fix: CI failures and review feedback

- Remove `memory doctor` from CI smoke test (command removed in v0.3.1)
- Simplify isolated_memory warning expression using sum of lengths
- Fix ruff formatting in test_rst.py and test_scaffold.py

Author: bburda

.github/workflows/ci.yml

@@ -103,7 +103,6 @@ jobs:
           memory --dir /tmp/test-memory get FACT_ci_test_fact
           memory --dir /tmp/test-memory tags
           memory --dir /tmp/test-memory list
-          memory --dir /tmp/test-memory doctor
 
   test-mcp:
     runs-on: ubuntu-latest

src/ai_memory_protocol/scaffold.py

@@ -232,7 +232,7 @@ def _write(path: Path, content: str) -> None:
     "isolated_decision": "type == 'dec' and len(relates) == 0 and len(supersedes) == 0 and len(supersedes_back) == 0",
     "draft_too_short": "status == 'draft' and (description == '' or len(description) < 20)",
     "suspicious_high_confidence": "confidence == 'high' and type in ['mem', 'risk', 'goal', 'q']",
-    "isolated_memory": "status != 'draft' and len(relates) == 0 and len(supersedes) == 0 and len(supersedes_back) == 0 and len(depends) == 0 and len(depends_back) == 0 and len(supports) == 0 and len(supports_back) == 0 and len(contradicts) == 0 and len(contradicts_back) == 0 and len(example_of) == 0 and len(example_of_back) == 0",
+    "isolated_memory": "status != 'draft' and (len(relates) + len(supersedes) + len(supersedes_back) + len(depends) + len(depends_back) + len(supports) + len(supports_back) + len(contradicts) + len(contradicts_back) + len(example_of) + len(example_of_back)) == 0",
 }}
 """
 

tests/test_rst.py

@@ -250,7 +250,9 @@ def test_replace_body(self, tmp_workspace: Path) -> None:
         )
         append_to_rst(tmp_workspace, "fact", directive)
 
-        ok, msg = update_body_in_rst(tmp_workspace, "FACT_test_fact", "Updated body with new content.")
+        ok, msg = update_body_in_rst(
+            tmp_workspace, "FACT_test_fact", "Updated body with new content."
+        )
         assert ok, msg
         content = (tmp_workspace / "memory" / "facts.rst").read_text()
         assert "Updated body with new content." in content

tests/test_scaffold.py

@@ -72,6 +72,7 @@ def test_custom_author(self, tmp_path: Path) -> None:
 class TestConfPyWarnings:
     def test_scaffold_includes_needs_warnings(self, tmp_path: Path) -> None:
         from ai_memory_protocol.scaffold import init_workspace
+
         ws = tmp_path / "test_ws"
         init_workspace(ws, "Test", "Author")
         conf_content = (ws / "conf.py").read_text()