Merge branch 'main' into 143-remove-admiraltest-from-renv-and-rprofile

.github/workflows/check-templates.yml

@@ -7,6 +7,16 @@ on:
         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
@@ -18,6 +28,29 @@ on:
       - 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:
@@ -164,3 +197,250 @@ jobs:
             }
           }
         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"]
+              });
+            }

.github/workflows/spellcheck.yml

@@ -10,6 +10,11 @@ on:
         default: '4.1'
         required: false
         type: string
+      exclude:
+        description: 'List of paths to exclude (comma seperated list)'
+        default: ''
+        required: false
+        type: string
   push:
     branches:
       - main
@@ -97,3 +102,4 @@ jobs:
         uses: insightsengineering/r-spellcheck-action@v3
         with:
           additional_options: ""
+          exclude: "${{ inputs.exclude }}"