Merge pull request #2 from CliMA/dy/project_stub

Add preliminary files for setting up package

.dev/Project.toml

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

.dev/clima_formatter_options.jl

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+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

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+#!/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

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+#!/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/CodeCov.yml

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+name: CodeCov
+
+on:
+  push:
+    branches:
+      - main
+    tags: '*'
+  pull_request:
+  merge_group:
+
+jobs:
+  codecov:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Julia
+      uses: julia-actions/setup-julia@latest
+      with:
+        version: '1.10'
+
+    - name: Test with coverage
+      env:
+        JULIA_PROJECT: "@."
+      run: |
+        julia --project=@. -e 'using Pkg; Pkg.instantiate()'
+        julia --project=@. -e 'using Pkg; Pkg.test(coverage=true)'
+
+    - name: Generate coverage file
+      env:
+        JULIA_PROJECT: "@."
+      run: julia --project=@. -e 'using Pkg; Pkg.add("Coverage");
+                                  using Coverage;
+                                  LCOV.writefile("coverage-lcov.info", Codecov.process_folder())'
+      if: success()
+
+    - name: Submit coverage
+      uses: codecov/codecov-action@v3
+      with:
+        token: ${{secrets.CODECOV_TOKEN}}
+      if: success()
+

.github/workflows/CompatHelper.yml

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+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/workflows/JuliaFormatter.yml

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+name: JuliaFormatter
+
+on:
+  push:
+    branches:
+      - main
+    tags: '*'
+  pull_request:
+  merge_group:
+
+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/checkout@v4
+
+    - uses: dorny/paths-filter@v2
+      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: '1.10'
+
+    - 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

.github/workflows/TagBot.yml

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+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 }}

.github/workflows/ci.yml

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+name: ci
+on:
+  push:
+    branches:
+      - main
+    tags: '*'
+  pull_request:
+  merge_group:
+
+jobs:
+  test:
+    name: ci ${{ matrix.version }} - ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.10'
+        os:
+          - ubuntu-latest
+          - macOS-latest
+          - windows-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: actions/cache@v1
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-test-${{ env.cache-name }}-
+            ${{ runner.os }}-test-
+            ${{ runner.os }}-
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
+        with:
+          file: lcov.info

.github/workflows/invalidations.yml

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+name: Invalidations
+
+on:
+  pull_request:
+
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: always.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  evaluate:
+    # Only run on PRs to the default branch.
+    # In the PR trigger above branches can be specified only explicitly whereas this check should work for master, main, or any other default branch
+    if: github.base_ref == github.event.repository.default_branch
+    runs-on: ubuntu-latest
+    steps:
+    - uses: julia-actions/setup-julia@v1
+      with:
+        version: '1'
+    - uses: actions/checkout@v4
+    - uses: julia-actions/julia-buildpkg@v1
+    - uses: julia-actions/julia-invalidations@v1
+      id: invs_pr
+
+    - uses: actions/checkout@v4
+      with:
+        ref: ${{ github.event.repository.default_branch }}
+    - uses: julia-actions/julia-buildpkg@v1
+    - uses: julia-actions/julia-invalidations@v1
+      id: invs_default
+
+    - name: Report invalidation counts
+      run: |
+        echo "Invalidations on default branch: ${{ steps.invs_default.outputs.total }} (${{ steps.invs_default.outputs.deps }} via deps)" >> $GITHUB_STEP_SUMMARY
+        echo "This branch: ${{ steps.invs_pr.outputs.total }} (${{ steps.invs_pr.outputs.deps }} via deps)" >> $GITHUB_STEP_SUMMARY
+    - name: Check if the PR does increase number of invalidations
+      if: steps.invs_pr.outputs.total > steps.invs_default.outputs.total
+      run: exit 1

.gitignore

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+# Files generated by invoking Julia with --code-coverage
+*.jl.cov
+*.jl.*.cov
+
+# Files generated by invoking Julia with --track-allocation
+*.jl.mem
+*.html
+
+# 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/
+
+# File generated by Pkg, the package manager, based on a corresponding Project.toml
+# It records a fixed state of all packages used by the project. As such, it should not be
+# committed for packages, but should be committed for applications that require a static
+# environment.
+Manifest.toml

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Charles Kawczynski
+
+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.