add YAML validation workflow and sorting script; update setup for pre-commit hooks

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

@@ -0,0 +1,86 @@
+name: Validate YAML Formatting
+on:
+  pull_request:
+    paths:
+      - 'Unpublished/**/rule.yml'
+      - 'Published/**/rule.yml'
+    types: [opened, synchronize, reopened]
+  workflow_dispatch: {}
+jobs:
+  check-yaml-format:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      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'
+      - name: Install pyyaml
+        run: pip install pyyaml
+      - name: Detect changed rule.yml files
+        id: changed-files
+        run: |
+          if [ "${{ github.event_name }}" = "pull_request" ]; then
+            FILES=$(git diff --name-only origin/${{ github.base_ref }}...HEAD \
+              | grep -E '^(Published|Unpublished)/.*/rule\.yml$' || true)
+          else
+            FILES=$(git diff --name-only HEAD~1 HEAD \
+              | grep -E '^(Published|Unpublished)/.*/rule\.yml$' || true)
+          fi
+          if [ -z "$FILES" ]; then
+            echo "No rule.yml files changed."
+            echo "has_files=false" >> $GITHUB_OUTPUT
+          else
+            echo "has_files=true" >> $GITHUB_OUTPUT
+            echo "$FILES" > /tmp/changed_rule_files.txt
+          fi
+      - name: Check YAML sorting and formatting
+        id: format-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
+        continue-on-error: true
+      - name: Post format check 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 marker = '<!-- yaml-format-check -->';
+            let body = marker + '\n';
+            if (outcome === 'success') {
+              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.';
+            }
+            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({
+                owner: context.repo.owner, repo: context.repo.repo,
+                issue_number: context.issue.number, body,
+              });
+            }
+      - name: Fail if format check failed
+        if: steps.format-check.outcome == 'failure'
+        run: |
+          echo "YAML format check failed. Run 'python scripts/sort_yaml.py' to fix."
+          exit 1

.pre-commit-config.yaml

@@ -0,0 +1,11 @@
+repos:
+  - repo: local
+    hooks:
+      - id: sort-yaml-rules
+        name: Sort and format rule YAML files
+        language: python
+        entry: python scripts/sort_yaml.py --check
+        types: [yaml]
+        files: ".*/rule\\.yml$"
+        additional_dependencies: [pyyaml]
+        pass_filenames: true

.vscode/extensions.json

@@ -2,6 +2,7 @@
   "recommendations": [
     "redhat.vscode-yaml",
     "GrapeCity.gc-excelviewer",
-    "mechatroner.rainbow-csv"
+    "mechatroner.rainbow-csv",
+    "emeraldwalk.runonsave"
   ]
 }

.vscode/settings.json

@@ -1,5 +1,14 @@
 {
   "yaml.schemas": {
     "https://raw.githubusercontent.com/cdisc-org/cdisc-rules-engine/refs/heads/main/resources/schema/rule-merged/CORE-base.json": "rule.yml"
+  },
+  "emeraldwalk.runonsave": {
+    "commands": [
+      {
+        "match": "rule\\.yml$",
+        "isAsync": false,
+        "cmd": "${workspaceFolder}/venv/bin/python ${workspaceFolder}/scripts/sort_yaml.py ${file}"
+      }
+    ]
   }
 }

.vscode/tasks.json

@@ -0,0 +1,28 @@
+{
+  "version": "2.0.0",
+  "tasks": [
+    {
+      "label": "Sort & Format rule.yml",
+      "type": "shell",
+      "command": "${workspaceFolder}/venv/bin/python",
+      "args": ["${workspaceFolder}/scripts/sort_yaml.py", "${file}"],
+      "presentation": {
+        "reveal": "silent",
+        "panel": "shared"
+      },
+      "problemMatcher": []
+    },
+    {
+      "label": "Sort & Format ALL rule.yml files",
+      "type": "shell",
+      "command": "${workspaceFolder}/venv/bin/python",
+      "args": ["${workspaceFolder}/scripts/sort_yaml.py"],
+      "presentation": {
+        "reveal": "always",
+        "panel": "shared"
+      },
+      "problemMatcher": []
+    }
+  ]
+}
+

scripts/sort_yaml.py

@@ -0,0 +1,176 @@
+#!/usr/bin/env python3
+"""
+Sort and format rule YAML files alphabetically and recursively by key name.
+
+This matches the auto-format/auto-sort behavior of the CDISC conformance rules editor.
+
+Usage:
+    # Format files in-place (default: all rule.yml under Published/ and Unpublished/)
+    python scripts/sort_yaml.py
+
+    # Format specific files
+    python scripts/sort_yaml.py path/to/rule.yml another/rule.yml
+
+    # Check mode: exit with code 1 if any file is not formatted correctly
+    python scripts/sort_yaml.py --check [files...]
+"""
+
+import sys
+import argparse
+from pathlib import Path
+
+try:
+    import yaml
+except ImportError:
+    print("ERROR: pyyaml is not installed. Run: pip install pyyaml", file=sys.stderr)
+    sys.exit(1)
+
+
+# ---------------------------------------------------------------------------
+# Custom YAML Dumper
+# ---------------------------------------------------------------------------
+
+class _SortedDumper(yaml.Dumper):
+    """YAML Dumper that produces consistent, human-readable output."""
+    pass
+
+
+def _str_representer(dumper: yaml.Dumper, data: str):
+    """Represent strings: use literal block style for multi-line, plain otherwise.
+    Strings that look like YAML scalars (booleans, numbers) are quoted.
+    """
+    if "\n" in data:
+        return dumper.represent_scalar("tag:yaml.org,2002:str", data, style="|")
+    return dumper.represent_scalar("tag:yaml.org,2002:str", data)
+
+
+_SortedDumper.add_representer(str, _str_representer)
+
+
+# ---------------------------------------------------------------------------
+# Core logic
+# ---------------------------------------------------------------------------
+
+def sort_recursive(obj):
+    """Recursively sort dict keys alphabetically. Lists are preserved as-is."""
+    if isinstance(obj, dict):
+        return {k: sort_recursive(obj[k]) for k in sorted(obj.keys(), key=str)}
+    if isinstance(obj, list):
+        return [sort_recursive(item) for item in obj]
+    return obj
+
+
+def canonical(content: str) -> str:
+    """Return the canonical (sorted + formatted) representation of a YAML string."""
+    data = yaml.safe_load(content)
+    if data is None:
+        return content
+    sorted_data = sort_recursive(data)
+    return yaml.dump(
+        sorted_data,
+        Dumper=_SortedDumper,
+        default_flow_style=False,
+        allow_unicode=True,
+        indent=2,
+        sort_keys=False,  # we already sorted manually
+        width=100,
+    )
+
+
+def find_rule_files(root: Path) -> list[Path]:
+    """Find all rule.yml files under Published/ and Unpublished/."""
+    files = []
+    for folder in ("Published", "Unpublished"):
+        folder_path = root / folder
+        if folder_path.exists():
+            files.extend(folder_path.rglob("rule.yml"))
+    return sorted(files)
+
+
+def process_files(files: list[Path], check_mode: bool) -> int:
+    """Format (or check) the given files. Returns exit code."""
+    changed = []
+    errors = []
+
+    for path in files:
+        try:
+            original = path.read_text(encoding="utf-8")
+            formatted = canonical(original)
+        except Exception as exc:
+            errors.append(f"  {path}: {exc}")
+            continue
+
+        if original != formatted:
+            changed.append(path)
+            if not check_mode:
+                path.write_text(formatted, encoding="utf-8")
+                print(f"  Formatted: {path}")
+
+    if errors:
+        print("\nERROR: Failed to process the following files:", file=sys.stderr)
+        for e in errors:
+            print(e, file=sys.stderr)
+        return 1
+
+    if check_mode:
+        if changed:
+            print(
+                "\nThe following rule.yml files are not correctly sorted/formatted:\n",
+                file=sys.stderr,
+            )
+            for p in changed:
+                print(f"  {p}", file=sys.stderr)
+            print(
+                "\nRun `python scripts/sort_yaml.py` to fix them automatically.",
+                file=sys.stderr,
+            )
+            return 1
+        else:
+            print("All rule.yml files are correctly sorted and formatted.")
+    else:
+        if not changed:
+            print("All rule.yml files are already correctly sorted and formatted.")
+
+    return 0
+
+
+# ---------------------------------------------------------------------------
+# Entry point
+# ---------------------------------------------------------------------------
+
+def main():
+    parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
+    parser.add_argument(
+        "--check",
+        action="store_true",
+        help="Check mode: exit 1 if any file needs formatting, without modifying files.",
+    )
+    parser.add_argument(
+        "files",
+        nargs="*",
+        type=Path,
+        help="rule.yml files to process. Defaults to all rule.yml files under Published/ and Unpublished/.",
+    )
+    args = parser.parse_args()
+
+    repo_root = Path(__file__).resolve().parent.parent
+
+    if args.files:
+        files = [p.resolve() for p in args.files]
+    else:
+        files = find_rule_files(repo_root)
+
+    if not files:
+        print("No rule.yml files found.")
+        return 0
+
+    mode = "Checking" if args.check else "Formatting"
+    print(f"{mode} {len(files)} rule.yml file(s)...")
+
+    sys.exit(process_files(files, check_mode=args.check))
+
+
+if __name__ == "__main__":
+    main()
+
+

setup/bash_setup.sh

@@ -145,4 +145,15 @@ fi
 
 VENV_PYTHON=$(which python)
 
+echo "Installing pre-commit..."
+pip install pre-commit --index-url https://pypi.org/simple/ --quiet 2>/dev/null || \
+  pip install pre-commit --quiet 2>/dev/null || true
+if command -v pre-commit >/dev/null 2>&1; then
+    pre-commit install
+    echo "Pre-commit hook installed."
+else
+    echo "Warning: pre-commit not found on PATH after install; skipping hook setup."
+    echo "You can install it manually with: pip install pre-commit && pre-commit install"
+fi
+
 echo "Setup completed successfully!"

setup/windows_setup.bat

@@ -177,6 +177,18 @@ if !errorlevel! neq 0 (
     exit /b 1
 )
 
+echo.
+echo Installing pre-commit...
+python -m pip install pre-commit --index-url https://pypi.org/simple/ --quiet 2>nul || python -m pip install pre-commit --quiet 2>nul
+where pre-commit >nul 2>&1
+if !errorlevel! equ 0 (
+    pre-commit install
+    echo Pre-commit hook installed.
+) else (
+    echo Warning: pre-commit not found on PATH; skipping hook setup.
+    echo You can install it manually with: pip install pre-commit ^&^& pre-commit install
+)
+
 echo.
 echo Setup completed successfully!
 pause