Update branch from dev

.Rbuildignore

@@ -1,6 +1,8 @@
-^chef\.Rproj$
-^\.Rproj\.user$
 ^LICENSE\.md$
+^\.Rproj\.user$
+^\.github$
+^\.pre-commit-config\.yaml$
 ^_pkgdown\.yml$
+^chef\.Rproj$
 ^docs$
 ^pkgdown$

.githooks/pre-commit

@@ -0,0 +1,32 @@
+#!/bin/bash
+#
+# An example hook script to verify what is about to be committed.
+# Called by "git commit" with no arguments.  The hook should
+# exit with non-zero status after issuing an appropriate message if
+# it wants to stop the commit.
+#
+# To enable this hook, rename this file to "pre-commit".
+
+export LOCAL_BRANCH=$(git rev-parse --abbrev-ref HEAD)
+# Array of protected branches
+protected_branches=(
+  "main"
+  "stage"
+  "dev"
+)
+
+
+
+
+for branch in "${protected_branches[@]}"; do
+    if [[ "$LOCAL_BRANCH" == "$branch"* ]]; then
+        echo "Pre-commit hook: Attempt to commit to a protected branch: ${LOCAL_BRANCH}"
+        echo ""
+        echo "Checkout a new feature/branchname and push from there."
+        echo "Then go to github and create a pull request."
+        exit 1
+    fi
+done
+
+
+exit 0

.githooks/pre-push

@@ -0,0 +1,58 @@
+#!/bin/bash
+
+# An example hook script to verify what is about to be pushed.  Called by "git
+# push" after it has checked the remote status, but before anything has been
+# pushed.  If this script exits with a non-zero status nothing will be pushed.
+#
+# This hook is called with the following parameters:
+#
+# $1 -- Name of the remote to which the push is being done
+# $2 -- URL to which the push is being done
+#
+# If pushing without using a named remote those arguments will be equal.
+#
+# Information about the commits which are being pushed is supplied as lines to
+# the standard input in the form:
+#
+#   <local ref> <local oid> <remote ref> <remote oid>
+#
+# This sample shows how to prevent push of commits where the log message starts
+# with "WIP" (work in progress).
+
+remote="$1"
+url="$2"
+
+# Array of protected branches
+protected_branches=(
+  "refs/heads/main/"
+  "refs/heads/main"
+  "refs/heads/stage/"
+  "refs/heads/stage"
+  "refs/heads/dev/"
+  "refs/heads/dev"
+  "refs/heads/testing/precommit"
+)
+
+while read local_ref local_sha remote_ref remote_sha; do
+    for branch in "${protected_branches[@]}"; do
+        if [[ "$remote_ref" == "$branch"* ]]; then
+        echo "Pre-push hook: Attempt to commit to a protected branch: ${LOCAL_BRANCH}"
+        echo ""
+        echo "Checkout a new feature/branchname and push from there."
+		echo ""
+		echo "You can use the following commands to place the changes on a new branch:"
+		echo "git reset --soft HEAD"
+		echo "git checkout -b feature/branchname"
+		echo "git add ."
+		echo "git commit -m 'Your commit message'"
+		echo "git push origin feature/branchname"
+        echo "Then go to github and create a pull request."
+        exit 1
+            exit 1
+        fi
+    done
+done
+
+exit 0
+
+exit 0

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/Check.yaml

@@ -0,0 +1,47 @@
+
+
+
+on:
+  push:
+    branches: [main, stage, dev]
+  pull_request:
+    branches: [main, stage, dev]
+  workflow_dispatch:
+
+name: Check
+
+jobs:
+  audit:
+    name: Audit Dependencies 🕵️‍♂️
+    uses: insightsengineering/r.pkg.template/.github/workflows/audit.yaml@main
+
+  licenses:
+    name: License Check 🃏
+    uses: insightsengineering/r.pkg.template/.github/workflows/licenses.yaml@main
+
+  check-reuse:
+    name: RMD check 📦
+    uses: ./.github/workflows/R-CMD-check.yaml
+
+  test:
+    name: Test 🧪
+    uses: ./.github/workflows/Test.yaml
+
+  gitleaks:
+    name: gitleaks 💧
+    uses: insightsengineering/r.pkg.template/.github/workflows/gitleaks.yaml@main
+    with:
+      check-for-pii: true
+
+  vbump:
+    name: Version Bump 🤜🤛
+    if: github.event_name == 'push' && github.ref != 'refs/heads/main'
+    uses: insightsengineering/r.pkg.template/.github/workflows/version-bump.yaml@main
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+  # roxygen:
+  #   name: Roxygen 📦
+  #   uses: ./.github/workflows/Roxygen.yaml
+
+

.github/workflows/PR_cleanup.yaml

@@ -0,0 +1,13 @@
+name: PR cleanup
+
+on:
+  pull_request:
+    types: [closed, synchronize]
+
+jobs:
+  delete_pr_artifacts:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: stefanluptak/delete-old-pr-artifacts@v1
+        with:
+          workflow_filename: Check.yaml

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  workflow_call:
+
+name: R-CMD-check
+
+# concurrency:
+#   group: roxygen-${{ github.event.pull_request.number || github.ref }}
+#   cancel-in-progress: true
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: ubuntu-latest,   r: 'release'}
+          # - {os: ubuntu-latest,   r: 'oldrel-1'}
+          # - {os: ubuntu-latest,   r: 'oldrel-2'}
+          # - {os: ubuntu-latest,   r: 'oldrel-3'}
+          # - {os: ubuntu-latest,   r: 'oldrel-4'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.github/workflows/Roxygen.yaml

@@ -0,0 +1,180 @@
+---
+    name: Roxygen 🅾
+
+    on:
+      workflow_call:
+        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
+          auto-update:
+            description: If man pages are not up-to-date, they will be automatically updated and committed back to the branch.
+            required: false
+            default: false
+            type: boolean
+          # sd-direction:
+          #   description: The direction to use to install staged dependencies. Choose between 'upstream', 'downstream' and 'all'
+          #   required: false
+          #   type: string
+          #   default: upstream
+          package-subdirectory:
+            description: Subdirectory in the repository, where the R package is located.
+            required: false
+            type: string
+            default: "."
+        secrets:
+          REPO_GITHUB_TOKEN:
+            description: |
+              Github token with read access to repositories, required for staged.dependencies installation
+            required: false
+
+    # concurrency:
+    #   group: roxygen-${{ github.event.pull_request.number || github.ref }}
+    #   cancel-in-progress: true
+
+    jobs:
+      roxygen:
+        name: Manual pages check 🏁
+        runs-on: ubuntu-latest
+        if: >
+          !contains(github.event.commits[0].message, '[skip roxygen]')
+            && github.event.pull_request.draft == false
+        container:
+          image: ghcr.io/insightsengineering/rstudio:latest
+
+        steps:
+          - name: Setup token 🔑
+            id: github-token
+            run: |
+              if [ "${{ 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/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 }}
+            #   token: ${{ steps.github-token.outputs.token }}
+
+          - name: Checkout repo 🛎
+            uses: actions/checkout@v4
+            if: github.event_name != 'pull_request'
+            # with:
+            #   ref: ${{ steps.branch-name.outputs.head_ref_branch }}
+            #   path: ${{ github.event.repository.name }}
+
+          - name: Setup R
+            uses: r-lib/actions/setup-r@v2
+            with:
+              use-public-rspm: true
+
+          - name: Setup R dependencies
+            uses: r-lib/actions/setup-r-dependencies@v2
+            with:
+              extra-packages: any::roxygen2
+
+        #   - name: Restore SD cache 💰
+        #     uses: actions/cache@v4
+        #     with:
+        #       key: sd-${{ runner.os }}-${{ github.event.repository.name }}
+        #       path: ~/.staged.dependencies
+
+        #   - name: Run Staged dependencies 🎦
+        #     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: ${{ inputs.sd-direction }}
+
+          - name: Generate man pages 📄
+            run: |
+              logfile <- "roxygen_${{ github.event.repository.name }}.log"
+              con <- file(logfile)
+              sink(con, append = TRUE, split = TRUE)
+              sink(con, append = TRUE, type = "message")
+              roxygen2::roxygenize('.')
+              sink()
+              sink(type = "message")
+              logs <- readLines(logfile)
+              cat("🪵 Log output of 'roxygen2::roxygenize()':\n")
+              system2("cat", logfile)
+              error_marker <- grep("Error:", logs)
+              warnings_marker <- grep("Warning message", logs)
+              if (length(warnings_marker) > 0) {
+                cat("⚠ One or more warnings were generated during the roxygen build:\n")
+                cat(logs[warnings_marker[[1]]:length(logs)], sep = "\n")
+                stop("Please 🙏 fix the warnings shown below this message 👇")
+              }
+              if (length(error_marker) > 0) {
+                cat("☠ One or more errors were generated during the roxygen build:\n")
+                cat(logs[error_marker[[1]]:length(logs)], sep = "\n")
+                stop("Please 🙏 fix the errors shown below this message 👇")
+              }
+            shell: Rscript {0}
+            working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
+
+          - name: Roxygen check 🅾
+            run: |
+              AUTO_UPDATE=${{ inputs.auto-update }}
+              if [[ -n `git status -s | grep -E "man|DESCRIPTION"` ]]
+              then {
+                ROXYGEN_VERSION="$(Rscript -e 'packageVersion("roxygen2")' | awk '{print $NF}')"
+                echo "🙈 Manuals are not up-to-date with roxygen comments!"
+                echo "🔀 The following differences were noted:"
+                git diff man/* DESCRIPTION
+                # Attempt to commit and push man-page updates
+                if [ "${AUTO_UPDATE}" == "true" ]
+                then {
+                  echo "Regenerating man pages via auto-update"
+                  git config --global user.name "github-actions"
+                  git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
+                  git config pull.rebase false
+                  BRANCH_NAME="${{ steps.branch-name.outputs.head_ref_branch }}"
+                  git pull origin ${BRANCH_NAME} || true
+                  git add -A man/ DESCRIPTION
+                  git commit -m "[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update"
+                  git push -v origin HEAD:${BRANCH_NAME} || \
+                    (echo "⚠️ Could not push to ${BRANCH_NAME} on $(git remote -v show -n origin | grep Push)" && \
+                    AUTO_UPDATE=failed)
+                }
+                fi
+                # If auto-update is disabled or is unsuccessful, let 'em know to fix manually
+                if [ "${AUTO_UPDATE}" != "true" ]
+                then {
+                  echo -e "\n💻 Please rerun the following command on your workstation and push your changes"
+                  echo "--------------------------------------------------------------------"
+                  echo "roxygen2::roxygenize('.')"
+                  echo "--------------------------------------------------------------------"
+                  echo "ℹ roxygen2 version that was used in this workflow: $ROXYGEN_VERSION"
+                  echo "🙏 Please ensure that the 'RoxygenNote' field in the DESCRIPTION file matches this version"
+                  exit 1
+                }
+                fi
+              } else {
+                echo "💚 Manuals are up-to-date with roxygen comments"
+              }
+              fi
+            shell: bash
+            working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}