Merge branch 'developer' into improve_assign_peptide_type_243 #86

	on:
	push:
	paths: [".[rR]", ".[qrR]md", ".[rR]markdown", ".[rR]nw", "**.[rR]profile"]

	name: Style
	env:
	GITHUB_ACTOR: "actions-user"

	jobs:
	style:
	runs-on: ubuntu-latest
	permissions:
	contents: write
	env:
	GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
	steps:
	- name: Checkout repo
	uses: actions/checkout@v4
	with:
	fetch-depth: 0

	- name: Setup R
	uses: r-lib/actions/setup-r@v2
	with:
	use-public-rspm: true

	- name: Install dependencies
	uses: r-lib/actions/setup-r-dependencies@v2
	with:
	extra-packages: any::styler, any::roxygen2
	needs: styler

	- name: Enable styler cache
	run: styler::cache_activate()
	shell: Rscript {0}

	- name: Determine cache location
	id: styler-location
	run: \|
	cat(
	"location=",
	styler::cache_info(format = "tabular")$location,
	"\n",
	file = Sys.getenv("GITHUB_OUTPUT"),
	append = TRUE,
	sep = ""
	)
	shell: Rscript {0}

	- name: Cache styler
	uses: actions/cache@v4
	with:
	path: ${{ steps.styler-location.outputs.location }}
	key: ${{ runner.os }}-styler-${{ github.sha }}
	restore-keys: \|
	${{ runner.os }}-styler-
	${{ runner.os }}-

	- name: Style
	run: styler::style_pkg()
	shell: Rscript {0}

	- name: Commit and push changes
	run: \|
	if FILES_TO_COMMIT=($(git diff-index --name-only ${{ github.sha }} \
	\| egrep --ignore-case '\.(R\|[qR]md\|Rmarkdown\|Rnw\|Rprofile)$'))
	then
	git config --local user.name "$GITHUB_ACTOR"
	git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
	git commit ${FILES_TO_COMMIT[*]} -m "Style code (GHA)"
	git pull --ff-only
	git push origin
	else
	echo "No changes to commit."
	fi

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