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refresh the CI a bit
1 parent 1fff45f commit 67e5469

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‎.github/ISSUE_TEMPLATE/custom.md‎

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‎.github/ISSUE_TEMPLATE/feature_request.md‎

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‎.github/workflows/CompatHelper.yml‎

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@@ -37,8 +37,7 @@ jobs:
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- name: "Run CompatHelper"
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run: |
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import CompatHelper
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CompatHelper.main(master_branch="develop")
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CompatHelper.main()
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shell: julia --color=yes {0}
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}

‎.github/workflows/ci.yml‎

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push:
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branches:
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- master
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pull_request:
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jobs:
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test:
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fail-fast: false
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matrix:
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version:
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- 'nightly'
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- '1' # This is always the latest stable release in the 1.X series
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- '1.10' # LTS
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#- 'nightly'
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os:
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- ubuntu-latest
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- macOS-latest
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#- macOS-latest
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#- windows-latest
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arch:
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- x64
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v4
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- uses: julia-actions/setup-julia@v1
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with:
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version: ${{ matrix.version }}
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arch: ${{ matrix.arch }}
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- uses: actions/cache@v1
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env:
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cache-name: cache-artifacts
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with:
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path: ~/.julia/artifacts
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key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
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restore-keys: |
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${{ runner.os }}-test-${{ env.cache-name }}-
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${{ runner.os }}-test-
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${{ runner.os }}-
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- uses: julia-actions/cache@v2
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- uses: julia-actions/julia-buildpkg@latest
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- run: |
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git config --global user.name Tester
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git config --global user.email te@st.er
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- uses: julia-actions/julia-runtest@latest
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continue-on-error: ${{ matrix.version == 'nightly' }}
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- uses: julia-actions/julia-processcoverage@v1
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- uses: codecov/codecov-action@v1
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- uses: codecov/codecov-action@v4
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with:
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file: lcov.info
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files: lcov.info
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token: ${{ secrets.CODECOV_TOKEN }}

‎.github/workflows/docker.yml‎

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name: Publish Docker image
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name: build docker image
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on:
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push:
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tags:
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- "v*"
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release:
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types: [published, created]
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branches:
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- master
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tags: '*'
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env:
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REGISTRY: ghcr.io
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IMAGE_NAME: lcsb-biocore/gigasom.jl # lowercase of ${{ github.repository }}
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jobs:
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push_to_registry:
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name: Push Docker image to GitHub Packages
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build:
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runs-on: ubuntu-latest
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permissions:
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contents: read
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packages: write
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steps:
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- name: Check out the repo
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uses: actions/checkout@v2
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- name: Push to GitHub Registry
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uses: mr-smithers-excellent/docker-build-push@v5
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with:
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image: gigasom.jl
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tags: latest
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registry: ghcr.io
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username: cylon-x
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password: ${{ secrets.docker_token }}
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- name: Checkout
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uses: actions/checkout@v4
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- name: log into docker registry
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uses: docker/login-action@v3
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with:
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registry: ${{ env.REGISTRY }}
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username: ${{ github.actor }}
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password: ${{ secrets.GITHUB_TOKEN }}
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- name: extract metadata
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id: meta
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uses: docker/metadata-action@v5
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with:
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images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
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- name: build and push the docker container
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uses: docker/build-push-action@v6
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with:
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context: .
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push: true
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tags: ${{ steps.meta.outputs.tags }}
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labels: ${{ steps.meta.outputs.labels }}

‎.github/workflows/docs.yml‎

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# ref: https://juliadocs.github.io/Documenter.jl/stable/man/hosting/#GitHub-Actions-1
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name: Documentation
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on:
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pull_request:
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push:
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branches:
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- develop
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- master
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tags: '*'
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release:
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types: [published, created]
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v4
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- uses: julia-actions/setup-julia@latest
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with:
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version: 1.7
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- uses: julia-actions/cache@v2
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- name: Install dependencies
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run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
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run: julia --color=yes --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
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- name: Build and deploy
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env:
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DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
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run: julia --project=docs/ docs/make.jl
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run: julia --color=yes --project=docs/ docs/make.jl

‎.github/workflows/pr-format.yml‎

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on:
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pull_request:
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issue_comment:
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types: [created]
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name: Formatting
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jobs:
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formatting:
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if: github.event_name == 'pull_request' || (github.event_name == 'issue_comment' && github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'COLLABORATOR' || github.event.comment.author_association == 'OWNER' || github.event.issue.user.id == github.event.comment.user.id) && startsWith(github.event.comment.body, '/format') )
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runs-on: ubuntu-latest
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steps:
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- name: Clone the repository
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uses: actions/checkout@v4
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- name: Checkout the pull request code # this checks out the actual branch so that one can commit into it
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if: github.event_name == 'issue_comment'
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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run: |
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gh pr checkout ${{ github.event.issue.number }}
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- name: Install JuliaFormatter and format
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run: |
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julia --color=yes -e 'import Pkg; Pkg.add("JuliaFormatter")'
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julia --color=yes -e 'using JuliaFormatter; format(".")'
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- name: Remove trailing whitespace
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run: |
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find -name '*.jl' -or -name '*.md' -or -name '*.toml' -or -name '*.yml' | while read filename ; do
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# remove any trailing spaces
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sed --in-place -e 's/\s*$//' "$filename"
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# add a final newline if missing
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if [[ -s "$filename" && $(tail -c 1 "$filename" |wc -l) -eq 0 ]] ; then
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echo >> "$filename"
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fi
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# squash superfluous final newlines
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sed -i -e :a -e '/^\n*$/{$d;N;};/\n$/ba' "$filename"
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done
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- name: Fail on formatting problems
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if: github.event_name == 'pull_request'
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run: |
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if git diff --exit-code --quiet
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then echo "Looks OK"
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else echo "Formatting fixes required!"; git diff -p ; exit 1
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fi
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- name: Commit fixes
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if: github.event_name == 'issue_comment'
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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run: |
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if [ `git status -s | wc -l` -ne 0 ] ; then
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git config --local user.name "$GITHUB_ACTOR"
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git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
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git commit -a -m "automatic formatting" -m "triggered by @$GITHUB_ACTOR on PR #${{ github.event.issue.number }}"
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if git push
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then gh pr comment ${{ github.event.issue.number }} --body \
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":heavy_check_mark: Auto-formatting triggered by [this comment](${{ github.event.comment.html_url }}) succeeded, commited as `git rev-parse HEAD`"
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else gh pr comment ${{ github.event.issue.number }} --body \
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":x: Auto-formatting triggered by [this comment](${{ github.event.comment.html_url }}) failed, perhaps someone pushed to the PR in the meantime?"
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fi
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else
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gh pr comment ${{ github.event.issue.number }} --body \
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":sunny: Auto-formatting triggered by [this comment](${{ github.event.comment.html_url }}) succeeded, but the code was already formatted correctly."
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fi

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