setup-r-deps: replace github-token param with GITHUB_PAT env var
#1379
Workflow file for this run
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| --- | |
| 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" | |
| 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 ${{ env.PKGBUILD }} | |
| shell: bash | |
| - name: Rebuild R package 🏗 | |
| if: > | |
| (inputs.disable-unit-test-reports != 'true' || | |
| startsWith(github.ref, 'refs/tags/v')) && | |
| github.event_name != 'pull_request' | |
| run: | | |
| # Undo changes to DESCRIPTION and tests/testthat.R | |
| git checkout DESCRIPTION | |
| if [ -f "tests/testthat.R" ]; then | |
| git checkout tests/testthat.R | |
| fi | |
| if [ "${{ 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') | |
| 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 |