Merge #61

61: The great formatting. r=ilopezgp a=ilopezgp

Let's use the formatting that makes other CliMA packages look so nice.

Co-authored-by: Ignacio Lopez Gomez <[email protected]>

.dev/Project.toml

@@ -0,0 +1,5 @@
+[deps]
+JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
+
+[compat]
+JuliaFormatter = "0.3"

.dev/clima_formatter_options.jl

@@ -0,0 +1,8 @@
+clima_formatter_options = (
+    indent = 4,
+    margin = 120,
+    always_for_in = true,
+    whitespace_typedefs = true,
+    whitespace_ops_in_indices = true,
+    remove_extra_newlines = false,
+)

.dev/climaformat.jl

@@ -0,0 +1,85 @@
+#!/usr/bin/env julia
+#
+# This is an adapted version of format.jl from JuliaFormatter with the
+# following license:
+#
+#    MIT License
+#    Copyright (c) 2019 Dominique Luna
+#
+#    Permission is hereby granted, free of charge, to any person obtaining a
+#    copy of this software and associated documentation files (the
+#    "Software"), to deal in the Software without restriction, including
+#    without limitation the rights to use, copy, modify, merge, publish,
+#    distribute, sublicense, and/or sell copies of the Software, and to permit
+#    persons to whom the Software is furnished to do so, subject to the
+#    following conditions:
+#
+#    The above copyright notice and this permission notice shall be included
+#    in all copies or substantial portions of the Software.
+#
+#    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+#    OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+#    MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN
+#    NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
+#    DAMAGES OR OTHER 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.
+#
+using Pkg
+Pkg.activate(@__DIR__)
+Pkg.instantiate()
+
+using JuliaFormatter
+
+include("clima_formatter_options.jl")
+
+help = """
+Usage: climaformat.jl [flags] [FILE/PATH]...
+
+Formats the given julia files using the CLIMA formatting options.  If paths
+are given it will format the julia files in the paths. Otherwise, it will
+format all changed julia files.
+
+    -v, --verbose
+        Print the name of the files being formatted with relevant details.
+
+    -h, --help
+        Print this message.
+"""
+
+function parse_opts!(args::Vector{String})
+    i = 1
+    opts = Dict{Symbol, Union{Int, Bool}}()
+    while i ≤ length(args)
+        arg = args[i]
+        if arg[1] != '-'
+            i += 1
+            continue
+        end
+        if arg == "-v" || arg == "--verbose"
+            opt = :verbose
+        elseif arg == "-h" || arg == "--help"
+            opt = :help
+        else
+            error("invalid option $arg")
+        end
+        if opt in (:verbose, :help)
+            opts[opt] = true
+            deleteat!(args, i)
+        end
+    end
+    return opts
+end
+
+opts = parse_opts!(ARGS)
+if haskey(opts, :help)
+    write(stdout, help)
+    exit(0)
+end
+if isempty(ARGS)
+    filenames = readlines(`git ls-files "*.jl"`)
+else
+    filenames = ARGS
+end
+
+format(filenames; clima_formatter_options..., opts...)

.dev/hooks/pre-commit

@@ -0,0 +1,41 @@
+#!/usr/bin/env julia
+#
+# Called by git-commit with no arguments.  This checks to make sure that all
+# .jl files are indented correctly before a commit is made.
+#
+# To enable this hook, make this file executable and copy it in
+# $GIT_DIR/hooks.
+
+toplevel_directory = chomp(read(`git rev-parse --show-toplevel`, String))
+
+using Pkg
+Pkg.activate(joinpath(toplevel_directory, ".dev"))
+Pkg.instantiate()
+
+using JuliaFormatter
+
+include(joinpath(toplevel_directory, ".dev", "clima_formatter_options.jl"))
+
+needs_format = false
+
+for diffoutput in split.(readlines(`git diff --name-status --cached`))
+    status = diffoutput[1]
+    filename = diffoutput[end]
+    (!startswith(status, "D") && endswith(filename, ".jl")) || continue
+
+    a = read(`git show :$filename`, String)
+    b = format_text(a; clima_formatter_options...)
+
+    if a != b
+        fullfilename = joinpath(toplevel_directory, filename)
+
+        @error """File $filename needs to be indented with:
+            julia $(joinpath(toplevel_directory, ".dev", "climaformat.jl")) $fullfilename
+        and added to the git index via
+            git add $fullfilename
+        """
+        global needs_format = true
+    end
+end
+
+exit(needs_format ? 1 : 0)

.github/workflows/JuliaFormatter.yml

@@ -0,0 +1,44 @@
+name: JuliaFormatter
+
+on:
+  push:
+    branches:
+      - main
+      - trying
+      - staging
+    tags: '*'
+  pull_request:
+
+jobs:
+  format:
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    steps:
+    - name: Cancel Previous Runs
+      uses: styfle/[email protected]
+      with:
+        access_token: ${{ github.token }}
+
+    - uses: actions/[email protected]
+
+    - uses: dorny/[email protected]
+      id: filter
+      with:
+        filters: |
+          julia_file_change:
+            - added|modified: '**.jl'
+ 
+    - uses: julia-actions/setup-julia@latest
+      if: steps.filter.outputs.julia_file_change == 'true'
+      with:
+        version: 1.6.0
+
+    - name: Apply JuliaFormatter
+      if: steps.filter.outputs.julia_file_change == 'true'
+      run: |
+        julia --project=.dev .dev/climaformat.jl .
+
+    - name: Check formatting diff
+      if: steps.filter.outputs.julia_file_change == 'true'
+      run: |
+        git diff --color=always --exit-code

bors.toml

@@ -1,6 +1,7 @@
 status = [
   'docs-build',
   'test_success',
+  'format',
 ]
 delete_merged_branches = true
 timeout_sec = 3600

docs/make.jl

@@ -1,8 +1,7 @@
 # reference in tree version of CalibrateEmulateSample
 prepend!(LOAD_PATH, [joinpath(@__DIR__, "..")])
 
-using
-    EnsembleKalmanProcesses,
+using EnsembleKalmanProcesses,
     Documenter,
     Plots,  # so that Literate.jl does not capture precompilation output
     Literate
@@ -11,13 +10,11 @@ using
 # This happens as examples will use Plots.jl to make plots and movies.
 # See: https://github.com/jheinen/GR.jl/issues/278
 ENV["GKSwstype"] = "100"
-    
+
 const EXAMPLES_DIR = joinpath(@__DIR__, "..", "examples")
-const OUTPUT_DIR   = joinpath(@__DIR__, "src/literated")
+const OUTPUT_DIR = joinpath(@__DIR__, "src/literated")
 
-examples_for_literation = [
-    "LossMinimization/loss_minimization.jl"
-]
+examples_for_literation = ["LossMinimization/loss_minimization.jl"]
 
 for example in examples_for_literation
     example_filepath = joinpath(EXAMPLES_DIR, example)
@@ -28,17 +25,17 @@ end
 
 api = [
     "EnsembleKalmanProcessModule" => "API/EnsembleKalmanProcessModule.md",
-    "ParameterDistribution"       => "API/ParameterDistribution.md",
-    "Observations"                => "API/Observations.md",
-    "DataStorage"                 => "API/DataStorage.md",
-] 
+    "ParameterDistribution" => "API/ParameterDistribution.md",
+    "Observations" => "API/Observations.md",
+    "DataStorage" => "API/DataStorage.md",
+]
 
 examples = [
-    "Template"          => "examples/template_example.md",
-    "Cloudy"            => "examples/Cloudy_example.md",
-    "Lorenz"            => "examples/lorenz_example.md",
+    "Template" => "examples/template_example.md",
+    "Cloudy" => "examples/Cloudy_example.md",
+    "Lorenz" => "examples/lorenz_example.md",
     "Minimization Loss" => "literated/loss_minimization.md",
-    "HPC interfacing example: ClimateMachine" => "examples/ClimateMachine_example.md"
+    "HPC interfacing example: ClimateMachine" => "examples/ClimateMachine_example.md",
 ]
 
 pages = [
@@ -56,28 +53,25 @@ pages = [
 
 #----------
 
-format = Documenter.HTML(
-    collapselevel = 1,
-    prettyurls = !isempty(get(ENV, "CI", ""))
-)
+format = Documenter.HTML(collapselevel = 1, prettyurls = !isempty(get(ENV, "CI", "")))
 
 makedocs(
-   sitename = "EnsembleKalmanProcesses.jl",
+    sitename = "EnsembleKalmanProcesses.jl",
     authors = "CliMA Contributors",
-     format = format,
-      pages = pages,
+    format = format,
+    pages = pages,
     modules = [EnsembleKalmanProcesses],
     doctest = true,
-     strict = true,
-      clean = true,
-  checkdocs = :none,
+    strict = true,
+    clean = true,
+    checkdocs = :none,
 )
 
 if !isempty(get(ENV, "CI", ""))
-  deploydocs(
-            repo = "github.com/CliMA/EnsembleKalmanProcesses.jl.git",
+    deploydocs(
+        repo = "github.com/CliMA/EnsembleKalmanProcesses.jl.git",
         versions = ["stable" => "v^", "v#.#.#", "dev" => "dev"],
-    push_preview = true,
-       devbranch = "main",
-  )
+        push_preview = true,
+        devbranch = "main",
+    )
 end