feat: extend linter config, add auto-changelog workflow and Conventional Commits guidelines

.github/workflows/auto-changelog.yml

@@ -0,0 +1,154 @@
+name: auto-changelog
+
+on:
+  workflow_call:
+    secrets:
+      ANTHROPIC_API_KEY:
+        required: true
+      PRIVATE_ACCESS_TOKEN:
+        required: true
+
+jobs:
+  auto-changelog:
+    runs-on: ubuntu-24.04
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          token: ${{ secrets.PRIVATE_ACCESS_TOKEN }}
+          ref: ${{ github.head_ref }}
+
+      - name: Check if version bump and NEWS.md entry are present
+        id: check
+        run: |
+          PKG_NAME=$(grep "^Package:" DESCRIPTION | sed 's/Package: //')
+          CURRENT_VERSION=$(grep "^Version:" DESCRIPTION | sed 's/Version: //')
+          MAIN_VERSION=$(git show origin/main:DESCRIPTION | grep "^Version:" | sed 's/Version: //')
+
+          echo "pkg_name=$PKG_NAME" >> "$GITHUB_OUTPUT"
+          echo "current_version=$CURRENT_VERSION" >> "$GITHUB_OUTPUT"
+          echo "main_version=$MAIN_VERSION" >> "$GITHUB_OUTPUT"
+
+          VERSION_BUMPED=false
+          NEWS_OK=false
+
+          if [ "$CURRENT_VERSION" != "$MAIN_VERSION" ]; then
+            VERSION_BUMPED=true
+          fi
+
+          if grep -q "^## $PKG_NAME $CURRENT_VERSION" NEWS.md; then
+            NEWS_OK=true
+          fi
+
+          if [ "$VERSION_BUMPED" = "true" ] && [ "$NEWS_OK" = "true" ]; then
+            echo "skip=true" >> "$GITHUB_OUTPUT"
+          else
+            echo "skip=false" >> "$GITHUB_OUTPUT"
+          fi
+
+      - name: Generate version bump and NEWS entry via Claude
+        if: steps.check.outputs.skip == 'false'
+        id: claude
+        env:
+          ANTHROPIC_API_KEY: ${{ secrets.ANTHROPIC_API_KEY }}
+        run: |
+          PKG_NAME="${{ steps.check.outputs.pkg_name }}"
+          MAIN_VERSION="${{ steps.check.outputs.main_version }}"
+
+          # Limit diff to 6000 chars to stay within token limits; write to file to avoid shell injection
+          git diff origin/main...HEAD -- . \
+            ':(exclude)NEWS.md' \
+            ':(exclude)DESCRIPTION' \
+            ':(exclude)*.lock' \
+            ':(exclude)*.rdb' \
+            | head -c 6000 > /tmp/pr_diff.txt
+
+          PKG_NAME_ENV="$PKG_NAME" MAIN_VERSION_ENV="$MAIN_VERSION" python3 - <<PYEOF
+          import os, json, urllib.request
+
+          pkg_name = os.environ["PKG_NAME_ENV"]
+          main_version = os.environ["MAIN_VERSION_ENV"]
+
+          with open("/tmp/pr_diff.txt") as f:
+            diff = f.read()
+
+          prompt = (
+            f"You are a changelog writer for an R package called '{pkg_name}'"
+            f" (current version on main: {main_version}).\n\n"
+            "Based on the following git diff from a pull request, determine:\n"
+            "1. The version bump type: patch (bug fixes, docs, refactoring),"
+            " minor (new features), major (breaking changes)\n"
+            "2. One short, clear bullet point for NEWS.md describing what changed"
+            " (start with a verb, no period at end)\n\n"
+            'Respond ONLY with valid JSON, no other text:\n'
+            '{"bump_type": "patch|minor|major", "entry": "short description"}\n\n'
+            "Git diff:\n" + diff[:5000]
+          )
+
+          payload = json.dumps({
+            "model": "claude-haiku-4-5-20251001",
+            "max_tokens": 256,
+            "messages": [{"role": "user", "content": prompt}]
+          }).encode()
+
+          req = urllib.request.Request(
+            "https://api.anthropic.com/v1/messages",
+            data=payload,
+            headers={
+              "x-api-key": os.environ["ANTHROPIC_API_KEY"],
+              "anthropic-version": "2023-06-01",
+              "content-type": "application/json"
+            }
+          )
+
+          with urllib.request.urlopen(req) as resp:
+            result = json.loads(resp.read())
+
+          parsed = json.loads(result["content"][0]["text"])
+          bump_type = parsed["bump_type"]
+          entry = parsed["entry"]
+
+          with open(os.environ["GITHUB_OUTPUT"], "a") as f:
+            f.write(f"bump_type={bump_type}\n")
+            f.write(f"entry={entry}\n")
+
+          print(f"bump_type={bump_type}, entry={entry}")
+          PYEOF
+
+      - name: Bump version in DESCRIPTION and prepend NEWS.md entry
+        if: steps.check.outputs.skip == 'false'
+        run: |
+          PKG_NAME="${{ steps.check.outputs.pkg_name }}"
+          MAIN_VERSION="${{ steps.check.outputs.main_version }}"
+          BUMP_TYPE="${{ steps.claude.outputs.bump_type }}"
+          ENTRY="${{ steps.claude.outputs.entry }}"
+          DATE=$(date +%Y-%m-%d)
+
+          MAJOR=$(echo "$MAIN_VERSION" | cut -d. -f1)
+          MINOR=$(echo "$MAIN_VERSION" | cut -d. -f2)
+          PATCH=$(echo "$MAIN_VERSION" | cut -d. -f3)
+
+          if [ "$BUMP_TYPE" = "major" ]; then
+            NEW_VERSION="$((MAJOR + 1)).0.0"
+          elif [ "$BUMP_TYPE" = "minor" ]; then
+            NEW_VERSION="${MAJOR}.$((MINOR + 1)).0"
+          else
+            NEW_VERSION="${MAJOR}.${MINOR}.$((PATCH + 1))"
+          fi
+
+          sed -i "s/^Version: .*/Version: $NEW_VERSION/" DESCRIPTION
+          sed -i "s/^Date: .*/Date: $DATE/" DESCRIPTION
+
+          printf '## %s %s - %s\n* %s\n\n' "$PKG_NAME" "$NEW_VERSION" "$DATE" "$ENTRY" \
+            | cat - NEWS.md > NEWS.md.tmp && mv NEWS.md.tmp NEWS.md
+
+      - name: Commit and push
+        if: steps.check.outputs.skip == 'false'
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          git add DESCRIPTION NEWS.md
+          git commit -m "chore: bump version and update NEWS.md"
+          git push

.github/workflows/conventional-commit-check.yml

@@ -0,0 +1,23 @@
+name: conventional-commit-check
+
+on:
+  workflow_call:
+
+jobs:
+  check-pr-title:
+    runs-on: ubuntu-24.04
+    steps:
+      - name: Check PR title format
+        env:
+          PR_TITLE: ${{ github.event.pull_request.title }}
+        run: |
+          PATTERN='^(feat|fix|refactor|docs|test|chore|ci|perf|build|revert)(\([^)]+\))?: .+'
+          if echo "$PR_TITLE" | grep -qE "$PATTERN"; then
+            echo "PR title follows Conventional Commits: '$PR_TITLE'"
+          else
+            echo "::warning::PR title '$PR_TITLE' does not follow Conventional Commits format."
+            echo "::warning::Expected: <type>: <description>  (e.g. 'feat: add new linter')"
+            echo "::warning::Valid types: feat, fix, refactor, docs, test, chore, ci, perf, build, revert"
+            echo "::warning::See the style guide vignette for details. This check is informational only."
+          fi
+          exit 0

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: gDRstyle
 Type: Package
 Title: A package with style requirements for the gDR suite 
-Version: 1.11.2
-Date: 2026-05-05
+Version: 1.11.4
+Date: 2026-05-08
 Authors@R: c(
     person("Allison", "Vuong", role=c("aut")),
     person("Dariusz", "Scigocki", role=c("aut")),
@@ -27,7 +27,8 @@ Imports:
     checkmate,
     desc,
     git2r,
-    lintr (>= 3.0.0),
+    cyclocomp,
+    lintr (>= 3.2.0),
     rcmdcheck,
     remotes,
     yaml,

NAMESPACE

@@ -5,6 +5,7 @@ export(checkDependencies)
 export(checkPackage)
 export(installAllDeps)
 export(installLocalPackage)
+export(lintNewsEntries)
 export(lintPkgDirs)
 export(roxygen_tag_linter)
 importFrom(BiocStyle,html_document)

NEWS.md

@@ -1,3 +1,11 @@
+## gDRstyle 1.11.4 - 2026-05-18
+* apply updated gDRstyle rules
+
+## gDRstyle 1.11.3 - 2026-05-08
+* extend linter config with additional rules and update style guide accordingly
+* add auto-changelog GitHub Actions reusable workflow using Claude API
+* add lintNewsEntries to enforce brevity and style in NEWS.md entries
+
 ## gDRstyle 1.11.2 - 2026-05-05
 * support vector notation for `length` field in `note.json`
 
@@ -176,4 +184,4 @@
 * fix WARNINGS and NOTES in check- 
 
 ## gDRstyle 0.1.3.9 - 2023-01-05
-* the note test is stricter
+* the note test is stricter

R/build_tools.R

@@ -18,7 +18,7 @@ setReposOpt <- function(additionalRepos = NULL) {
 #' @return \code{NULL} or info about error
 #' @keywords internal
 #' @noRd
-setTokenVar <- function(base_dir, 
+setTokenVar <- function(base_dir,
                         filename = ".github_access_token.txt") {
   # Use GitHub access_token if available
   gh_access_token_file <- file.path(base_dir, filename)
@@ -51,7 +51,7 @@ setTokenVar <- function(base_dir,
 #' @return \code{NULL} or info about error
 #' @keywords internal
 #' @noRd
-verify_version <- function(name, 
+verify_version <- function(name,
                            required_version) {
   pkg_version <- utils::packageVersion(name)
 
@@ -67,24 +67,24 @@ verify_version <- function(name,
 
 is_version_ok <- function(pkg_ver, req) {
   valid_ver_regex <- .standard_regexps()$valid_numeric_version
-  
+
   req <- if (grepl(paste0("^", valid_ver_regex, "$"), req)) {
     paste0("==", req)
   } else {
     req
   }
-  
+
   fun <- trimws(sub("\\d.*", "", req))
   req_ver <- trimws(sub(fun, "", req))
-  
+
   if (!grepl("==|<|>|<=|>=", fun)) stop("Invalid comparison operator")
 
   get(fun, mode = "function")(pkg_ver, req_ver)
 }
 
 #' Create a new ssh key credential object
-#' 
-#' @param use_ssh logical, if use ssh keys 
+#'
+#' @param use_ssh logical, if use ssh keys
 #'
 #' @return A list of class cred_ssh_key
 #' @keywords internal
@@ -108,7 +108,7 @@ getSshKeys <- function(use_ssh) {
 #' installLocalPackage(system.file(
 #' package = "gDRstyle", "tst_pkgs", "dummy_pkg"
 #' ))
-#' 
+#'
 #' @return \code{NULL}
 #' @keywords install
 #' @export
@@ -189,7 +189,7 @@ installAllDeps <- function(additionalRepos = NULL,
 #' @return \code{NULL}
 #' @keywords internal
 #' @noRd
-install_cran <- function(name, 
+install_cran <- function(name,
                          pkg) {
   if (is.null(pkg$repos)) {
     pkg$repos <- getOption("repos")
@@ -211,7 +211,7 @@ install_cran <- function(name,
 #' @return \code{NULL}
 #' @keywords internal
 #' @noRd
-install_bioc <- function(name, 
+install_bioc <- function(name,
                          pkg) {
   if (is.null(pkg$ver)) {
     pkg$ver <- BiocManager::version()
@@ -232,18 +232,18 @@ install_bioc <- function(name,
 #' @return \code{NULL}
 #' @keywords internal
 #' @noRd
-install_github <- function(name, 
+install_github <- function(name,
                            pkg) {
   if (is.null(pkg$ref)) {
     pkg$ref <- "HEAD"
   }
-  
+
   host_url <- if (!is.null(pkg$host)) {
     pkg$host
   } else {
     "api.github.com"
   }
-  
+
   remotes::install_github(
     repo = pkg$url,
     ref = pkg$ref,
@@ -264,8 +264,8 @@ install_github <- function(name,
 #' @return \code{NULL}
 #' @keywords internal
 #' @noRd
-install_git <- function(name, 
-                        pkg, 
+install_git <- function(name,
+                        pkg,
                         keys) {
   remotes::install_git(
     url = pkg$url,
@@ -286,7 +286,7 @@ install_git <- function(name,
 #' @return \code{NULL}
 #' @keywords internal
 #' @noRd
-install_gitlab <- function(name, 
+install_gitlab <- function(name,
                            pkg) {
   repo <- paste(tempdir(), "install_pkg_git", name, sep = .Platform$file.sep)
   url <- if (!is.null(pkg$url) && grepl("code.roche.com", pkg$url)) {

R/check.R

@@ -55,7 +55,7 @@ test_notes_check <- function(check_results,
 
     if (!all(is_note_valid)) {
       stop("Check found unexpected NOTEs: \n",
-           paste0(check_results$notes[!is_note_valid], collapse = " "))
+           paste(check_results$notes[!is_note_valid], collapse = " "))
     }
   }
 }
@@ -233,6 +233,7 @@ checkPackage <- function(pkgName,
     utils::timestamp()
     with_shiny <- file.exists(file.path(pkgDir, "inst", "shiny"))
     gDRstyle::lintPkgDirs(pkgDir, shiny = with_shiny)
+    gDRstyle::lintNewsEntries(pkgDir)
   } else {
     message("Lint skipped")
   }