MeshCell{Array{Int,1}}, 1}(undef, Nsubcells * length(realelems))
-  ind = LinearIndices((1:Nqr, 1:Nqs))
-  for e ∈ realelems
-    offset = (e-1) * Nqr * Nqs
-    for j = 1:Nqs-1
-      for i = 1:Nqr-1
-        cells[i + (j-1)*(Nqr-1) + (e-1)*Nsubcells] =
-        MeshCell(VTKCellTypes.VTK_PIXEL, offset .+ ind[i:i+1,j:j+1][:])
-      end
+    cells =
+        Array{MeshCell{Array{Int, 1}}, 1}(undef, Nsubcells * length(realelems))
+    ind = LinearIndices((1:Nqr, 1:Nqs))
+    for e in realelems
+        offset = (e - 1) * Nqr * Nqs
+        for j in 1:(Nqs - 1)
+            for i in 1:(Nqr - 1)
+                cells[i + (j - 1) * (Nqr - 1) + (e - 1) * Nsubcells] = MeshCell(
+                    VTKCellTypes.VTK_PIXEL,
+                    offset .+ ind[i:(i + 1), j:(j + 1)][:],
+                )
+            end
+        end
     end
-  end
 
-  if x3 == nothing
-    vtkfile = vtk_grid("$(base_name)", @view(x1[:]), @view(x2[:]), cells;
-                       compress=false)
-  else
-    vtkfile = vtk_grid("$(base_name)", @view(x1[:]), @view(x2[:]), @view(x3[:]),
-                       cells; compress=false)
-  end
-  for (name, v) ∈ fields
-    vtk_point_data(vtkfile, v, name)
-  end
-  outfiles = vtk_save(vtkfile)
+    if x3 == nothing
+        vtkfile = vtk_grid(
+            "$(base_name)",
+            @view(x1[:]),
+            @view(x2[:]),
+            cells;
+            compress = false,
+        )
+    else
+        vtkfile = vtk_grid(
+            "$(base_name)",
+            @view(x1[:]),
+            @view(x2[:]),
+            @view(x3[:]),
+            cells;
+            compress = false,
+        )
+    end
+    for (name, v) in fields
+        vtk_point_data(vtkfile, v, name)
+    end
+    outfiles = vtk_save(vtkfile)
 end
 
 #=
 This is the 3D WriteMesh routine
 =#
-function writemesh(base_name, x1, x2, x3; fields=(), realelems=1:size(x1)[end])
-  (Nqr, Nqs, Nqt, _) = size(x1)
-  (Nr, Ns, Nt) = (Nqr-1, Nqs-1, Nqt-1)
-  Nsubcells = Nr * Ns * Nt
-  cells = Array{MeshCell{Array{Int,1}}, 1}(undef, Nsubcells * length(realelems))
-  ind = LinearIndices((1:Nqr, 1:Nqs, 1:Nqt))
-  for e ∈ realelems
-    offset = (e-1) * Nqr * Nqs * Nqt
-    for k = 1:Nt
-      for j = 1:Ns
-        for i = 1:Nr
-          cells[i + (j-1) * Nr + (k-1) * Nr * Ns + (e-1) * Nsubcells] =
-            MeshCell(VTKCellTypes.VTK_VOXEL,
-                     offset .+ ind[i:i+1, j:j+1, k:k+1][:])
+function writemesh(
+    base_name,
+    x1,
+    x2,
+    x3;
+    fields = (),
+    realelems = 1:size(x1)[end],
+)
+    (Nqr, Nqs, Nqt, _) = size(x1)
+    (Nr, Ns, Nt) = (Nqr - 1, Nqs - 1, Nqt - 1)
+    Nsubcells = Nr * Ns * Nt
+    cells =
+        Array{MeshCell{Array{Int, 1}}, 1}(undef, Nsubcells * length(realelems))
+    ind = LinearIndices((1:Nqr, 1:Nqs, 1:Nqt))
+    for e in realelems
+        offset = (e - 1) * Nqr * Nqs * Nqt
+        for k in 1:Nt
+            for j in 1:Ns
+                for i in 1:Nr
+                    cells[i + (j - 1) * Nr + (k - 1) * Nr * Ns + (e - 1) *
+                                                                 Nsubcells] =
+                        MeshCell(
+                            VTKCellTypes.VTK_VOXEL,
+                            offset .+ ind[i:(i + 1), j:(j + 1), k:(k + 1)][:],
+                        )
+                end
+            end
         end
-      end
     end
-  end
 
-  vtkfile = vtk_grid("$(base_name)", @view(x1[:]), @view(x2[:]), @view(x3[:]),
-                     cells; compress=false)
-  for (name, v) ∈ fields
-    vtk_point_data(vtkfile, v, name)
-  end
-  outfiles = vtk_save(vtkfile)
+    vtkfile = vtk_grid(
+        "$(base_name)",
+        @view(x1[:]),
+        @view(x2[:]),
+        @view(x3[:]),
+        cells;
+        compress = false,
+    )
+    for (name, v) in fields
+        vtk_point_data(vtkfile, v, name)
+    end
+    outfiles = vtk_save(vtkfile)
 end