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Initialize repo #2
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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: | ||
| GITHUB_TOKEN: | ||
|
Check failure on line 21 in .github/workflows/build-check-install.yaml
|
||
| 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/" | ||
| required: false | ||
| type: string | ||
| default: "" | ||
| 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: r-cmd-${{ 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.GITHUB_TOKEN }}" == "" ]; then | ||
| echo "GITHUB_TOKEN is empty. Substituting it with GITHUB_TOKEN." | ||
| echo "token=${{ secrets.GITHUB_TOKEN }}" >> $GITHUB_OUTPUT | ||
| else | ||
| echo "Using GITHUB_TOKEN." | ||
| echo "token=${{ secrets.GITHUB_TOKEN }}" >> $GITHUB_OUTPUT | ||
| fi | ||
| shell: bash | ||
| - name: Get branch names 🌿 | ||
| id: branch-name | ||
| uses: tj-actions/branch-names@v7 | ||
| - name: Checkout gh-pages 🛎 | ||
| if: >- | ||
| inputs.publish-unit-test-report-gh-pages == true | ||
| && github.event_name != 'pull_request' | ||
| id: checkout-gh-pages | ||
| uses: actions/checkout@v4 | ||
| 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 }}" | ||
| 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}" >> $GITHUB_ENV | ||
| shell: bash | ||
| - name: Restore npm cache 💰 | ||
| if: >- | ||
| inputs.publish-unit-test-report-gh-pages == true | ||
| && github.event_name != 'pull_request' | ||
| uses: actions/cache@v3 | ||
| with: | ||
| key: npm-${{ 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: Checkout repo (PR) 🛎 | ||
| uses: actions/checkout@v4 | ||
| 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 }} | ||
| - name: Checkout repo 🛎 | ||
| uses: actions/checkout@v4 | ||
| if: github.event_name != 'pull_request' | ||
| with: | ||
| ref: ${{ steps.branch-name.outputs.head_ref_branch }} | ||
| path: ${{ github.event.repository.name }} | ||
| - name: Restore SD cache 💰 | ||
| if: inputs.install-deps-from-package-repositories == '' | ||
| uses: actions/cache@v3 | ||
| with: | ||
| key: sd-${{ runner.os }}-${{ github.event.repository.name }} | ||
| path: ~/.staged.dependencies | ||
| - name: Run Staged dependencies 🎦 | ||
| if: inputs.install-deps-from-package-repositories == '' | ||
| uses: insightsengineering/staged-dependencies-action@v1 | ||
| 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: ${{ inputs.sd-direction }} | ||
| - name: Install dependencies from package repositories 🗄️ | ||
| if: inputs.install-deps-from-package-repositories != '' | ||
| run: | | ||
| split_to_map <- function(args) { | ||
| tmp <- strsplit(x = unlist(strsplit(args, ",")), "=") | ||
| content <- unlist(lapply(tmp, function(x) x[2])) | ||
| names(content) <- unlist(lapply(tmp, function(x) x[1])) | ||
| return(content) | ||
| } | ||
| devtools::install_dev_deps(".", repos = split_to_map("${{ 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@v3 | ||
| 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: Set TESTING_DEPTH ⚙ | ||
| env: | ||
| COMMIT_NEWEST_MESSAGE: ${{ github.event.head_commit.message }} | ||
| COMMIT_OLDEST_MESSAGE: ${{ github.event.commits[0].message }} | ||
| run: | | ||
| # set TESTING_DEPTH for PR | ||
| if [[ ! -z "${GITHUB_HEAD_REF}" ]]; then | ||
| TESTING_DEPTH=3 | ||
| echo "TESTING_DEPTH=3" >> $GITHUB_ENV | ||
| COMMIT_NEWEST_MESSAGE=$(git log --format=%B -n 1 ${{ github.event.after }}) | ||
| fi | ||
| if [[ $COMMIT_NEWEST_MESSAGE == *"[skip tests]"* ]]; then | ||
| echo "NO_TESTS=1" >> $GITHUB_ENV | ||
| fi | ||
| # default TESTING_DEPTH | ||
| if [[ -z "${TESTING_DEPTH}" ]]; then | ||
| echo "TESTING_DEPTH=1" >> $GITHUB_ENV | ||
| fi | ||
| shell: bash | ||
| working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }} | ||
| - 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/checkout@v4 | ||
| 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: ${{ env.junit_xml_storage }} | ||
| force: true | ||
| continue-on-error: true | ||
| - name: Check whether JUnit XML report exists 🚦 | ||
| id: check-junit-xml | ||
| uses: andstor/file-existence-action@v2 | ||
| with: | ||
| files: "${{ 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@v3 | ||
| with: | ||
| name: unit-test-report | ||
| 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/checkout@v3 | ||
| 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@v3 | ||
| 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' -print0 | while IFS= read -r -d $'\0' file; do | ||
| printf "==================================\n$file\n==================================\n" | ||
| cat $file | ||
| done | ||
| shell: bash | ||
| - name: Catch warnings in R CMD check output 🗳 | ||
| id: catch-errors | ||
| run: | | ||
| check_log <- "${{ 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@v3 | ||
| with: | ||
| path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}/${{ env.PKGBUILD }} | ||
| name: ${{ env.PKGBUILD }} | ||
| publish-junit-html-report: | ||
| name: Publish JUnit HTML report 📰 | ||
| runs-on: ubuntu-latest | ||
| needs: build-install-check | ||
| if: > | ||
| needs.build-install-check.outputs.publish-unit-test-html-report == 'true' | ||
| && github.event_name != 'pull_request' | ||
| # Only one job can publish to gh-pages branch concurrently. | ||
| concurrency: | ||
| group: ghpages | ||
| steps: | ||
| - name: Setup token 🔑 | ||
| id: github-token | ||
| run: | | ||
| if [ "${{ secrets.GITHUB_TOKEN }}" == "" ]; then | ||
| echo "GITHUB_TOKEN is empty. Substituting it with GITHUB_TOKEN." | ||
| echo "token=${{ secrets.GITHUB_TOKEN }}" >> $GITHUB_OUTPUT | ||
| else | ||
| echo "Using GITHUB_TOKEN." | ||
| echo "token=${{ secrets.GITHUB_TOKEN }}" >> $GITHUB_OUTPUT | ||
| fi | ||
| shell: bash | ||
| - name: Download JUnit HTML report as artifact ⤵️ | ||
| uses: actions/download-artifact@v3 | ||
| with: | ||
| name: unit-test-report | ||
| 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@v3 | ||
| with: | ||
| github_token: ${{ steps.github-token.outputs.token }} | ||
| publish_dir: ./unit-test-report | ||
| destination_dir: ${{ needs.build-install-check.outputs.current-branch-or-tag }}/unit-test-report | ||
| - 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@v3 | ||
| with: | ||
| github_token: ${{ steps.github-token.outputs.token }} | ||
| publish_dir: ./unit-test-report | ||
| destination_dir: ${{ inputs.latest-tag-alt-name }}/unit-test-report | ||
| - 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@v3 | ||
| with: | ||
| github_token: ${{ steps.github-token.outputs.token }} | ||
| publish_dir: ./unit-test-report | ||
| destination_dir: ${{ inputs.release-candidate-alt-name }}/unit-test-report | ||
| - name: Upload JUnit HTML report to GitHub pages (non-multiversion) 🗞️ | ||
| if: needs.build-install-check.outputs.multiversion-docs == 'false' | ||
| uses: peaceiris/actions-gh-pages@v3 | ||
| with: | ||
| github_token: ${{ steps.github-token.outputs.token }} | ||
| publish_dir: ./unit-test-report | ||
| destination_dir: unit-test-report | ||
| upload-release-assets: | ||
| name: Upload build tar.gz | ||
| needs: build-install-check | ||
| runs-on: ubuntu-latest | ||
| if: > | ||
| startsWith(github.ref, 'refs/tags/v') | ||
| && (!contains(github.event.commits[0].message, '[skip r-cmd]')) | ||
| && github.event.pull_request.draft == false | ||
| steps: | ||
| - name: Checkout repo 🛎 | ||
| uses: actions/checkout@v4 | ||
| - name: Get package build filename 📦 | ||
| run: | | ||
| echo "PKGBUILD=$(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@v3 | ||
| 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 | ||
