fix(core): remove runtime ALTER TABLE from vector init (#728)

Signed-off-by: phernandez <paul@basicmachines.co>

Author: phernandez

src/basic_memory/repository/postgres_search_repository.py

@@ -292,6 +292,10 @@ async def _ensure_vector_tables(self) -> None:
                     ) from exc
 
                 # --- Chunks table (dimension-independent, may already exist via migration) ---
+                # Trigger: fresh Postgres projects may not have vector chunk tables yet.
+                # Why: runtime can bootstrap missing tables, but schema evolution must stay
+                # in Alembic to avoid concurrent ALTER TABLE deadlocks during indexing.
+                # Outcome: new installs create the current schema; upgrades rely on migration.
                 await session.execute(
                     text(
                         """
@@ -318,47 +322,6 @@ async def _ensure_vector_tables(self) -> None:
                         """
                     )
                 )
-                await session.execute(
-                    text(
-                        """
-                        ALTER TABLE search_vector_chunks
-                        ADD COLUMN IF NOT EXISTS entity_fingerprint TEXT
-                        """
-                    )
-                )
-                await session.execute(
-                    text(
-                        """
-                        ALTER TABLE search_vector_chunks
-                        ADD COLUMN IF NOT EXISTS embedding_model TEXT
-                        """
-                    )
-                )
-                await session.execute(
-                    text(
-                        """
-                        UPDATE search_vector_chunks
-                        SET entity_fingerprint = COALESCE(entity_fingerprint, ''),
-                            embedding_model = COALESCE(embedding_model, '')
-                        """
-                    )
-                )
-                await session.execute(
-                    text(
-                        """
-                        ALTER TABLE search_vector_chunks
-                        ALTER COLUMN entity_fingerprint SET NOT NULL
-                        """
-                    )
-                )
-                await session.execute(
-                    text(
-                        """
-                        ALTER TABLE search_vector_chunks
-                        ALTER COLUMN embedding_model SET NOT NULL
-                        """
-                    )
-                )
 
                 # --- Embeddings table (dimension-dependent, created at runtime) ---
                 # Trigger: provider dimensions may differ from what was previously deployed.

tests/repository/test_postgres_search_repository_unit.py

@@ -6,6 +6,7 @@
 """
 
 import asyncio
+from contextlib import asynccontextmanager
 from unittest.mock import AsyncMock, MagicMock, patch
 
 import pytest
@@ -169,6 +170,43 @@ async def test_skips_when_already_initialized(self):
         assert repo._vector_tables_initialized is True
 
 
+class TestEnsureVectorTablesSchemaBootstrapping:
+    """Guard the runtime setup path against inline schema migration drift."""
+
+    @pytest.mark.asyncio
+    async def test_initialization_never_alters_chunk_table_schema(self, monkeypatch):
+        repo = _make_repo(
+            semantic_enabled=True,
+            embedding_provider=StubEmbeddingProvider(),
+        )
+        session = AsyncMock()
+
+        @asynccontextmanager
+        async def fake_scoped_session(session_maker):
+            yield session
+
+        monkeypatch.setattr(
+            "basic_memory.repository.postgres_search_repository.db.scoped_session",
+            fake_scoped_session,
+        )
+        monkeypatch.setattr(repo, "_get_existing_embedding_dims", AsyncMock(return_value=None))
+
+        await repo._ensure_vector_tables()
+
+        executed_sql = [str(call.args[0]) for call in session.execute.await_args_list]
+
+        assert any(
+            "CREATE TABLE IF NOT EXISTS search_vector_chunks" in sql for sql in executed_sql
+        )
+        assert any(
+            "CREATE TABLE IF NOT EXISTS search_vector_embeddings" in sql
+            for sql in executed_sql
+        )
+        assert not any("ALTER TABLE search_vector_chunks" in sql for sql in executed_sql)
+        session.commit.assert_awaited_once()
+        assert repo._vector_tables_initialized is True
+
+
 # --- _run_vector_query empty embedding (line 395-396) ----------------------