In Progress: Fixes

.gitattributes

@@ -1,2 +1,8 @@
 # Explicitly force LF for files
 *.csv     text eol=lf
+
+# Force LF line endings for text files, regardless of local core.autocrlf
+* text=auto eol=lf
+
+*.yml     text eol=lf
+*.yaml    text eol=lf

.github/ISSUE_TEMPLATE/1-rule-issue.yml

@@ -45,4 +45,4 @@ body:
     attributes:
       label: Test Data
       description: "If reporting a bug, attach your test data files here (CSV, Excel, etc.). You can drag and drop multiple files directly into this field."
-      placeholder: Drag and drop files here, or describe the test data inline.
+      placeholder: Drag and drop files here, or describe the test data inline.

.github/ISSUE_TEMPLATE/config.yml

@@ -1 +1 @@
-blank_issues_enabled: false
+blank_issues_enabled: false

.github/workflows/auto-format-yaml.yml

@@ -0,0 +1,35 @@
+name: Auto-format Rule YAML
+on:
+  workflow_dispatch: {}
+jobs:
+  format-yaml:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ github.head_ref || github.ref_name }}
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - run: pip install ruamel.yaml
+
+      - name: Sort rule.yml files
+        run: python scripts/sort_yaml.py
+
+      - uses: actions/setup-node@v4
+      - name: Run Prettier to format rule.yml files
+        run: |
+          npm i prettier
+          npx prettier "Published/**/rule.yml" "Unpublished/**/rule.yml" --write
+
+      - name: Commit and push formatting fixes
+        run: |
+          git config user.name github-actions
+          git config user.email github-actions@cdisc.org
+          git add Published Unpublished
+          git diff-index --quiet HEAD || git commit -m "chore: sort and format rule.yml files"
+          git push

.github/workflows/publish.yml

@@ -97,4 +97,4 @@ jobs:
       - name: Push
         if: steps.newdirs.outputs.HAS_NEW_DIRS == 'true'
         run: |
-          git push
+          git push

.github/workflows/submodule_update.yml

@@ -33,4 +33,4 @@ jobs:
           body: |
             Automated update of the `engine` submodule to the latest commit on `cdisc-rules-engine/main`.
           branch: auto/update-engine-submodule
-          base: main
+          base: main

.github/workflows/validate-rule-contributions.yml

@@ -3,7 +3,7 @@ name: Validate Rule Contributions
 on:
   pull_request:
     paths:
-      - 'Unpublished/**'
+      - "Unpublished/**"
     types: [opened, synchronize, reopened]
   workflow_dispatch: {}
 
@@ -27,7 +27,7 @@ jobs:
       - name: Set up Python 3.12
         uses: actions/setup-python@v5
         with:
-          python-version: '3.12'
+          python-version: "3.12"
 
       - name: Install engine dependencies
         run: |

.github/workflows/validate-yaml-format.yml

@@ -11,17 +11,27 @@ jobs:
     runs-on: ubuntu-latest
     permissions:
       contents: read
+      issues: write
       pull-requests: write
     steps:
       - name: Checkout
         uses: actions/checkout@v4
         with:
           fetch-depth: 0
+
       - name: Set up Python 3.12
         uses: actions/setup-python@v5
         with:
           python-version: "3.12"
       - run: pip install ruamel.yaml
+
+      - name: Set up Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: "20"
+      - name: Install Prettier
+        run: npm install -g prettier
+
       - name: Detect changed rule.yml files
         id: changed-files
         run: |
@@ -39,47 +49,116 @@ jobs:
             echo "has_files=true" >> $GITHUB_OUTPUT
             echo "$FILES" > /tmp/changed_rule_files.txt
           fi
-      - name: Check YAML sorting and formatting
-        id: format-check
+
+      - name: Check YAML sorting
+        id: sort-check
         if: steps.changed-files.outputs.has_files == 'true'
         run: |
-          FILES=$(cat /tmp/changed_rule_files.txt | tr '\n' ' ')
-          python scripts/sort_yaml.py --check $FILES
+          mapfile -t FILES < /tmp/changed_rule_files.txt
+          python scripts/sort_yaml.py --check "${FILES[@]}" 2> /tmp/sort_stderr.txt
         continue-on-error: true
-      - name: Post format check result to PR
+
+      - name: Check Prettier formatting
+        id: prettier-check
+        if: steps.changed-files.outputs.has_files == 'true'
+        run: |
+          : > /tmp/prettier_unformatted.txt
+          while read -r f; do
+            [ -z "$f" ] && continue
+            if ! prettier --check "$f" > /dev/null 2>&1; then
+              echo "  $f" >> /tmp/prettier_unformatted.txt
+            fi
+          done < /tmp/changed_rule_files.txt
+          if [ -s /tmp/prettier_unformatted.txt ]; then
+            echo "passed=false" >> $GITHUB_OUTPUT
+          else
+            echo "passed=true" >> $GITHUB_OUTPUT
+          fi
+
+      - name: Post result to PR
         if: always() && github.event_name == 'pull_request' && steps.changed-files.outputs.has_files == 'true'
         uses: actions/github-script@v7
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           script: |
-            const outcome = '${{ steps.format-check.outcome }}';
+            const fs = require('fs');
+
+            function truncatedList(path, maxChars = 3000) {
+              let raw = '';
+              try { raw = fs.readFileSync(path, 'utf8'); } catch (e) { return ''; }
+              const lines = raw.split('\n').filter(l => l.trim().length > 0);
+              let out = [];
+              let total = 0;
+              for (const line of lines) {
+                if (total + line.length > maxChars) {
+                  out.push(`...and ${lines.length - out.length} more`);
+                  break;
+                }
+                out.push(line);
+                total += line.length + 1;
+              }
+              return out.join('\n');
+            }
+
+            const sortOk = '${{ steps.sort-check.outcome }}' === 'success';
+            const prettierOk = '${{ steps.prettier-check.outputs.passed }}' === 'true';
             const marker = '<!-- yaml-format-check -->';
             let body = marker + '\n';
-            if (outcome === 'success') {
+
+            if (sortOk && prettierOk) {
               body += '## \u2705 YAML Format Check Passed\n\nAll changed `rule.yml` files are correctly sorted and formatted.';
             } else {
               body += '## \u274c YAML Format Check Failed\n\n';
-              body += 'One or more `rule.yml` files are not correctly sorted/formatted alphabetically by key.\n\n';
-              body += 'Run the following command locally to fix them:\n\n```bash\npython scripts/sort_yaml.py\n```\n\nThen commit and push.';
+              if (!sortOk) {
+                const sortList = truncatedList('/tmp/sort_stderr.txt');
+                body += '**Sorting issue** — one or more `rule.yml` files are not sorted alphabetically by key.\n\n';
+                body += 'Run the following command locally to fix them:\n\n```bash\npython scripts/sort_yaml.py\n```\n\n';
+                if (sortList) body += '<details><summary>Details</summary>\n\n```\n' + sortList + '\n```\n</details>\n\n';
+              }
+              if (!prettierOk) {
+                const prettierList = truncatedList('/tmp/prettier_unformatted.txt');
+                body += '**Formatting issue** — the following files are not formatted with Prettier:\n\n';
+                body += '```\n' + prettierList + '\n```\n\n';
+                body += 'Install the [Prettier VS Code extension](https://marketplace.visualstudio.com/items?itemName=esbenp.prettier-vscode) and enable "Format On Save", then re-save these files and push.\n\n';
+                body += 'Alternatively, trigger the **Auto-format Rule YAML** workflow to fix them automatically.';
+              }
             }
-            const { data: comments } = await github.rest.issues.listComments({
-              owner: context.repo.owner, repo: context.repo.repo,
-              issue_number: context.issue.number,
-            });
-            const existing = comments.find(c => c.user.type === 'Bot' && c.body.includes(marker));
-            if (existing) {
-              await github.rest.issues.updateComment({
-                owner: context.repo.owner, repo: context.repo.repo,
-                comment_id: existing.id, body,
-              });
-            } else {
-              await github.rest.issues.createComment({
+
+            if (body.length > 60000) {
+              body = body.slice(0, 60000) + '\n\n...(comment truncated — see workflow run logs for full details)';
+            }
+
+            core.info(`Comment body length: ${body.length}`);
+            core.info(`Issue number: ${context.issue.number}`);
+
+            try {
+              const { data: comments } = await github.rest.issues.listComments({
                 owner: context.repo.owner, repo: context.repo.repo,
-                issue_number: context.issue.number, body,
+                issue_number: context.issue.number,
               });
+              core.info(`Found ${comments.length} existing comments on this PR.`);
+              const existing = comments.find(c => c.user.type === 'Bot' && c.body.includes(marker));
+              if (existing) {
+                core.info(`Updating existing comment id ${existing.id}`);
+                const res = await github.rest.issues.updateComment({
+                  owner: context.repo.owner, repo: context.repo.repo,
+                  comment_id: existing.id, body,
+                });
+                core.info(`Updated comment: ${res.data.html_url}`);
+              } else {
+                core.info('No existing marker comment found — creating a new one.');
+                const res = await github.rest.issues.createComment({
+                  owner: context.repo.owner, repo: context.repo.repo,
+                  issue_number: context.issue.number, body,
+                });
+                core.info(`Created comment: ${res.data.html_url}`);
+              }
+            } catch (err) {
+              core.setFailed(`Failed to post PR comment: ${err.message}`);
             }
-      - name: Fail if format check failed
-        if: steps.format-check.outcome == 'failure'
+
+      - name: Fail if any check failed
+        if: steps.sort-check.outcome == 'failure' || steps.prettier-check.outputs.passed == 'false'
         run: |
-          echo "YAML format check failed. Run 'python scripts/sort_yaml.py' to fix."
+          echo "YAML sort and/or Prettier format check failed. See PR comment for details."
           exit 1

.github/workflows/validate-yaml-schema.yml

@@ -3,8 +3,8 @@ name: Validate YAML against Schema
 on:
   pull_request:
     paths:
-      - 'Published/**/rule.yml'
-      - 'Unpublished/**/rule.yml'
+      - "Published/**/rule.yml"
+      - "Unpublished/**/rule.yml"
     types: [opened, synchronize, reopened]
   workflow_dispatch:
     inputs:
@@ -14,7 +14,7 @@ on:
           (e.g. "Published/CORE-000001/rule.yml"). Leave blank to validate
           all changed rule files detected from the last commit.
         required: false
-        default: ''
+        default: ""
 
 # Only one run per PR branch at a time; cancel superseded runs.
 concurrency:
@@ -32,7 +32,7 @@ jobs:
     env:
       # draft/2020-12 schema — switch to rule-merged if you need $defs inlined
       SCHEMA_URL: >-
-          https://raw.githubusercontent.com/cdisc-org/cdisc-rules-engine/refs/heads/main/resources/schema/rule-merged/CORE-base.json
+        https://raw.githubusercontent.com/cdisc-org/cdisc-rules-engine/refs/heads/main/resources/schema/rule-merged/CORE-base.json
 
     steps:
       # -----------------------------------------------------------------------
@@ -49,7 +49,7 @@ jobs:
       - name: Set up Python 3.12
         uses: actions/setup-python@v6
         with:
-          python-version: '3.12'
+          python-version: "3.12"
 
       # -----------------------------------------------------------------------
       # 3. Install validation dependencies

.pre-commit-config.yaml

@@ -2,9 +2,9 @@ repos:
   - repo: local
     hooks:
       - id: sort-yaml-rules
-        name: Sort and format rule YAML files
+        name: Sort rule YAML files
         language: python
-        entry: python scripts/sort_yaml.py --check
+        entry: python scripts/sort_yaml.py --no-format
         types: [yaml]
         files: ".*/rule\\.yml$"
         additional_dependencies: [ruamel.yaml]

.prettierrc

@@ -0,0 +1,16 @@
+{
+  "printWidth": 100,
+  "tabWidth": 2,
+  "useTabs": false,
+  "singleQuote": false,
+  "endOfLine": "lf",
+  "overrides": [
+    {
+      "files": ["*.yml", "*.yaml"],
+      "options": {
+        "printWidth": 100,
+        "tabWidth": 2
+      }
+    }
+  ]
+}

.vscode/extensions.json

@@ -1,8 +1,9 @@
 {
   "recommendations": [
     "redhat.vscode-yaml",
+    "esbenp.prettier-vscode",
     "GrapeCity.gc-excelviewer",
     "mechatroner.rainbow-csv",
     "emeraldwalk.runonsave"
   ]
-}
+}

.vscode/settings.json

@@ -1,4 +1,5 @@
 {
+  "extensions.autoUpdate": true,
   "yaml.schemas": {
     "https://raw.githubusercontent.com/cdisc-org/cdisc-rules-engine/refs/heads/main/resources/schema/rule-merged/CORE-base.json": "rule.yml"
   },
@@ -10,5 +11,10 @@
         "cmd": "${workspaceFolder}/venv/bin/python ${workspaceFolder}/scripts/sort_yaml.py ${file}"
       }
     ]
-  }
+  },
+  "[yaml]": {
+    "editor.defaultFormatter": "esbenp.prettier-vscode",
+    "editor.formatOnSave": true
+  },
+  "yaml.format.enable": false
 }