rdrr.io links fix #463
Workflow file for this run
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| on: | |
| workflow_dispatch: | |
| workflow_call: | |
| inputs: | |
| r-version: | |
| description: 'The version of R to use' | |
| default: '4.1' | |
| required: false | |
| type: string | |
| push-templates-data: | |
| description: 'Push generated templates data to pharmaverseadam repo' | |
| default: false | |
| required: false | |
| type: boolean | |
| exclude-templates-data: | |
| description: 'List of data generated by templates to exclude (templates script will run, but results will not be push to pharmaverseadam repo) - comma seperated list' | |
| default: '' | |
| required: false | |
| type: string | |
| push: | |
| branches: | |
| - main | |
| - devel | |
| - pre-release | |
| pull_request: | |
| branches: | |
| - main | |
| - devel | |
| - pre-release | |
| env: | |
| # branch name for PR | |
| source-branch: update_templates_data | |
| repo: pharmaverseadam | |
| target-branch: main | |
| reviewers: > | |
| { | |
| "admiralonco": { | |
| "reviewers": ["bundfussr", "manciniedoardo"] | |
| }, | |
| "admiralophtha": { | |
| "reviewers": ["manciniedoardo"] | |
| }, | |
| "admiral": { | |
| "reviewers": ["manciniedoardo", "bms63"] | |
| }, | |
| "admiralvaccine": { | |
| "reviewers": ["ahasoplakus", "arjoon-r", "manciniedoardo"] | |
| } | |
| } | |
| # data folder name for templates | |
| templates_data_folder: ./data/ | |
| name: Check Templates | |
| concurrency: | |
| group: templates-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| get_r_version: | |
| name: Get R version | |
| runs-on: ubuntu-latest | |
| if: > | |
| !contains(github.event.commits[0].message, '[skip check_templates]') | |
| outputs: | |
| r-version: ${{ steps.normalizer.outputs.R_VERSION }} | |
| steps: | |
| - name: Normalize inputs | |
| id: normalizer | |
| run: | | |
| R_VERSION="${{ inputs.r-version }}" | |
| if [ "$R_VERSION" == "" ] | |
| then { | |
| R_VERSION="4.1" | |
| } | |
| fi | |
| echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT | |
| shell: bash | |
| check_templates: | |
| name: Verify | |
| if: > | |
| !contains(github.event.commits[0].message, '[skip check_templates]') | |
| runs-on: ubuntu-latest | |
| container: | |
| image: "ghcr.io/pharmaverse/admiralci-${{needs.get_r_version.outputs.r-version}}:latest" | |
| needs: get_r_version | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| ##################### BEGIN boilerplate steps ##################### | |
| - name: Get branch names | |
| id: branch-name | |
| uses: tj-actions/[email protected] | |
| - name: Checkout repo (PR) 🛎 | |
| uses: actions/checkout@v3 | |
| if: github.event_name == 'pull_request' | |
| with: | |
| ref: ${{ steps.branch-name.outputs.head_ref_branch }} | |
| repository: ${{ github.event.pull_request.head.repo.full_name }} | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| if: github.event_name != 'pull_request' | |
| with: | |
| ref: ${{ steps.branch-name.outputs.head_ref_branch }} | |
| fetch-depth: 0 | |
| - name: Add safe directory | |
| run: | | |
| git config --global --add safe.directory "${GITHUB_WORKSPACE}" # open issue: git dubious ownership running in docker container context: https://github.com/actions/runner/issues/2033 | |
| shell: bash | |
| - name: Normalize inputs | |
| id: normalizer | |
| run: | | |
| function remove_substring() { | |
| echo "${1//$2}" | |
| } | |
| BRANCH=${{ steps.branch-name.outputs.head_ref_branch }} | |
| if [ "${BRANCH}" == "" ] | |
| then { | |
| BRANCH=$(git name-rev HEAD | awk '{print $NF}') | |
| } | |
| fi | |
| if [[ $BRANCH == remotes/pull/* ]] | |
| then { | |
| PR=$(remove_substring "$BRANCH" "/merge") | |
| PR=$(remove_substring "$PR" "remotes/") | |
| PR=$(echo $PR | sed 's/pull/pulls/') | |
| echo "Accessing repos/${GITHUB_REPOSITORY}/${PR}" | |
| BRANCH=$(gh api -X GET repos/${GITHUB_REPOSITORY}/${PR} | jq -r '.head.ref') | |
| } | |
| fi | |
| echo "BRANCH is $BRANCH" | |
| R_VERSION="${{ inputs.r-version }}" | |
| if [ "$R_VERSION" == "" ] | |
| then { | |
| R_VERSION="4.1" | |
| } | |
| fi | |
| echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT | |
| echo "SD_GIT_REF=$BRANCH" >> $GITHUB_OUTPUT | |
| shell: bash | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Restore cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| ~/.staged.dependencies | |
| key: staged-deps | |
| restore-keys: staged-deps | |
| - name: Run Staged dependencies | |
| uses: insightsengineering/staged-dependencies-action@v1 | |
| with: | |
| run-system-dependencies: false | |
| enable-check: false | |
| git-ref: ${{ steps.normalizer.outputs.SD_GIT_REF }} | |
| renv-restore: false | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| ##################### END boilerplate steps ##################### | |
| - name: Install package | |
| run: | | |
| R CMD build --no-build-vignettes --no-manual . | |
| R CMD INSTALL *.tar.gz | |
| - name: Run Template Scripts | |
| run: | | |
| desc <- read.dcf("DESCRIPTION") | |
| package_name <- as.character(desc[, "Package"]) | |
| templates <- list.files( | |
| system.file("templates", package = package_name), | |
| pattern = "\\.R$", | |
| ignore.case = TRUE, | |
| full.names = TRUE | |
| ) | |
| if (length(templates) > 0) { | |
| exit_codes <- purrr::map_chr(templates, function(file) { | |
| cmd <- sprintf("Rscript --vanilla %s", file) | |
| system(cmd) | |
| }) | |
| if (any(exit_codes == 1L)) { | |
| failed_scripts <- basename(templates)[which(exit_codes == 1L)] | |
| err_msg <- sprintf( | |
| "Executing the following template scripts failed:\n%s", | |
| paste("-", failed_scripts, collapse = "\n") | |
| ) | |
| stop(err_msg, call. = FALSE) | |
| } | |
| } | |
| shell: Rscript {0} | |
| - name: Add other data formats and suffixes, exclude data | |
| if: inputs.push-templates-data | |
| run: | | |
| library(readxl) | |
| library(zip) | |
| loadRData <- function(fileName){ | |
| load(fileName) | |
| get(ls()[ls() != "fileName"]) | |
| } | |
| print(file.path("${{ github.workspace }}", "tmp")) | |
| print(file.path(Sys.getenv("GITHUB_WORKSPACE"), "tmp")) | |
| folder_path <- file.path(Sys.getenv("GITHUB_WORKSPACE"), "tmp") | |
| rda_files <- list.files(path = folder_path, pattern = "\\.rda$") | |
| ex_files <- unlist(strsplit("${{ inputs.exclude-templates-data }}", ",")) # files to exclude | |
| for (rda_file in rda_files) { | |
| # delete file if part of inputs.exclude-templates-data | |
| if (gsub("\\.rda$", "", rda_file) %in% ex_files) { | |
| file.remove(file.path(folder_path, rda_file)) | |
| cat("Deleted:", rda_file, "\n") | |
| } | |
| else { | |
| print(sprintf("converting file %s", rda_file)) | |
| data <- loadRData(file.path(folder_path, rda_file)) | |
| suffix <- gsub("pharmaverse/admiral", "", "${{ github.repository }}") | |
| if (nchar(suffix) > 0) { | |
| rda_file_renamed <- gsub("\\.rda$", sprintf("_%s.rda", suffix), rda_file) | |
| csv_file <- gsub("\\.rda$", sprintf("_%s.csv", suffix), rda_file) | |
| file.rename(file.path(folder_path, rda_file), file.path(folder_path, rda_file_renamed)) | |
| } | |
| else { | |
| csv_file <- gsub("\\.rda$", ".csv", rda_file) | |
| rda_file_renamed <- rda_file | |
| } | |
| write.csv(data, file = file.path(folder_path, csv_file), row.names = FALSE) | |
| # rename content of rda file | |
| rda_var <- gsub("\\.rda$", "", rda_file_renamed) | |
| print(rda_var) | |
| assign(rda_var, data) | |
| do.call(save, list(rda_var, file = file.path(folder_path, sprintf("%s.rda", rda_var)), compress = "bzip2")) | |
| # create associated documentation inside R folder | |
| dataset_name <- gsub("\\.rda$", "", rda_file_renamed) | |
| doc_string <- paste( | |
| sprintf("#' Dataset %s", dataset_name), | |
| "#'", | |
| sprintf("#' %s dataset", dataset_name), | |
| "#'", | |
| sprintf("#' @name %s", dataset_name), | |
| "#' @docType data", | |
| sprintf("#' @format A data frame with %s columns:", ncol(data)), | |
| "#' \\describe{", | |
| paste(sapply(names(data), function(col_name) { | |
| paste(sprintf("#' \\item{ %s }{%s}", col_name, col_name)) | |
| }, USE.NAMES = FALSE), collapse="\n"), | |
| "#' }", | |
| "#'", sprintf("#' @source Generated from ${{ github.repository }}."), | |
| "#' @references None", | |
| "#'", sprintf("#' @examples\n#' data(\"%s\")", dataset_name), | |
| sep = '\n', | |
| sprintf("\"%s\"", dataset_name) | |
| ) | |
| doc_dir <- "datasets_doc" | |
| if (!file.exists(doc_dir)) { | |
| dir.create(doc_dir, recursive = TRUE) | |
| } | |
| writeLines(doc_string, con = file.path(doc_dir, paste0(dataset_name, ".R"))) | |
| } | |
| } | |
| shell: Rscript {0} | |
| # zip templates data | |
| - name: zip artifacts data | |
| if: inputs.push-templates-data | |
| run: | | |
| find "$GITHUB_WORKSPACE/tmp" -type f \( -name "*.rda" -o -name "*.csv" \) -exec zip -j "$GITHUB_WORKSPACE/data.zip" {} \; | |
| find "$GITHUB_WORKSPACE/datasets_doc" -type f \( -name "*.R" \) -exec zip -j "$GITHUB_WORKSPACE/doc.zip" {} \; | |
| # store templates data as artifacts | |
| - name: Archive templates data | |
| if: inputs.push-templates-data | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: data_templates | |
| path: ${{ github.workspace }}/data.zip | |
| # store templates data as artifacts | |
| - name: Archive doc | |
| if: inputs.push-templates-data | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: doc_templates | |
| path: ${{ github.workspace }}/doc.zip | |
| - name: Checkout repo (PR) 🛎 | |
| if: inputs.push-templates-data | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: main | |
| repository: "${{ github.repository_owner }}/${{ env.repo }}" | |
| fetch-depth: 2 | |
| token: ${{ secrets.PHARMAVERSE_BOT }} | |
| - name: Add safe directory | |
| if: inputs.push-templates-data | |
| run: | | |
| git config --global --add safe.directory "${GITHUB_WORKSPACE}" | |
| shell: bash | |
| - name: Download data artifacts | |
| if: inputs.push-templates-data | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: data_templates | |
| - name: Download doc artifacts | |
| if: inputs.push-templates-data | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: doc_templates | |
| # detect diffs om templates data | |
| - name: Check templates changes | |
| if: inputs.push-templates-data | |
| id: changes | |
| run: | | |
| head_data_folder=$(git ls-tree -r HEAD data) # check if data folder exists on remote main branch | |
| unzip -o "${GITHUB_WORKSPACE}/data.zip" -d "${GITHUB_WORKSPACE}/inst/extdata/" | |
| unzip -o "${GITHUB_WORKSPACE}/doc.zip" -d "${GITHUB_WORKSPACE}/R" | |
| # move every rda files inside data folder | |
| mkdir -p data | |
| for rda_file in inst/extdata/*.rda; do | |
| filename=$(basename "$rda_file") | |
| mv "$rda_file" "data/$filename" | |
| done | |
| if [ -z "${head_data_folder}" ] | |
| then { | |
| echo "data folder not existing on main branch yet - init mode (all templates data files will be pushed)" | |
| diff_files=$(ls "${GITHUB_WORKSPACE}/data") | |
| } else { | |
| git add data R | |
| diff_files_data=$(git status data | grep 'data/.*\.rda$') | |
| diff_files_doc=$(git status R | grep 'R/.*\.R$') | |
| diff_files="${diff_files_data}${diff_files_doc}" | |
| } | |
| fi | |
| if [ -z "$diff_files" ] | |
| then { | |
| echo "No changes detected after running templates. Stop here" | |
| echo "diff=false" >> $GITHUB_OUTPUT | |
| } else { | |
| echo "Changes detected, new PR will be created" | |
| echo "list of files with new updates: $diff_files" | |
| echo "diff=true" >> $GITHUB_OUTPUT | |
| } | |
| fi | |
| shell: bash {0} | |
| - name: Generate man pages | |
| if: inputs.push-templates-data | |
| run: | | |
| Rscript -e "roxygen2::roxygenize('.', roclets = c('rd', 'collate', 'namespace'))" | |
| git add man | |
| shell: bash {0} | |
| - name: Update spellchecks list | |
| if: inputs.push-templates-data | |
| run: | | |
| spelling::update_wordlist(pkg=".", confirm=FALSE) | |
| shell: Rscript {0} | |
| - name: set source-branch name | |
| if: inputs.push-templates-data | |
| id: branch | |
| run: | | |
| repo_name=$(basename "${{ github.repository }}") | |
| echo "source-branch=${{ env.source-branch }}_${repo_name}@devel" >> $GITHUB_OUTPUT | |
| shell: bash {0} | |
| # if diff detected, push changes | |
| - name: Commit and push changes in {{ env.repo }} | |
| if: ${{ inputs.push-templates-data && steps.changes.outputs.diff == 'true' }} | |
| uses: stefanzweifel/git-auto-commit-action@v4 | |
| with: | |
| commit_message: templates data updates from ${{ github.repository }} | |
| file_pattern: 'inst/extdata/* data/* R/* inst/WORDLIST' | |
| commit_user_name: pharmaverse-bot | |
| commit_user_email: [email protected] | |
| branch: "${{ steps.branch.outputs.source-branch }}" | |
| create_branch: true | |
| - name: Create Pull Request | |
| if: ${{ inputs.push-templates-data && steps.changes.outputs.diff == 'true' }} | |
| uses: actions/github-script@v6 | |
| with: | |
| github-token: ${{ secrets.PHARMAVERSE_BOT }} | |
| script: | | |
| // Look for any open PRs | |
| const repo_owner = "${{ github.repository_owner }}"; | |
| const target_repo_name = "${{ env.repo }}"; | |
| const result = await github.rest.pulls.list({ | |
| owner: repo_owner, | |
| repo: target_repo_name, | |
| state: "open" | |
| }) | |
| let create_new_pr = true; | |
| for (const pr of result.data) { | |
| // Look for distinct PR branch name | |
| if (pr.head.ref === "${{ steps.branch.outputs.source-branch }}") { | |
| console.log("PR with head ref " + pr.head.ref + " already exists"); | |
| create_new_pr = false; | |
| break; | |
| } | |
| } | |
| // If no PR with distinguished branch name has been found | |
| // create a new PR to track changes to renv.lock. | |
| if (create_new_pr) { | |
| console.log("Creating a new PR"); | |
| const result2 = await github.rest.pulls.create({ | |
| title: 'Templates data updates from ${{ github.repository }}', | |
| owner: repo_owner, | |
| repo: target_repo_name, | |
| head: '${{ steps.branch.outputs.source-branch }}', | |
| base: '${{ env.target-branch }}', | |
| body: [ | |
| 'This PR has been automatically generated by ', | |
| 'check-templates workflow from ${{ github.repository }}.', | |
| '\n\nPlease review the changes.' | |
| ].join('') | |
| }); | |
| // Assign reviewers to the PR | |
| let rev = process.env.reviewers; | |
| let reviewers_dict = JSON.parse(rev); | |
| let current_repo_name_full = "${{ github.repository }}"; | |
| let current_repo_name = current_repo_name_full.split('/').pop(); | |
| const result3 = await github.rest.pulls.requestReviewers({ | |
| owner: repo_owner, | |
| repo: target_repo_name, | |
| pull_number: result2.data.number, | |
| reviewers: reviewers_dict[current_repo_name]["reviewers"] | |
| }); | |
| } |