fix-the-autoannotate-metadata-workflow (#421)

* testing wf

* testing

* testing...

* Update Molecules/membrane/BOGUS/metadata.yaml

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* Added CAS key secret to allow retrieval of CAS numbers in autocomplete_metadata git wf

* Remove the test directory. Now only the changes to the workflow remain.

---------

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

Author: mdondrup

.github/workflows/AutocompleteMetadata.yml

@@ -52,91 +52,17 @@ jobs:
         if: steps.files.outputs.changed_files != ''
         env:
           CHANGED_FILES: ${{ steps.files.outputs.changed_files }}
+          CAS_API_KEY: ${{ secrets.CAS_API_KEY }}
         run: |
           printf '%s\n' "$CHANGED_FILES" | while IFS= read -r f; do
             [ -n "$f" ] && python "$RUNNER_TEMP/Databank/developer/autocomplete_metadata.py" "$f"
           done
 
       - name: Suggest changes on PR
         if: steps.files.outputs.changed_files != ''
-        env:
-          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          PR_NUMBER: ${{ github.event.pull_request.number }}
-          HEAD_SHA: ${{ github.event.pull_request.head.sha }}
-        run: |
-          python3 << 'PYEOF'
-          import subprocess, json, re, os, sys
-
-          repo = os.environ['GITHUB_REPOSITORY']
-          pr_number = os.environ['PR_NUMBER']
-          head_sha = os.environ['HEAD_SHA']
-
-          diff_output = subprocess.check_output(['git', 'diff', 'HEAD', '--unified=0'], text=True)
-          print('=== git diff HEAD ===')
-          print(diff_output or '(empty — autocomplete made no changes)')
-
-          def head_line(filepath, line_num):
-              out = subprocess.check_output(['git', 'show', f'HEAD:{filepath}'], text=True)
-              lines = out.splitlines(keepends=True)
-              return lines[line_num - 1] if 0 < line_num <= len(lines) else ''
-
-          comments = []
-          current_file = None
-          current_old_start = 0
-          minus_lines = []
-          plus_lines = []
-
-          def flush_hunk():
-              if current_file is None or (not minus_lines and not plus_lines):
-                  return
-              if not minus_lines:
-                  # Pure addition after line current_old_start — anchor to that line
-                  anchor_num = max(current_old_start, 1)
-                  anchor = head_line(current_file, anchor_num)
-                  body = '```suggestion\n' + anchor + ''.join(plus_lines) + '```'
-                  comment = {'path': current_file, 'body': body, 'side': 'RIGHT', 'line': anchor_num}
-              else:
-                  start_line = current_old_start
-                  end_line = current_old_start + len(minus_lines) - 1
-                  body = '```suggestion\n' + ''.join(plus_lines) + '```'
-                  comment = {'path': current_file, 'body': body, 'side': 'RIGHT', 'line': end_line}
-                  if start_line != end_line:
-                      comment['start_line'] = start_line
-                      comment['start_side'] = 'RIGHT'
-              print(f'  hunk -> {current_file}:{comment["line"]} ({len(minus_lines)} removed, {len(plus_lines)} added)')
-              comments.append(comment)
-
-          for line in diff_output.splitlines(keepends=True):
-              if line.startswith('diff --git'):
-                  flush_hunk(); minus_lines = []; plus_lines = []
-              elif line.startswith('+++ '):
-                  current_file = line[6:].rstrip('\n')
-              elif line.startswith('@@ '):
-                  flush_hunk(); minus_lines = []; plus_lines = []
-                  m = re.match(r'@@ -(\d+)(?:,\d+)? ', line)
-                  if m:
-                      current_old_start = int(m.group(1))
-              elif line.startswith('-') and not line.startswith('---'):
-                  minus_lines.append(line[1:])
-              elif line.startswith('+') and not line.startswith('+++'):
-                  plus_lines.append(line[1:])
-
-          flush_hunk()
-
-          print(f'Built {len(comments)} suggestion(s)')
-          if not comments:
-              print('No changes to suggest'); sys.exit(0)
-
-          review = {'commit_id': head_sha, 'body': '', 'event': 'COMMENT', 'comments': comments}
-          result = subprocess.run(
-              ['gh', 'api', f'repos/{repo}/pulls/{pr_number}/reviews',
-               '--method', 'POST', '--input', '-'],
-              input=json.dumps(review), text=True, capture_output=True
-          )
-          print('API response:', result.stdout[:300])
-          if result.stderr:
-              print('API error:', result.stderr[:300], file=sys.stderr)
-          if result.returncode != 0:
-              sys.exit(1)
-          print(f'Posted {len(comments)} inline suggestion(s)')
-          PYEOF
+        uses: reviewdog/action-suggester@v1
+        with:
+          tool_name: addmetadata
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          fail_level: any          # surface errors instead of exiting 0
+          reviewdog_flags: -tee    # echo reviewdog's stdout/stderr to the log