feat: Add option to disable package rebuilds and uploads #1382

Workflow file for this run

.github/workflows/build-check-install.yaml at 7d64b47

	---
	name: R CMD Check 🧬

	on:
	push:
	tags:
	- "v*"
	branches:
	- main
	pull_request:
	types:
	- opened
	- synchronize
	- reopened
	- ready_for_review
	branches:
	- main
	workflow_dispatch:
	workflow_call:
	secrets:
	REPO_GITHUB_TOKEN:
	description: \|
	Github token with read access to repositories, required for staged.dependencies installation
	required: false
	inputs:
	install-system-dependencies:
	description: Check for and install system dependencies
	required: false
	default: false
	type: boolean
	enable-staged-dependencies-check:
	description: Enable staged dependencies YAML check
	required: false
	default: false
	type: boolean
	R_CHECK_FORCE_SUGGESTS:
	description: If true, give an error if suggested packages are not available
	required: false
	default: true
	type: boolean
	skip-r-cmd-check:
	description: Skip the R CMD check step in this workflow
	required: false
	default: false
	type: boolean
	skip-r-cmd-install:
	description: Skip the R CMD INSTALL step in this workflow
	required: false
	default: true
	type: boolean
	enforce-note-blocklist:
	description: Whether to check for specific NOTEs via regexes that should cause the pipeline to fail
	required: false
	default: false
	type: boolean
	note-blocklist:
	description: \|
	List of regular expressions appearing in NOTEs that should cause the pipeline to fail.
	Example usage:
	note-blocklist: \|
	checking package dependencies ... NOTE( )+Depends: includes the non-default packages
	checking R code for possible problems ... NOTE( )+.*: no visible global function definition for
	checking for unstated dependencies in vignettes ... NOTE( )+\'.*\' import not declared from
	checking dependencies in R code ... NOTE( )+Namespace in Imports field not imported from
	checking installed package size ... NOTE( )+installed size is
	required: false
	default: ""
	type: string
	additional-r-cmd-check-params:
	description: Additional flags or parameters to add to R CMD check
	required: false
	default: ""
	type: string
	disable-unit-test-reports:
	description: Do not produce unit test reports
	required: false
	default: false
	type: boolean
	additional-env-vars:
	description: \|
	Extra environment variables, as a 'key=value' pair, with each pair on a new line.
	Example usage:
	additional-env-vars: \|
	ABC=123
	XYZ=456
	required: false
	default: ""
	type: string
	junit-xml-storage:
	description: Branch name to store JUnit XML reports
	required: false
	default: "_junit_xml_reports"
	type: string
	junit-xml-diff-branch:
	description: Against which branch should the JUnit XML report from the current branch be compared?
	required: false
	default: main
	type: string
	junit-xml-comparison:
	description: Turn on JUnit XML comparison
	required: false
	default: true
	type: boolean
	junit-xml-negative-threshold:
	description: \|
	If time difference during JUnit XML comparison is between negative-threshold and 0: it's treated as 0.
	This means that if test suite/case executes up to negative-threshold seconds faster,
	this time difference is ignored as insignificant, and test suite/case is not shown in the table
	required: false
	default: 1.0
	type: string
	junit-xml-positive-threshold:
	description: \|
	If time difference during JUnit XML comparison is between 0 and positive-threshold: it's treated as 0.
	This means that if test suite/case executes up to positive-threshold seconds slower,
	this time difference is ignored as insignificant, and test suite/case is not shown in the table
	required: false
	default: 1.0
	type: string
	sd-direction:
	description: The direction to use to install staged dependencies. Choose between 'upstream', 'downstream' and 'all'
	required: false
	type: string
	default: upstream
	install-deps-from-package-repositories:
	description: \|
	Set this to a comma-separated named list of R packages repositories to use for installing dependencies.
	Example: "R-universe=https://insightsengineering.r-universe.dev/,CRAN=https://cloud.r-project.org/"
	If the value is non-empty, it takes precedence over deps-installation-method.
	required: false
	type: string
	default: ""
	deps-installation-method:
	description: \|
	Which method for installing R package dependencies to use? Supported values are:
	staged-dependencies
	setup-r-dependencies
	required: false
	type: string
	default: staged-dependencies
	lookup-refs:
	description: \|
	List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'.
	required: false
	type: string
	default: ""
	skip-desc-branch:
	description: \|
	Passed to `insightsengineering/setup-r-dependencies`.
	Used only if deps-installation-method == 'setup-r-dependencies'.
	required: false
	type: boolean
	default: false
	skip-desc-dev:
	description: \|
	Passed to `insightsengineering/setup-r-dependencies`.
	Used only if deps-installation-method == 'setup-r-dependencies'.
	required: false
	type: boolean
	default: false
	repository-list:
	description: \|
	Passed to `insightsengineering/setup-r-dependencies`.
	Used only if deps-installation-method == 'setup-r-dependencies'.
	required: false
	type: string
	default: "PPM=PPM@latest"
	cache-version:
	description: \|
	Passed to `insightsengineering/setup-r-dependencies`.
	Used only if deps-installation-method == 'setup-r-dependencies'.
	required: false
	type: string
	default: "1"
	unit-test-report-brand:
	description: Image URL to use in unit test report for branding. If empty, the default xunit-viewer brand will be used.
	required: false
	type: string
	default: ""
	publish-unit-test-report-gh-pages:
	description: Publish HTML unit test report to GitHub Pages alongside pkgdown docs.
	required: false
	type: boolean
	default: true
	latest-tag-alt-name:
	description: \|
	The name of directory to store unit test report when running for latest tag.
	The variable is named this way to keep it consistent with r-pkgdown-multiversion input name.
	required: false
	type: string
	default: "latest-tag"
	release-candidate-alt-name:
	description: \|
	The name of directory to store unit test report when running for rc tag.
	The variable is named this way to keep it consistent with r-pkgdown-multiversion input name.
	required: false
	type: string
	default: "release-candidate"
	package-subdirectory:
	description: Subdirectory in the repository, where the R package is located.
	required: false
	type: string
	default: ""
	additional-caches:
	description: \|
	Additional cache directories. One cache path per new line.
	Example usage:
	additional-caches: \|
	~/awesome-cache
	/tmp/some-cache
	required: false
	type: string
	default: ""
	concurrency-group:
	description: \|
	Concurrency group name in case a calling workflow would like to use multiple instances of this workflow simultaneously.
	required: false
	type: string
	default: ""
	enable-sd:
	description: \|
	Whether the installation of package dependencies via staged.dependencies should be enabled.
	Has no effect if deps-installation-method == 'setup-r-dependencies' or
	install-deps-from-package-repositories is set to non-empty value.
	required: false
	type: boolean
	default: true
	update-r-packages:
	description: \|
	Whether R packages installed in the container should be updated to their latest version from CRAN/BioC.
	required: false
	type: boolean
	default: false
	unit-test-report-directory:
	description: \|
	Directory name on gh-pages branch where the unit test report will be uploaded.
	If the unit test report directory is different than the default 'unit-test-report',
	it has to be added to the additional-unit-test-report-directories pkgdown workflow input.
	Additionally, if the non-default unit test report should be shown in the GitHub Pages
	documentation drop-down, it has to be added to _pkgdown.yaml.
	required: false
	type: string
	default: "unit-test-report"
	disable-package-rebuild-and-upload:
	description: This will disable the package rebuild and upload step for versioned tags.
	required: false
	type: boolean
	default: false

	concurrency:
	group: r-cmd-${{ inputs.concurrency-group }}-${{ github.event.pull_request.number \|\| github.ref }}
	cancel-in-progress: true

	jobs:
	build-install-check:
	strategy:
	fail-fast: false
	matrix:
	config:
	- image: ghcr.io/insightsengineering/rstudio
	tag: latest
	name: ${{ matrix.config.image }}, version ${{ matrix.config.tag }}
	runs-on: ubuntu-latest
	if: >
	!contains(github.event.commits[0].message, '[skip r-cmd]')
	&& github.event.pull_request.draft == false
	container:
	image: ${{ matrix.config.image }}:${{ matrix.config.tag }}
	outputs:
	publish-unit-test-html-report: ${{ steps.junit-output.outputs.junit-upload }}
	current-branch-or-tag: ${{ steps.current-branch-or-tag.outputs.ref-name }}
	is-latest-tag: ${{ steps.current-branch-or-tag.outputs.is-latest-tag }}
	is-rc-tag: ${{ steps.current-branch-or-tag.outputs.is-rc-tag }}
	multiversion-docs: ${{ steps.current-branch-or-tag.outputs.multiversion-docs }}

	steps:
	- name: Setup token 🔑
	id: github-token
	run: \|
	if [ "${{ secrets.REPO_GITHUB_TOKEN }}" == "" ]; then
	echo "REPO_GITHUB_TOKEN is empty. Substituting it with GITHUB_TOKEN."
	echo "token=${{ secrets.GITHUB_TOKEN }}" >> $GITHUB_OUTPUT
	else
	echo "Using REPO_GITHUB_TOKEN."
	echo "token=${{ secrets.REPO_GITHUB_TOKEN }}" >> $GITHUB_OUTPUT
	fi
	shell: bash

	- name: Get branch names 🌿
	id: branch-name
	uses: tj-actions/branch-names@v7

	- name: Checkout repo (PR) 🛎
	uses: actions/[email protected]
	if: github.event_name == 'pull_request'
	with:
	ref: ${{ steps.branch-name.outputs.head_ref_branch }}
	path: ${{ github.event.repository.name }}
	repository: ${{ github.event.pull_request.head.repo.full_name }}
	fetch-depth: 0

	- name: Checkout repo 🛎
	uses: actions/[email protected]
	if: github.event_name != 'pull_request'
	with:
	ref: ${{ steps.branch-name.outputs.head_ref_branch }}
	path: ${{ github.event.repository.name }}

	- name: Check commit message 💬
	run: \|
	git config --global --add safe.directory $(pwd)
	export head_commit_message="$(git show -s --format=%B \| tr '\r\n' ' ' \| tr '\n' ' ')"
	echo "head_commit_message = $head_commit_message"
	if [[ $head_commit_message == "$SKIP_INSTRUCTION" ]]; then
	echo "Skip instruction detected - cancelling the workflow."
	exit 1
	fi
	shell: bash
	working-directory: ${{ github.event.repository.name }}
	env:
	SKIP_INSTRUCTION: "[skip r-cmd]"

	- name: Checkout gh-pages 🛎
	if: >-
	inputs.publish-unit-test-report-gh-pages == true
	&& github.event_name != 'pull_request'
	id: checkout-gh-pages
	uses: actions/[email protected]
	with:
	ref: gh-pages
	path: gh-pages
	repository: ${{ github.event.pull_request.head.repo.full_name }}
	continue-on-error: true

	- name: Get current branch or tag 🏷️
	if: >-
	inputs.publish-unit-test-report-gh-pages == true
	&& github.event_name != 'pull_request'
	id: current-branch-or-tag
	run: \|
	if [ "${{ steps.branch-name.outputs.is_tag }}" == "true" ]; then
	echo "Current tag: ${{ steps.branch-name.outputs.tag }}"
	echo "ref-name=${{ steps.branch-name.outputs.tag }}" >> $GITHUB_OUTPUT
	current_tag="${{ steps.branch-name.outputs.tag }}"
	if [ "$(echo "$current_tag" \| grep -E "^v([0-9]+\.)?([0-9]+\.)?([0-9]+)$")" != "" ]; then
	echo "Running for latest-tag."
	echo "is-latest-tag=true" >> $GITHUB_OUTPUT
	elif [ "$(echo "$current_tag" \| grep -E "^v([0-9]+\.)?([0-9]+\.)?([0-9]+)(-rc[0-9]+)$")" != "" ]; then
	echo "Running for rc-tag."
	echo "is-rc-tag=true" >> $GITHUB_OUTPUT
	fi
	else
	echo "Current branch: ${{ steps.branch-name.outputs.current_branch }}"
	echo "ref-name=${{ steps.branch-name.outputs.current_branch }}" >> $GITHUB_OUTPUT
	fi
	# Check if pkgdown multiversion docs are used at all.
	if [ $(grep -rl '<!-- start dropdown for versions -->' gh-pages \| wc -l) -gt 0 ]; then
	echo "multiversion-docs=true" >> $GITHUB_OUTPUT
	else
	echo "multiversion-docs=false" >> $GITHUB_OUTPUT
	fi
	shell: bash

	- name: Normalize variables 📏
	run: \|
	junit_xml_storage_input="${{ inputs.junit-xml-storage }}"
	junit_xml_diff_branch_input="${{ inputs.junit-xml-diff-branch }}"
	junit_xml_comparison_input="${{ inputs.junit-xml-comparison }}"
	junit_xml_positive_threshold="${{ inputs.junit-xml-positive-threshold }}"
	junit_xml_negative_threshold="${{ inputs.junit-xml-negative-threshold }}"
	enable_sd="${{ inputs.enable-sd }}"
	deps_installation_method="${{ inputs.deps-installation-method }}"
	echo "junit_xml_storage=${junit_xml_storage_input:-_junit_xml_reports}" >> $GITHUB_ENV
	echo "junit_xml_diff_branch=${junit_xml_diff_branch_input:-main}" >> $GITHUB_ENV
	echo "junit_xml_comparison=${junit_xml_comparison_input:-true}" >> $GITHUB_ENV
	echo "junit_xml_positive_threshold=${junit_xml_positive_threshold:-1.0}" >> $GITHUB_ENV
	echo "junit_xml_negative_threshold=${junit_xml_negative_threshold:-1.0}" >> $GITHUB_ENV
	echo "enable_sd=${enable_sd:-true}" >> $GITHUB_ENV
	echo "deps_installation_method=${deps_installation_method:-staged-dependencies}" >> $GITHUB_ENV
	shell: bash

	- name: Restore npm cache 💰
	if: >-
	inputs.publish-unit-test-report-gh-pages == true
	&& github.event_name != 'pull_request'
	uses: actions/cache@v4
	with:
	key: npm-${{ runner.os }}-${{ github.job }}
	restore-keys: \|
	npm-${{ runner.os }}-
	path: node_modules

	- name: Setup NodeJS ☊
	if: >-
	inputs.publish-unit-test-report-gh-pages == true
	&& github.event_name != 'pull_request'
	uses: actions/setup-node@v4
	id: npm-cache
	with:
	node-version: 20

	- name: Install xunit-viewer ⚙️
	if: >-
	steps.npm-cache.outputs.cache-hit != 'true'
	&& inputs.publish-unit-test-report-gh-pages == true
	&& github.event_name != 'pull_request'
	run: npm i -g xunit-viewer
	shell: bash

	- name: Restore SD cache 💰
	if: >-
	inputs.install-deps-from-package-repositories == ''
	&& env.deps_installation_method == 'staged-dependencies'
	uses: actions/cache@v4
	with:
	key: sd-${{ runner.os }}-${{ github.event.repository.name }}
	path: ~/.staged.dependencies

	- name: Update R packages 🗓️
	if: >-
	inputs.update-r-packages == true
	run: \|
	update.packages()
	shell: Rscript {0}

	- name: Run Staged dependencies 🎦
	if: >-
	env.enable_sd == 'true'
	&& inputs.install-deps-from-package-repositories == ''
	&& env.deps_installation_method == 'staged-dependencies'
	uses: insightsengineering/staged-dependencies-action@v2
	env:
	GITHUB_PAT: ${{ steps.github-token.outputs.token }}
	with:
	path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
	enable-check: ${{ inputs.enable-staged-dependencies-check }}
	run-system-dependencies: ${{ inputs.install-system-dependencies }}
	direction: ${{ inputs.sd-direction }}

	- name: Setup R dependencies 🎦
	if: >-
	env.deps_installation_method == 'setup-r-dependencies'
	&& inputs.install-deps-from-package-repositories == ''
	uses: insightsengineering/setup-r-dependencies@v1
	env:
	GITHUB_PAT: ${{ steps.github-token.outputs.token }}
	with:
	lookup-refs: ${{ inputs.lookup-refs }}
	repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
	skip-desc-branch: ${{ inputs.skip-desc-branch }}
	skip-desc-dev: ${{ inputs.skip-desc-dev }}
	repository-list: ${{ inputs.repository-list }}
	cache-version: ${{ inputs.cache-version }}

	- name: Install dependencies from package repositories 🗄️
	if: inputs.install-deps-from-package-repositories != ''
	run: \|
	split_to_map <- function(args) {
	tmp <- strsplit(x = unlist(strsplit(args, ",")), "=")
	content <- unlist(lapply(tmp, function(x) x[2]))
	names(content) <- unlist(lapply(tmp, function(x) x[1]))
	return(content)
	}
	devtools::install_dev_deps(".", repos = split_to_map("${{ inputs.install-deps-from-package-repositories }}"))
	shell: Rscript {0}
	working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}

	- name: Show session info and installed packages ℹ
	run: \|
	sessionInfo()
	as.data.frame(installed.packages()[, c("LibPath", "Version")])
	if (grepl("--as-cran", "${{ inputs.additional-r-cmd-check-params }}", fixed = TRUE)) {
	x <- desc::desc_del("Remotes")
	}
	if ("${{ inputs.disable-unit-test-reports }}" != "true") {
	x <- desc::desc_set_dep("xml2", "Suggests")
	}
	shell: Rscript {0}
	working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}

	- name: Get package name 📦
	run: \|
	echo "PKGBUILD=$(echo $(awk -F: '/Package:/{gsub(/[ ]+/,"") ; print $2}' DESCRIPTION)_"\
	"$(awk -F: '/Version:/{gsub(/[ ]+/,"") ; print $2}' DESCRIPTION).tar.gz)" >> $GITHUB_ENV
	echo "PKGNAME=$(echo $(awk -F: '/Package:/{gsub(/[ ]+/,"") ; print $2}' DESCRIPTION))" >> $GITHUB_ENV
	shell: bash
	working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}

	- name: Replace testthat.R for test reporting 🎚
	if: inputs.disable-unit-test-reports != 'true'
	run: \|
	if [ -f "tests/testthat.R" ]; then {
	# Overwrite testthat.R for JUnit XML reporting
	cat > tests/testthat.R <<EOF
	pkg_name <- "${{ env.PKGNAME }}"
	if (requireNamespace("testthat", quietly = TRUE)) {
	library(testthat)
	reporter <- MultiReporter\$new(list(
	CheckReporter\$new(),
	JunitReporter\$new(file = "junit-result.xml")
	))
	test_check(pkg_name, reporter = reporter)
	}
	EOF
	}
	cat tests/testthat.R
	fi
	shell: bash
	working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}

	- name: Restore any additional caches 📥
	if: inputs.additional-caches != ''
	uses: actions/cache@v4
	with:
	path: "${{ inputs.additional-caches }}"
	key: additional-caches-${{ runner.os }}

	- name: Build R package 🏗
	run: \|
	if [ "${{ inputs.additional-env-vars }}" != "" ]
	then {
	echo -e "${{ inputs.additional-env-vars }}" > /tmp/dotenv.env
	export $(tr '\n' ' ' < /tmp/dotenv.env)
	}
	fi
	R CMD build ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
	shell: bash

	- name: Run R CMD check 🏁
	run: \|
	if [ "${{ inputs.skip-r-cmd-check }}" == "true" ]
	then {
	echo "Skipping R CMD check as 'skip-r-cmd-check' was set to 'true'"
	exit 0
	}
	fi
	if [ "${{ inputs.R_CHECK_FORCE_SUGGESTS }}" == "" ]
	then {
	_R_CHECK_FORCE_SUGGESTS_="FALSE"
	}
	fi
	ADDITIONAL_PARAMS=${{ inputs.additional-r-cmd-check-params }}
	if [[ ! -z "${{ env.NO_TESTS }}" ]]
	then {
	ADDITIONAL_PARAMS="${ADDITIONAL_PARAMS} --no-tests"
	}
	fi
	if [ "${{ inputs.additional-env-vars }}" != "" ]
	then {
	echo -e "${{ inputs.additional-env-vars }}" > /tmp/dotenv.env
	export $(tr '\n' ' ' < /tmp/dotenv.env)
	}
	fi
	Rscript - <<EOF
	if ("${{ inputs.disable-unit-test-reports }}" != "true") {
	if (!require("xml2")) {
	install.packages("xml2", repos = "https://cloud.r-project.org", quiet = TRUE)
	}
	}
	EOF
	R CMD check ${ADDITIONAL_PARAMS} ${{ env.PKGBUILD }}
	shell: bash
	continue-on-error: true
	env:
	_R_CHECK_TESTS_NLINES_: 0
	_R_CHECK_VIGNETTES_NLINES_: 0
	_R_CHECK_FORCE_SUGGESTS_: ${{ inputs.R_CHECK_FORCE_SUGGESTS }}

	- name: Fetch report from ${{ env.junit_xml_storage }} ⤵️
	if: env.junit_xml_comparison == 'true'
	uses: actions/[email protected]
	with:
	path: ${{ env.junit_xml_storage }}
	fetch-depth: 0

	- name: Initialize storage branch ${{ env.junit_xml_storage }} 🗄️
	if: env.junit_xml_comparison == 'true'
	working-directory: ${{ env.junit_xml_storage }}
	run: \|
	git config --global --add safe.directory ${PWD}
	git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
	git config --global user.name "github-actions[bot]"
	# Switch to the branch if it already exists
	git switch ${{ env.junit_xml_storage }} \|\| true
	git pull origin ${{ env.junit_xml_storage }} \|\| true
	# Create the branch if it doesn't exist yet
	git checkout --orphan ${{ env.junit_xml_storage }} \|\| true
	# Ensure that the bare minimum components exist in the branch
	mkdir -p data
	touch README.md data/.gitkeep
	# Copy necessary files and folders to a temporary location
	mkdir -p /tmp/${{ github.sha }}
	echo "Copying data to /tmp/${{ github.sha }}"
	cp -r .git README.md data /tmp/${{ github.sha }}
	# Remove everything else
	# Attribution: https://unix.stackexchange.com/a/77313
	rm -rf ..?* .[!.]* *
	# Restore files from the temporary location
	echo "Copying data from /tmp/${{ github.sha }}"
	cp -r /tmp/${{ github.sha }}/.git /tmp/${{ github.sha }}/README.md /tmp/${{ github.sha }}/data .
	rm -rf /tmp/${{ github.sha }}
	git add --all -f
	git commit -m "Update storage branch: $(date)" \|\| true
	shell: bash

	- name: Push storage branch ${{ env.junit_xml_storage }} 🗄️
	if: env.junit_xml_comparison == 'true'
	uses: ad-m/github-push-action@master
	with:
	github_token: ${{ steps.github-token.outputs.token }}
	branch: ${{ env.junit_xml_storage }}
	directory: ${{ env.junit_xml_storage }}
	force: true
	continue-on-error: true

	- name: Check whether JUnit XML report exists 🚦
	id: check-junit-xml
	uses: andstor/file-existence-action@v3
	with:
	files: "${{ env.PKGNAME }}.Rcheck/tests/testthat/junit-result.xml"

	- name: Convert JUnit XML to HTML 📝
	if: >-
	steps.check-junit-xml.outputs.files_exists == 'true'
	&& inputs.publish-unit-test-report-gh-pages == true
	&& github.event_name != 'pull_request'
	run: \|
	brand_option=""
	if [ "${{ inputs.unit-test-report-brand }}" != "" ]; then
	brand_option='--brand ${{ inputs.unit-test-report-brand }}'
	fi
	xunit-viewer -r "${{ env.PKGNAME }}.Rcheck/tests/testthat/junit-result.xml" \
	-o index.html \
	-f "https://www.clipboardmaster.com/favicon.ico" \
	-t "${{ env.PKGNAME }} Unit Test Results" \
	$brand_option
	shell: bash

	- name: Publish JUnit XML as artifact 📰
	if: >-
	steps.check-junit-xml.outputs.files_exists == 'true'
	&& inputs.publish-unit-test-report-gh-pages == true
	&& github.event_name != 'pull_request'
	uses: actions/upload-artifact@v4
	with:
	name: unit-test-report-${{ inputs.concurrency-group }}
	path: "index.html"

	- name: Set output ⚙️
	id: junit-output
	if: >-
	steps.check-junit-xml.outputs.files_exists == 'true'
	&& inputs.publish-unit-test-report-gh-pages == true
	&& github.event_name != 'pull_request'
	run: echo "junit-upload=true" >> $GITHUB_OUTPUT

	- name: Publish Unit Test Summary 📑
	uses: EnricoMi/publish-unit-test-result-action@v2
	id: test-results
	# Second line of the condition skips the step if workflow is running in a fork.
	if: \|
	steps.check-junit-xml.outputs.files_exists == 'true' && github.event_name == 'pull_request' &&
	github.event.pull_request.head.repo.full_name == github.event.pull_request.base.repo.full_name
	with:
	check_name: Unit Tests Summary
	junit_files: "${{ env.PKGNAME }}.Rcheck/tests/testthat/junit-result.xml"

	- name: Fetch JUnit XML reports from ${{ env.junit_xml_storage }} ⤵️
	if: steps.check-junit-xml.outputs.files_exists == 'true' && env.junit_xml_comparison == 'true'
	uses: actions/[email protected]
	with:
	path: ${{ env.junit_xml_storage }}
	fetch-depth: 0

	- name: Set up ${{ env.junit_xml_storage }} branch for reports 🗃️
	if: steps.check-junit-xml.outputs.files_exists == 'true' && env.junit_xml_comparison == 'true'
	run: \|
	BRANCH=${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}}
	echo "diff_storage_branch=$BRANCH" >> $GITHUB_ENV
	mkdir -p ${{ env.junit_xml_storage }}/data/${BRANCH}
	shell: bash

	- name: Commit JUnit XML report 📄
	if: steps.check-junit-xml.outputs.files_exists == 'true' && env.junit_xml_comparison == 'true'
	working-directory: ${{ env.junit_xml_storage }}/data
	run: \|
	git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
	git config --global user.name "github-actions[bot]"
	git switch ${{ env.junit_xml_storage }} \|\| true
	git config pull.rebase false
	git pull origin ${{ env.junit_xml_storage }} \|\| true
	cp ../../${{ env.PKGNAME }}.Rcheck/tests/testthat/junit-result.xml \
	'./${{ env.diff_storage_branch }}/junit-result.xml'
	git add -f '${{ env.diff_storage_branch }}/junit-result.xml'
	git commit -m "Add/Update JUnit report: ${{ github.sha }}" \|\| true
	shell: bash

	- name: Push JUnit XML report to ${{ env.junit_xml_storage }} 📄
	if: steps.check-junit-xml.outputs.files_exists == 'true' && env.junit_xml_comparison == 'true'
	uses: ad-m/github-push-action@master
	with:
	github_token: ${{ steps.github-token.outputs.token }}
	branch: ${{ env.junit_xml_storage }}
	directory: ${{ env.junit_xml_storage }}/data
	continue-on-error: true

	- name: Run XML comparison 🔍
	if: steps.check-junit-xml.outputs.files_exists == 'true' && env.junit_xml_comparison == 'true'
	run: \|
	cp '${{ env.junit_xml_storage }}/data/${{ env.diff_storage_branch }}/junit-result.xml' new.xml
	if [ ! -f ${{ env.junit_xml_storage }}/data/${{ env.junit_xml_diff_branch }}/junit-result.xml ]; then
	# If XML for the branch against which we're comparing doesn't exist, we're skipping the comparison.
	echo "JUnit report for branch \`${{ env.junit_xml_diff_branch }}\` " \
	"doesn't exist on \`${{ env.junit_xml_storage }}\` branch yet." > output.md
	echo "Once this workflow runs on \`${{ env.junit_xml_diff_branch }}\` branch, " \
	"you'll see comparison of tests performance between \`${{ env.junit_xml_diff_branch }}\` " \
	"and \`${{ env.diff_storage_branch }}\` as a PR comment." >> output.md
	else
	cp ${{ env.junit_xml_storage }}/data/${{ env.junit_xml_diff_branch }}/junit-result.xml old.xml
	wget https://github.com/insightsengineering/junit-xml-diff/releases/download/v0.4.0/junit-xml-diff_0.4.0_linux_amd64.tar.gz \
	-O junit-xml-diff.tar.gz
	tar xzf junit-xml-diff.tar.gz
	./junit-xml-diff old.xml new.xml output.md '${{ env.junit_xml_diff_branch }}' \
	'${{ env.junit_xml_positive_threshold }}' '${{ env.junit_xml_negative_threshold }}'
	if [ "$(du -b output.md \| awk '{print $1}')" != "0" ]; then
	# Non-empty output which means that there is at least one test suite/case in the table.
	# Empty table won't be published since junit_xml_comparison_result_method won't be set.
	echo "junit_xml_comparison_result_method=comment" >> $GITHUB_ENV
	echo "" >> output.md
	echo "Results for commit ${{ github.sha }}" >> output.md
	echo "" >> output.md
	echo "♻️ This comment has been updated with latest results." >> output.md
	cp output.md output-artifact.md
	echo "Size of markdown: $(du -b output.md \| awk '{print $1}') bytes"
	if [ "$(du -b output.md \| awk '{print $1}')" -ge "60000" ]; then
	echo "The result of JUnit XML file comparison exceeded maximum size. " \
	"The report has therefore been uploaded as an R CMD check workflow artifact." > output.md
	echo "junit_xml_comparison_result_method=artifact" >> $GITHUB_ENV
	fi
	echo "Markdown output:"
	cat output.md
	else
	echo "No test suites/cases in JUnit XML file difference."
	fi
	fi

	- name: Post JUnit XML comparison as comment 💬
	if: >
	steps.check-junit-xml.outputs.files_exists == 'true' &&
	env.junit_xml_comparison == 'true' &&
	env.junit_xml_comparison_result_method == 'comment' &&
	!github.event.pull_request.head.repo.fork &&
	github.event_name == 'pull_request'
	uses: marocchino/sticky-pull-request-comment@v2
	with:
	header: markdown-table
	path: output.md
	continue-on-error: true

	- name: Upload JUnit XML comparison ⤴
	if: >
	steps.check-junit-xml.outputs.files_exists == 'true' &&
	env.junit_xml_comparison == 'true' &&
	env.junit_xml_comparison_result_method == 'artifact' &&
	!github.event.pull_request.head.repo.fork &&
	github.event_name == 'pull_request'
	uses: actions/upload-artifact@v4
	with:
	path: output-artifact.md
	name: junit-xml-report-comparison
	continue-on-error: true

	- name: Show R CMD check logs 🔎
	if: inputs.skip-r-cmd-check != true
	run: \|
	find ${{ env.PKGNAME }}.Rcheck -type f -regextype posix-egrep \
	-regex '.00install.out\|.00check.log\|.00build.out\|.-Ex.Rout\|.tests/testthat\.Rout.' \
	-print0 \| while IFS= read -r -d $'\0' file; do
	# Grouping allows to collapse/expand logs when needed.
	echo "::group::$file"
	cat $file
	echo "::endgroup::"
	done
	shell: bash

	- name: Catch warnings in R CMD check output 🗳
	id: catch-errors
	run: \|
	check_log <- "${{ env.PKGNAME }}.Rcheck/00check.log"
	if (file.exists(check_log)) {
	x <- tail(readLines(check_log), 1)
	if (grepl("ERROR", x)) {
	writeLines(readLines(check_log))
	stop("❌ R CMD check has errors. Please refer to the 'Show R CMD check logs 🔎' step above.")
	}
	if (grepl("WARNING", x)) {
	writeLines(readLines(check_log))
	stop("⚠ R CMD check has warnings. Please refer to the 'Show R CMD check logs 🔎' step above.")
	}
	if ("${{ inputs.enforce-note-blocklist }}" == "true") {
	print("Checking notes...")
	regexes <- "${{ inputs.note-blocklist }}"
	regexes <- unlist(strsplit(regexes, split = "\n"))
	lines <- paste(readLines(check_log), collapse = "\n")
	notes_result <- vapply(
	regexes,
	function(r){
	if (grepl(paste0(r, "\n"), lines, perl=T)) {
	print(r)
	return(TRUE)
	}
	return(FALSE)
	},
	logical(1)
	)
	if (any(notes_result)) {
	stop("NOTEs on the blocklist were found. Please refer to the 'Run R CMD check 🏁' step above.")
	}
	}
	}
	shell: Rscript {0}

	- name: Install R package 🚧
	run: \|
	if [ "${{ inputs.skip-r-cmd-install }}" == "true" ]
	then {
	echo "Skipping R CMD INSTALL as 'skip-r-cmd-install' was set to 'true'"
	exit 0
	}
	fi
	if [ "${{ inputs.additional-env-vars }}" != "" ]
	then {
	echo -e "${{ inputs.additional-env-vars }}" > /tmp/dotenv.env
	export $(tr '\n' ' ' < /tmp/dotenv.env)
	}
	fi
	R CMD INSTALL ${{ env.PKGBUILD }}
	shell: bash

	- name: Rebuild R package 🏗
	if: >
	(inputs.disable-unit-test-reports != 'true' \|\|
	startsWith(github.ref, 'refs/tags/v')) &&
	github.event_name != 'pull_request' &&
	inputs.disable-package-rebuild-and-upload != 'true'
	run: \|
	# Undo changes to DESCRIPTION and tests/testthat.R
	git checkout DESCRIPTION
	if [ -f "tests/testthat.R" ]; then
	git checkout tests/testthat.R
	fi
	if [ "${{ inputs.additional-env-vars }}" != "" ]
	then {
	echo -e "${{ inputs.additional-env-vars }}" > /tmp/dotenv.env
	export $(tr '\n' ' ' < /tmp/dotenv.env)
	}
	fi
	R CMD build .
	shell: bash
	working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}

	- name: Upload package build ⤴
	if: >
	startsWith(github.ref, 'refs/tags/v') &&
	inputs.disable-package-rebuild-and-upload != 'true'
	uses: actions/upload-artifact@v4
	with:
	path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}/${{ env.PKGBUILD }}
	name: ${{ env.PKGBUILD }}
	overwrite: true

	- name: Upload logs artifact 🗞️
	uses: actions/upload-artifact@v4
	with:
	path: \|
	${{ env.PKGNAME }}.Rcheck/*00install.out
	${{ env.PKGNAME }}.Rcheck/*00check.log
	${{ env.PKGNAME }}.Rcheck/*00build.out
	${{ env.PKGNAME }}.Rcheck/*-Ex.Rout
	${{ env.PKGNAME }}.Rcheck/tests/testthat.Rout
	${{ env.PKGNAME }}.Rcheck/tests/testthat.Rout.fail
	name: check-logs-${{ env.PKGNAME }}-${{ inputs.concurrency-group }}

	publish-junit-html-report:
	name: Publish JUnit HTML report 📰
	runs-on: ubuntu-latest
	needs: build-install-check
	if: >
	needs.build-install-check.outputs.publish-unit-test-html-report == 'true'
	&& github.event_name != 'pull_request'
	# Only one job can publish to gh-pages branch concurrently.
	concurrency:
	group: ghpages
	steps:
	- name: Setup token 🔑
	id: github-token
	run: \|
	if [ "${{ secrets.REPO_GITHUB_TOKEN }}" == "" ]; then
	echo "REPO_GITHUB_TOKEN is empty. Substituting it with GITHUB_TOKEN."
	echo "token=${{ secrets.GITHUB_TOKEN }}" >> $GITHUB_OUTPUT
	else
	echo "Using REPO_GITHUB_TOKEN."
	echo "token=${{ secrets.REPO_GITHUB_TOKEN }}" >> $GITHUB_OUTPUT
	fi
	shell: bash

	- name: Download JUnit HTML report as artifact ⤵️
	uses: actions/download-artifact@v4
	with:
	name: unit-test-report-${{ inputs.concurrency-group }}
	path: unit-test-report

	- name: Upload JUnit HTML report to GitHub pages 🗞️
	if: needs.build-install-check.outputs.multiversion-docs == 'true'
	uses: peaceiris/actions-gh-pages@v4
	with:
	github_token: ${{ steps.github-token.outputs.token }}
	publish_dir: ./unit-test-report
	destination_dir: ${{ needs.build-install-check.outputs.current-branch-or-tag }}/${{ inputs.unit-test-report-directory }}

	- name: Upload JUnit HTML report to GitHub pages (latest-tag) 🏷️
	if: >
	needs.build-install-check.outputs.is-latest-tag == 'true'
	&& needs.build-install-check.outputs.multiversion-docs == 'true'
	uses: peaceiris/actions-gh-pages@v4
	with:
	github_token: ${{ steps.github-token.outputs.token }}
	publish_dir: ./unit-test-report
	destination_dir: ${{ inputs.latest-tag-alt-name }}/${{ inputs.unit-test-report-directory }}

	- name: Upload JUnit HTML report to GitHub pages (release-candidate) 🏷️
	if: >
	needs.build-install-check.outputs.is-rc-tag == 'true'
	&& needs.build-install-check.outputs.multiversion-docs == 'true'
	uses: peaceiris/actions-gh-pages@v4
	with:
	github_token: ${{ steps.github-token.outputs.token }}
	publish_dir: ./unit-test-report
	destination_dir: ${{ inputs.release-candidate-alt-name }}/${{ inputs.unit-test-report-directory }}

	- name: Upload JUnit HTML report to GitHub pages (non-multiversion) 🗞️
	if: needs.build-install-check.outputs.multiversion-docs == 'false'
	uses: peaceiris/actions-gh-pages@v4
	with:
	github_token: ${{ steps.github-token.outputs.token }}
	publish_dir: ./unit-test-report
	destination_dir: ${{ inputs.unit-test-report-directory }}

	upload-release-assets:
	name: Upload build tar.gz
	needs: build-install-check
	runs-on: ubuntu-latest
	if: >
	startsWith(github.ref, 'refs/tags/v')
	&& (!contains(github.event.commits[0].message, '[skip r-cmd]'))
	&& github.event.pull_request.draft == false

	steps:
	- name: Checkout repo 🛎
	uses: actions/[email protected]

	- name: Get package build filename 📦
	run: \|
	echo "PKGBUILD=$(echo $(awk -F: '/Package:/{gsub(/[ ]+/,"") ; print $2}' DESCRIPTION)_"\
	"$(awk -F: '/Version:/{gsub(/[ ]+/,"") ; print $2}' DESCRIPTION).tar.gz)" >> $GITHUB_ENV
	shell: bash

	- name: Download artifact ⏬
	uses: actions/download-artifact@v4
	with:
	name: ${{ env.PKGBUILD }}

	- name: Check if release exists
	id: check-if-release-exists
	uses: insightsengineering/release-existence-action@v1

	- name: Upload binaries to release 🔼
	if: >-
	steps.check-if-release-exists.outputs.release-exists == 'true'
	uses: svenstaro/upload-release-action@v2
	with:
	repo_token: ${{ secrets.GITHUB_TOKEN }}
	file: ${{ env.PKGBUILD }}
	asset_name: ${{ env.PKGBUILD }}
	tag: ${{ github.ref }}
	overwrite: true

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feat: Add option to disable package rebuilds and uploads #1382

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feat: Add option to disable package rebuilds and uploads #1382

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