codespine 0.6.0__tar.gz → 0.6.2__tar.gz

{codespine-0.6.0 → codespine-0.6.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: codespine
-Version: 0.6.0
+Version: 0.6.2
 Summary: Local Java code intelligence indexer backed by a graph database
 Author: CodeSpine contributors
 License: MIT License

{codespine-0.6.0 → codespine-0.6.2}/codespine/__init__.py

@@ -1,4 +1,4 @@
 """CodeSpine package."""
 
 __all__ = ["__version__"]
-__version__ = "0.6.0"
+__version__ = "0.6.2"

{codespine-0.6.0 → codespine-0.6.2}/codespine/cli.py

@@ -751,17 +751,25 @@ def clear_project_cmd(project_id: str, allow_running: bool) -> None:
     if not allow_running and _is_running():
         click.secho("Stop MCP first ('codespine stop') to modify index.", fg="yellow")
         return
-    store = GraphStore(read_only=False)
-    recs = store.query_records(
-        "MATCH (p:Project) WHERE p.id = $pid RETURN p.id as id, p.path as path",
-        {"pid": project_id},
-    )
+    try:
+        store = GraphStore(read_only=False)
+        recs = store.query_records(
+            "MATCH (p:Project) WHERE p.id = $pid RETURN p.id as id, p.path as path",
+            {"pid": project_id},
+        )
+    except Exception as exc:
+        click.secho(f"DB is corrupted ({exc}). Use 'codespine force-reset' to wipe all data.", fg="red")
+        return
     if not recs:
         click.secho(f"Project '{project_id}' not found in index.", fg="yellow")
         return
     project_path = recs[0].get("path", "")
-    store.clear_analysis_artifacts()
-    store.clear_project(project_id)
+    try:
+        store.clear_analysis_artifacts()
+        store.clear_project(project_id)
+    except Exception as exc:
+        click.secho(f"DB write failed ({exc}). Use 'codespine force-reset' to recover.", fg="red")
+        return
     store.overlay_store.clear_project(project_id)
     meta_path = JavaIndexer._meta_cache_path(project_id)
     if os.path.exists(meta_path):
@@ -769,6 +777,8 @@ def clear_project_cmd(project_id: str, allow_running: bool) -> None:
             os.remove(meta_path)
         except OSError:
             pass
+    # Update the read replica so read-only callers (stats, MCP) see the change.
+    GraphStore.snapshot_to_read_replica()
     click.secho(f"Cleared project '{project_id}' (was at {project_path}).", fg="green")
 
 
@@ -784,9 +794,23 @@ def clear_index_cmd(allow_running: bool) -> None:
     if not allow_running and _is_running():
         click.secho("Stop MCP first ('codespine stop') to modify index.", fg="yellow")
         return
-    store = GraphStore(read_only=False)
-    projects = store.query_records("MATCH (p:Project) RETURN p.id as id")
-    store.rebuild_empty_db()
+    try:
+        store = GraphStore(read_only=False)
+        projects = store.query_records("MATCH (p:Project) RETURN p.id as id")
+    except Exception:
+        # DB is corrupted — can't even open it.  Force-delete everything.
+        click.secho("DB is corrupted. Running force-reset instead...", fg="yellow")
+        removed = GraphStore.force_delete_all_data()
+        click.secho(f"Force-reset complete. {len(removed)} path(s) removed. Index is now empty.", fg="green")
+        return
+    try:
+        store.rebuild_empty_db()
+    except Exception as exc:
+        # rebuild_empty_db failed even with fallbacks — force-delete.
+        click.secho(f"rebuild failed ({exc}). Running force-reset...", fg="yellow")
+        GraphStore.force_delete_all_data()
+        click.secho("Force-reset complete. Index is now empty.", fg="green")
+        return
     store.overlay_store.clear_all()
     for p in projects:
         meta_path = JavaIndexer._meta_cache_path(p["id"])
@@ -795,6 +819,9 @@ def clear_index_cmd(allow_running: bool) -> None:
                 os.remove(meta_path)
             except OSError:
                 pass
+    # Publish an empty read replica so that read-only callers (stats, MCP)
+    # immediately see the cleared state and the MCP daemon hot-reloads.
+    GraphStore.snapshot_to_read_replica()
     click.secho(f"Cleared {len(projects)} project(s). Index is now empty.", fg="green")
 
 

{codespine-0.6.0 → codespine-0.6.2}/codespine/db/store.py

@@ -550,21 +550,58 @@ class GraphStore:
     def rebuild_empty_db(self) -> None:
         self._recycle_conn()
         path = SETTINGS.db_path
+        # Remove the DB directory AND any stale WAL / lock files
         self._remove_db_path(path)
+        for suffix in (".wal", ".lock"):
+            sidecar = path + suffix
+            if os.path.exists(sidecar):
+                try:
+                    os.remove(sidecar)
+                except OSError:
+                    pass
+
+        # Also remove the read replica so that read-only callers (stats, MCP)
+        # don't continue to see stale data from before the wipe.
+        for stale in [
+            SETTINGS.db_snapshot_path,
+            SETTINGS.db_snapshot_path + ".tmp",
+            SETTINGS.db_snapshot_path + ".updated",
+        ]:
+            self._remove_db_path(stale)
+
         # Kuzu may retain stale internal state from a previous failed open of
-        # this path (e.g. after Ctrl+C mid-write).  If re-opening the just-
-        # deleted path raises, fall back to a clean /tmp location so the
-        # command succeeds rather than leaving the user stuck.
+        # this path (e.g. after Ctrl+C mid-write).  The in-process C++ state
+        # is poisoned and will raise "unordered_map::at: key not found" on any
+        # new kuzu.Database() call — even for a freshly deleted path.
+        #
+        # Strategy: try primary → try /tmp fallback → force-delete everything
+        # and re-import kuzu to get a clean C++ state.
         try:
             self.db = self._open_db(path)
-        except Exception as exc:
+        except Exception as exc1:
+            LOGGER.warning("rebuild_empty_db: primary path failed (%s)", exc1)
             fallback = os.path.join("/tmp", ".codespine_db")
-            LOGGER.warning(
-                "Could not open fresh DB at %s after rebuild (%s); falling back to %s",
-                path, exc, fallback,
-            )
             self._remove_db_path(fallback)
-            self.db = self._open_db(fallback)
+            for suffix in (".wal", ".lock"):
+                sidecar = fallback + suffix
+                if os.path.exists(sidecar):
+                    try:
+                        os.remove(sidecar)
+                    except OSError:
+                        pass
+            try:
+                self.db = self._open_db(fallback)
+            except Exception as exc2:
+                # Nuclear option: force-delete all files and reimport kuzu
+                # so the C++ runtime starts from a completely clean state.
+                LOGGER.warning("rebuild_empty_db: fallback also failed (%s); force-resetting", exc2)
+                self.force_delete_all_data()
+                import importlib
+                importlib.reload(kuzu)
+                try:
+                    self.db = kuzu.Database(path, buffer_pool_size=_WRITE_BUFFER_POOL_SIZE)
+                except TypeError:
+                    self.db = kuzu.Database(path)
         self._tls = threading.local()
         ensure_schema(self._conn())
 

{codespine-0.6.0 → codespine-0.6.2}/codespine/mcp/server.py

@@ -1227,9 +1227,13 @@ def build_mcp_server(store, repo_path_provider):
             timeout=60,
         )
         if proc.returncode != 0:
+            error_text = (proc.stderr.strip() or proc.stdout.strip())[:300]
             return {
                 "available": False,
-                "note": f"Reset failed: {proc.stderr.strip() or proc.stdout.strip()}",
+                "note": (
+                    f"Reset failed: {error_text}. "
+                    "If this is a buffer pool or DB corruption error, use force_reset_index() instead."
+                ),
             }
         return {
             "available": True,
@@ -1268,9 +1272,13 @@ def build_mcp_server(store, repo_path_provider):
             timeout=120,
         )
         if proc.returncode != 0:
+            error_text = (proc.stderr.strip() or proc.stdout.strip())[:300]
             return {
                 "available": False,
-                "note": f"Reset failed: {proc.stderr.strip() or proc.stdout.strip()}",
+                "note": (
+                    f"Reset failed: {error_text}. "
+                    "If this is a buffer pool or DB corruption error, use force_reset_index() instead."
+                ),
             }
 
         cleared = [{"project_id": p["id"], "path": p["path"]} for p in projects]

{codespine-0.6.0 → codespine-0.6.2}/codespine.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: codespine
-Version: 0.6.0
+Version: 0.6.2
 Summary: Local Java code intelligence indexer backed by a graph database
 Author: CodeSpine contributors
 License: MIT License

{codespine-0.6.0 → codespine-0.6.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "codespine"
-version = "0.6.0"
+version = "0.6.2"
 description = "Local Java code intelligence indexer backed by a graph database"
 readme = "README.md"
 requires-python = ">=3.10"