Set up repo, small plot

.dev/Project.toml

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

.dev/clima_formatter_options.jl

@@ -0,0 +1,8 @@
+clima_formatter_options = (
+    indent = 4,
+    margin = 80,
+    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/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)

.dev/up_deps.jl

@@ -0,0 +1,36 @@
+#=
+A simple script for updating the manifest
+files in all of our environments.
+=#
+
+root = dirname(@__DIR__)
+dirs = (
+    root,
+    joinpath(root, "test"),
+    joinpath(root, ".dev"),
+    joinpath(root, "perf"),
+    joinpath(root, "docs"),
+    joinpath(root, "examples"),
+)
+
+cd(root) do
+    for dir in dirs
+        reldir = relpath(dir, root)
+        @info "Updating environment `$reldir`"
+        cmd = if dir == root
+            `$(Base.julia_cmd()) --project -e """import Pkg; Pkg.update()"""`
+        elseif dir == joinpath(root, ".dev")
+            `$(Base.julia_cmd()) --project=$reldir -e """import Pkg; Pkg.update()"""`
+        else
+            `$(Base.julia_cmd()) --project=$reldir -e """import Pkg; Pkg.develop(;path=\".\"); Pkg.update()"""`
+        end
+        run(cmd)
+    end
+end
+
+# https://github.com/JuliaLang/Pkg.jl/issues/3014
+for dir in dirs
+    cd(dir) do
+        rm("LocalPreferences.toml"; force = true)
+    end
+end

.github/CompatHelper.yml

@@ -0,0 +1,16 @@
+name: CompatHelper
+on:
+  schedule:
+    - cron: '00 00 * * *'
+  workflow_dispatch:
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Pkg.add("CompatHelper")
+        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
+      - name: CompatHelper.main()
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}  # optional
+        run: julia -e 'using CompatHelper; CompatHelper.main()'

.github/TagBot.yml

@@ -0,0 +1,67 @@
+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+jobs:
+  TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}
+          changelog: |
+            ## {{ package }} {{ version }}
+            {% if previous_release %}
+            [Diff since {{ previous_release }}]({{ compare_url }})
+            {% endif %}
+            {% if custom %}
+            {{ custom }}
+            {% endif %}
+            ### 📢 API Changes:
+            {% if issues %}
+            {% for issue in issues if 'API' in issue.labels %}
+            - {{ issue.title }} (#{{ issue.number }})
+            {% endfor %}
+            {% endif %}
+            {% if pulls %}
+            {% for pull in pulls if 'API' in pull.labels %}
+            - {{ pull.title }} (#{{ pull.number }}) (@{{ pull.author.username }})
+            {% endfor %}
+            {% endif %}
+            ### 🚀 Features
+            {% if issues %}
+            {% for issue in issues if 'enhancement' in issue.labels or 'feature' in issue.labels %}
+            - {{ issue.title }} (#{{ issue.number }})
+            {% endfor %}
+            {% endif %}
+            {% if pulls %}
+            {% for pull in pulls if 'enhancement' in pull.labels or 'feature' in pull.labels %}
+            - {{ pull.title }} (#{{ pull.number }}) (@{{ pull.author.username }})
+            {% endfor %}
+            {% endif %}
+            ### 📑 Documentation
+            {% if issues %}
+            {% for issue in issues if 'documentation' in issue.labels %}
+            - {{ issue.title }} (#{{ issue.number }})
+            {% endfor %}
+            {% endif %}
+            {% if pulls %}
+            {% for pull in pulls if 'documentation' in pull.labels %}
+            - {{ pull.title }} (#{{ pull.number }}) (@{{ pull.author.username }})
+            {% endfor %}
+            {% endif %}
+            ### 🐛 Fixes
+            {% if issues %}
+            {% for issue in issues if 'bug' in issue.labels or 'bugfix' in issue.labels %}
+            - {{ issue.title }} (#{{ issue.number }})
+            {% endfor %}
+            {% endif %}
+            {% if pulls %}
+            {% for pull in pulls if 'bug' in pull.labels or 'bugfix' in pull.labels %}
+            - {{ pull.title }} (#{{ pull.number }}) (@{{ pull.author.username }})
+            {% endfor %}
+            {% endif %}

.github/julia_formatter.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/cancel-workflow-action@0.4.0
+      with:
+        access_token: ${{ github.token }}
+
+    - uses: actions/checkout@v2.2.0
+
+    - uses: dorny/paths-filter@v2.9.1
+      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: '1.8'
+
+    - 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

.gitignore

@@ -0,0 +1,22 @@
+# Simulation outputs 
+*.png
+*.hdf5
+
+# System-specific files and directories generated by the BinaryProvider and BinDeps packages
+# They contain absolute paths specific to the host computer, and so should not be committed
+deps/deps.jl
+deps/build.log
+deps/downloads/
+deps/usr/
+deps/src/
+
+# Build artifacts for creating documentation generated by the Documenter package
+docs/build/
+docs/site/
+
+# Julia package dependencies
+/Manifest.toml
+/*/Manifest.toml
+
+# misc
+.DS_Store

Project.toml

@@ -0,0 +1,4 @@
+name = "CalibrateClimaAtmos"
+uuid = "4347a170-ebd6-470c-89d3-5c705c0cacc2"
+authors = ["Climate Modeling Alliance"]
+version = "0.1.0"

examples/Project.toml

@@ -0,0 +1,2 @@
+[deps]
+ClimaAtmos = "b2c96348-7fb7-4fe0-8da9-78d88439e717"

plot/Project.toml

@@ -0,0 +1,4 @@
+[deps]
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+ClimaComms = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d"
+ClimaCore = "d414da3d-4745-48bb-8d80-42e94e092884"