fix(store): honor unified database configuration (#3904)

* fix(store): align store backend with database config

* fix(store): preserve no-config memory fallback

---------

Co-authored-by: Willem Jiang <willem.jiang@gmail.com>

README.md

@@ -253,6 +253,11 @@ make down   # Stop and remove containers
 
 Access: http://localhost:2026
 
+For persistent deployments, configure `database.backend` as `sqlite` or
+`postgres`. The selected backend is shared by the LangGraph checkpointer,
+LangGraph Store, and DeerFlow application data. The deprecated `checkpointer`
+section, when present, overrides the first two for backward compatibility.
+
 The unified nginx endpoint is same-origin by default and does not emit browser CORS headers. If you run a split-origin or port-forwarded browser client, set `GATEWAY_CORS_ORIGINS` to comma-separated exact origins such as `http://localhost:3000`; the Gateway then applies the CORS allowlist and matching CSRF origin checks.
 
 > [!IMPORTANT]

backend/AGENTS.md

@@ -250,6 +250,12 @@ Setup: Copy `config.example.yaml` to `config.yaml` in the **project root** direc
 
 Infrastructure fields are **restart-required**. The authoritative list lives in `packages/harness/deerflow/config/reload_boundary.py::STARTUP_ONLY_FIELDS` and is mirrored by the standardised `"startup-only:"` prefix on the corresponding `Field(description=...)` in `AppConfig`, so IDE hover on those fields surfaces the reason inline (no need to context-switch into this table). Currently registered: `database`, `checkpointer`, `run_events`, `stream_bridge`, `sandbox`, `log_level`, `channels`, `channel_connections`. Adding a new restart-required field requires updating the registry; drift is pinned by `tests/test_reload_boundary.py`.
 
+**Persistence backend resolution**: the unified `database` section selects the
+Gateway's LangGraph checkpointer, LangGraph Store, and DeerFlow SQL repositories.
+The deprecated `checkpointer` section remains backward compatible and, when
+present, overrides `database` for the LangGraph checkpointer and Store only;
+application repositories continue to use `database`.
+
 Configuration priority:
 1. Explicit `config_path` argument
 2. `DEER_FLOW_CONFIG_PATH` environment variable

backend/packages/harness/deerflow/runtime/store/async_provider.py

@@ -1,11 +1,11 @@
-"""Async Store factory — backend mirrors the configured checkpointer.
+"""Async Store factory — backend mirrors runtime persistence configuration.
 
-The store and checkpointer share the same ``checkpointer`` section in
-*config.yaml* so they always use the same persistence backend:
+The deprecated ``checkpointer`` section takes precedence when present;
+otherwise Store follows the unified ``database`` section in *config.yaml*:
 
-- ``type: memory``   → :class:`langgraph.store.memory.InMemoryStore`
-- ``type: sqlite``   → :class:`langgraph.store.sqlite.aio.AsyncSqliteStore`
-- ``type: postgres`` → :class:`langgraph.store.postgres.aio.AsyncPostgresStore`
+- ``memory``   → :class:`langgraph.store.memory.InMemoryStore`
+- ``sqlite``   → :class:`langgraph.store.sqlite.aio.AsyncSqliteStore`
+- ``postgres`` → :class:`langgraph.store.postgres.aio.AsyncPostgresStore`
 
 Usage (e.g. FastAPI lifespan)::
 
@@ -17,6 +17,7 @@ Usage (e.g. FastAPI lifespan)::
 
 from __future__ import annotations
 
+import asyncio
 import contextlib
 import logging
 from collections.abc import AsyncIterator
@@ -24,7 +25,14 @@ from collections.abc import AsyncIterator
 from langgraph.store.base import BaseStore
 
 from deerflow.config.app_config import AppConfig, get_app_config
-from deerflow.runtime.store.provider import POSTGRES_CONN_REQUIRED, POSTGRES_STORE_INSTALL, SQLITE_STORE_INSTALL, ensure_sqlite_parent_dir, resolve_sqlite_conn_str
+from deerflow.runtime.store.provider import (
+    POSTGRES_CONN_REQUIRED,
+    POSTGRES_STORE_INSTALL,
+    SQLITE_STORE_INSTALL,
+    _resolve_store_config,
+    ensure_sqlite_parent_dir,
+    resolve_sqlite_conn_str,
+)
 
 logger = logging.getLogger(__name__)
 
@@ -54,7 +62,7 @@ async def _async_store(config) -> AsyncIterator[BaseStore]:
             raise ImportError(SQLITE_STORE_INSTALL) from exc
 
         conn_str = resolve_sqlite_conn_str(config.connection_string or "store.db")
-        ensure_sqlite_parent_dir(conn_str)
+        await asyncio.to_thread(ensure_sqlite_parent_dir, conn_str)
 
         async with AsyncSqliteStore.from_conn_string(conn_str) as store:
             await store.setup()
@@ -87,28 +95,21 @@ async def _async_store(config) -> AsyncIterator[BaseStore]:
 
 @contextlib.asynccontextmanager
 async def make_store(app_config: AppConfig | None = None) -> AsyncIterator[BaseStore]:
-    """Async context manager that yields a Store whose backend matches the
-    configured checkpointer.
+    """Yield a Store selected from legacy or unified persistence config.
 
-    Reads from the same ``checkpointer`` section of *config.yaml* used by
-    :func:`deerflow.runtime.checkpointer.async_provider.make_checkpointer` so
-    that both singletons always use the same persistence technology::
+    The legacy ``checkpointer`` section takes precedence when configured;
+    otherwise the unified ``database`` section selects the backend, matching
+    :func:`deerflow.runtime.checkpointer.async_provider.make_checkpointer`::
 
         async with make_store(app_config) as store:
             app.state.store = store
 
-    Yields an :class:`~langgraph.store.memory.InMemoryStore` when no
-    ``checkpointer`` section is configured (emits a WARNING in that case).
+    An :class:`~langgraph.store.memory.InMemoryStore` is returned only when the
+    resolved backend is explicitly ``memory``.
     """
     if app_config is None:
         app_config = get_app_config()
 
-    if app_config.checkpointer is None:
-        from langgraph.store.memory import InMemoryStore
-
-        logger.warning("No 'checkpointer' section in config.yaml — using InMemoryStore for the store. Thread list will be lost on server restart. Configure a sqlite or postgres backend for persistence.")
-        yield InMemoryStore()
-        return
-
-    async with _async_store(app_config.checkpointer) as store:
+    config = _resolve_store_config(app_config)
+    async with _async_store(config) as store:
         yield store

backend/packages/harness/deerflow/runtime/store/provider.py

@@ -3,8 +3,9 @@
 Provides a **sync singleton** and a **sync context manager** for CLI tools
 and the embedded :class:`~deerflow.client.DeerFlowClient`.
 
-The backend mirrors the configured checkpointer so that both always use the
-same persistence technology.  Supported backends: memory, sqlite, postgres.
+The deprecated ``checkpointer`` section takes precedence when present;
+otherwise Store follows the unified ``database`` section. Supported backends:
+memory, sqlite, postgres.
 
 Usage::
 
@@ -27,8 +28,8 @@ from collections.abc import Iterator
 
 from langgraph.store.base import BaseStore
 
-from deerflow.config.app_config import get_app_config
-from deerflow.config.checkpointer_config import ensure_config_loaded
+from deerflow.config.app_config import AppConfig, get_app_config
+from deerflow.config.checkpointer_config import CheckpointerConfig, ensure_config_loaded, get_checkpointer_config
 from deerflow.runtime.store._sqlite_utils import ensure_sqlite_parent_dir, resolve_sqlite_conn_str
 
 logger = logging.getLogger(__name__)
@@ -43,6 +44,44 @@ POSTGRES_STORE_INSTALL = (
 )
 POSTGRES_CONN_REQUIRED = "checkpointer.connection_string is required for the postgres backend"
 
+
+def _resolve_store_config(app_config: AppConfig) -> CheckpointerConfig:
+    """Resolve the Store backend from legacy or unified application config.
+
+    The legacy ``checkpointer`` section remains authoritative when present so
+    Store and Checkpointer continue to use the same backend. Otherwise the
+    unified ``database`` section drives the Store as documented.
+    """
+    if app_config.checkpointer is not None:
+        return app_config.checkpointer
+
+    database = app_config.database
+    if database.backend == "memory":
+        return CheckpointerConfig(type="memory")
+    if database.backend == "sqlite":
+        return CheckpointerConfig(type="sqlite", connection_string=database.checkpointer_sqlite_path)
+    if database.backend == "postgres":
+        if not database.postgres_url:
+            raise ValueError("database.postgres_url is required for the postgres backend")
+        return CheckpointerConfig(type="postgres", connection_string=database.postgres_url)
+    raise ValueError(f"Unknown database backend: {database.backend!r}")
+
+
+def _get_store_config() -> CheckpointerConfig:
+    """Load Store config without holding the provider singleton lock."""
+    ensure_config_loaded()
+
+    # Preserve callers that initialise the legacy config singleton directly.
+    legacy_config = get_checkpointer_config()
+    if legacy_config is not None:
+        return legacy_config
+    try:
+        app_config = get_app_config()
+    except FileNotFoundError:
+        return CheckpointerConfig(type="memory")
+    return _resolve_store_config(app_config)
+
+
 # ---------------------------------------------------------------------------
 # Sync factory
 # ---------------------------------------------------------------------------
@@ -108,37 +147,26 @@ _store_lock = threading.Lock()
 def get_store() -> BaseStore:
     """Return the global sync Store singleton, creating it on first call.
 
-    Returns an :class:`~langgraph.store.memory.InMemoryStore` when no
-    checkpointer is configured in *config.yaml* (emits a WARNING in that case).
+    The legacy ``checkpointer`` section takes precedence when configured;
+    otherwise the unified ``database`` section selects the backend.
 
     Raises:
         ImportError: If the required package for the configured backend is not installed.
-        ValueError: If ``connection_string`` is missing for a backend that requires it.
+        ValueError: If the selected backend is missing its required connection value.
     """
     global _store, _store_ctx
 
     if _store is not None:
         return _store
 
-    # Config loading can reset both persistence singletons. Keep it outside
-    # this provider lock to avoid cross-provider lock-order inversion.
-    ensure_config_loaded()
+    # Config loading can reset both persistence singletons. Resolve the full
+    # config outside this provider lock to avoid lock-order inversion.
+    config = _get_store_config()
 
     with _store_lock:
         if _store is not None:
             return _store
 
-        from deerflow.config.checkpointer_config import get_checkpointer_config
-
-        config = get_checkpointer_config()
-
-        if config is None:
-            from langgraph.store.memory import InMemoryStore
-
-            logger.warning("No 'checkpointer' section in config.yaml — using InMemoryStore for the store. Thread list will be lost on server restart. Configure a sqlite or postgres backend for persistence.")
-            _store = InMemoryStore()
-            return _store
-
         store_ctx = _sync_store_cm(config)
         store = store_ctx.__enter__()
         _store_ctx = store_ctx
@@ -179,16 +207,9 @@ def store_context() -> Iterator[BaseStore]:
         with store_context() as store:
             store.put(("threads",), thread_id, {...})
 
-    Yields an :class:`~langgraph.store.memory.InMemoryStore` when no
-    checkpointer is configured in *config.yaml*.
+    The legacy ``checkpointer`` section takes precedence when configured;
+    otherwise the unified ``database`` section selects the backend.
     """
-    config = get_app_config()
-    if config.checkpointer is None:
-        from langgraph.store.memory import InMemoryStore
-
-        logger.warning("No 'checkpointer' section in config.yaml — using InMemoryStore for the store. Thread list will be lost on server restart. Configure a sqlite or postgres backend for persistence.")
-        yield InMemoryStore()
-        return
-
-    with _sync_store_cm(config.checkpointer) as store:
+    config = _resolve_store_config(get_app_config())
+    with _sync_store_cm(config) as store:
         yield store

backend/tests/test_checkpointer.py

@@ -3,8 +3,10 @@
 import sys
 import tomllib
 from concurrent.futures import ThreadPoolExecutor
+from contextlib import nullcontext
 from pathlib import Path
 from threading import Barrier, Event, Lock
+from types import SimpleNamespace
 from unittest.mock import AsyncMock, MagicMock, patch
 
 import pytest
@@ -17,6 +19,7 @@ from deerflow.config.checkpointer_config import (
     load_checkpointer_config_from_dict,
     set_checkpointer_config,
 )
+from deerflow.config.database_config import DatabaseConfig
 from deerflow.runtime.checkpointer import get_checkpointer, reset_checkpointer
 from deerflow.runtime.checkpointer.provider import POSTGRES_INSTALL
 from deerflow.runtime.store import get_store, reset_store
@@ -702,6 +705,156 @@ class TestAsyncCheckpointer:
         mock_saver.setup.assert_awaited_once()
 
 
+class TestStoreDatabaseConfig:
+    def test_sync_store_falls_back_to_memory_when_config_file_is_missing(self):
+        """The sync Store keeps its no-config fallback for embedded callers."""
+        from langgraph.store.memory import InMemoryStore
+
+        with (
+            patch("deerflow.runtime.store.provider.ensure_config_loaded"),
+            patch("deerflow.runtime.store.provider.get_checkpointer_config", return_value=None),
+            patch("deerflow.runtime.store.provider.get_app_config", side_effect=FileNotFoundError),
+        ):
+            assert isinstance(get_store(), InMemoryStore)
+
+    @pytest.mark.anyio
+    async def test_async_postgres_store_uses_database_config(self, caplog):
+        """Unified database postgres config must not fall back to InMemoryStore."""
+        from deerflow.runtime.store.async_provider import make_store
+
+        caplog.set_level("WARNING", logger="deerflow.runtime.store.async_provider")
+        app_config = SimpleNamespace(
+            checkpointer=None,
+            database=DatabaseConfig(backend="postgres", postgres_url="postgresql://localhost/db"),
+        )
+        mock_store = AsyncMock()
+        mock_cm = AsyncMock()
+        mock_cm.__aenter__.return_value = mock_store
+        mock_cm.__aexit__.return_value = False
+        mock_store_cls = MagicMock()
+        mock_store_cls.from_conn_string.return_value = mock_cm
+        mock_module = MagicMock(AsyncPostgresStore=mock_store_cls)
+
+        with patch.dict(sys.modules, {"langgraph.store.postgres.aio": mock_module}):
+            async with make_store(app_config) as store:
+                assert store is mock_store
+
+        mock_store_cls.from_conn_string.assert_called_once_with("postgresql://localhost/db")
+        mock_store.setup.assert_awaited_once()
+        assert "No 'checkpointer' section" not in caplog.text
+
+    @pytest.mark.anyio
+    async def test_async_sqlite_store_uses_unified_database_path(self, tmp_path):
+        """Unified database SQLite config must use the shared deerflow.db path."""
+        from deerflow.runtime.store.async_provider import make_store
+        from deerflow.runtime.store.provider import ensure_sqlite_parent_dir
+
+        db_config = DatabaseConfig(backend="sqlite", sqlite_dir=str(tmp_path))
+        app_config = SimpleNamespace(checkpointer=None, database=db_config)
+        mock_store = AsyncMock()
+        mock_cm = AsyncMock()
+        mock_cm.__aenter__.return_value = mock_store
+        mock_cm.__aexit__.return_value = False
+        mock_store_cls = MagicMock()
+        mock_store_cls.from_conn_string.return_value = mock_cm
+        mock_module = MagicMock(AsyncSqliteStore=mock_store_cls)
+
+        with (
+            patch.dict(sys.modules, {"langgraph.store.sqlite.aio": mock_module}),
+            patch(
+                "deerflow.runtime.store.async_provider.asyncio.to_thread",
+                new_callable=AsyncMock,
+            ) as mock_to_thread,
+        ):
+            async with make_store(app_config) as store:
+                assert store is mock_store
+
+        mock_to_thread.assert_awaited_once()
+        called_fn, called_path = mock_to_thread.await_args.args
+        assert called_fn is ensure_sqlite_parent_dir
+        assert called_path == db_config.checkpointer_sqlite_path
+        mock_store_cls.from_conn_string.assert_called_once_with(db_config.checkpointer_sqlite_path)
+        mock_store.setup.assert_awaited_once()
+
+    def test_sync_store_context_uses_database_config(self):
+        """The one-shot sync Store factory must follow unified database config."""
+        from deerflow.runtime.store.provider import store_context
+
+        app_config = SimpleNamespace(
+            checkpointer=None,
+            database=DatabaseConfig(backend="postgres", postgres_url="postgresql://localhost/db"),
+        )
+        expected_store = object()
+        factory = MagicMock(return_value=nullcontext(expected_store))
+
+        with (
+            patch("deerflow.runtime.store.provider.get_app_config", return_value=app_config),
+            patch("deerflow.runtime.store.provider._sync_store_cm", factory),
+            store_context() as store,
+        ):
+            assert store is expected_store
+
+        resolved = factory.call_args.args[0]
+        assert resolved.type == "postgres"
+        assert resolved.connection_string == "postgresql://localhost/db"
+
+    def test_sync_store_singleton_uses_database_config(self):
+        """The cached sync Store factory must resolve database config before locking."""
+        app_config = SimpleNamespace(
+            checkpointer=None,
+            database=DatabaseConfig(backend="postgres", postgres_url="postgresql://localhost/db"),
+        )
+        expected_store = object()
+        factory = MagicMock(return_value=nullcontext(expected_store))
+
+        with (
+            patch("deerflow.runtime.store.provider.ensure_config_loaded"),
+            patch("deerflow.runtime.store.provider.get_app_config", return_value=app_config),
+            patch("deerflow.runtime.store.provider._sync_store_cm", factory),
+        ):
+            assert get_store() is expected_store
+
+        resolved = factory.call_args.args[0]
+        assert resolved.type == "postgres"
+        assert resolved.connection_string == "postgresql://localhost/db"
+
+    def test_legacy_checkpointer_config_takes_precedence_for_store(self):
+        """Backward-compatible checkpointer config must override database for Store."""
+        from deerflow.runtime.store.provider import store_context
+
+        app_config = SimpleNamespace(
+            checkpointer=CheckpointerConfig(type="memory"),
+            database=DatabaseConfig(backend="postgres", postgres_url="postgresql://localhost/db"),
+        )
+        expected_store = object()
+        factory = MagicMock(return_value=nullcontext(expected_store))
+
+        with (
+            patch("deerflow.runtime.store.provider.get_app_config", return_value=app_config),
+            patch("deerflow.runtime.store.provider._sync_store_cm", factory),
+            store_context() as store,
+        ):
+            assert store is expected_store
+
+        resolved = factory.call_args.args[0]
+        assert resolved.type == "memory"
+        assert resolved.connection_string is None
+
+    def test_explicit_memory_database_uses_in_memory_store(self):
+        """Explicit memory mode remains an intentional non-persistent Store."""
+        from langgraph.store.memory import InMemoryStore
+
+        from deerflow.runtime.store.provider import store_context
+
+        app_config = SimpleNamespace(
+            checkpointer=None,
+            database=DatabaseConfig(backend="memory"),
+        )
+        with patch("deerflow.runtime.store.provider.get_app_config", return_value=app_config):
+            with store_context() as store:
+                assert isinstance(store, InMemoryStore)
+
+
 # ---------------------------------------------------------------------------
 # app_config.py integration
 # ---------------------------------------------------------------------------

backend/tests/test_runtime_lifecycle_e2e.py

@@ -274,6 +274,15 @@ def isolated_app(isolated_deer_flow_home: Path, monkeypatch: pytest.MonkeyPatch)
     return create_app()
 
 
+def test_lifespan_uses_sqlite_store_from_database_config(isolated_app):
+    """Gateway startup must bind LangGraph Store to the unified database backend."""
+    from langgraph.store.sqlite.aio import AsyncSqliteStore
+    from starlette.testclient import TestClient
+
+    with TestClient(isolated_app):
+        assert isinstance(isolated_app.state.store, AsyncSqliteStore)
+
+
 @pytest.fixture
 def isolated_app_with_title(isolated_deer_flow_home: Path, monkeypatch: pytest.MonkeyPatch):
     config_path = isolated_deer_flow_home.parent / "config-title-enabled.yaml"

config.example.yaml

@@ -1299,12 +1299,12 @@ skill_evolution:
 # Checkpointer Configuration (DEPRECATED — use `database` instead)
 # ============================================================================
 # Legacy standalone checkpointer config. Kept for backward compatibility.
-# Prefer the unified `database` section below, which drives BOTH the
-# LangGraph checkpointer AND DeerFlow application data (runs, feedback,
-# events) from a single backend setting.
+# Prefer the unified `database` section below, which drives the LangGraph
+# checkpointer, LangGraph Store, and DeerFlow application data (runs,
+# feedback, events) from a single backend setting.
 #
 # If both `checkpointer` and `database` are present, `checkpointer`
-# takes precedence for LangGraph state persistence only.
+# takes precedence for the LangGraph checkpointer and Store only.
 #
 # checkpointer:
 #   type: sqlite
@@ -1317,8 +1317,8 @@ skill_evolution:
 # ============================================================================
 # Database
 # ============================================================================
-# Unified storage backend for LangGraph checkpointer and DeerFlow
-# application data (runs, threads metadata, feedback, etc.).
+# Unified storage backend for the LangGraph checkpointer, LangGraph Store,
+# and DeerFlow application data (runs, threads metadata, feedback, etc.).
 #
 # backend: memory  -- No persistence, data lost on restart
 # backend: sqlite  -- Single-node deployment, files in sqlite_dir
@@ -1329,7 +1329,7 @@ skill_evolution:
 #   sqlite_dir: .deer-flow/data
 #
 # SQLite mode uses a single deerflow.db file with WAL journal mode
-# for both checkpointer and application data.
+# for the checkpointer, Store, and application data.
 #
 # Postgres mode: put your connection URL in .env as DATABASE_URL,
 # then reference it here with $DATABASE_URL.
@@ -1354,7 +1354,8 @@ skill_evolution:
 #   (--all-packages propagates the extra into workspace members — see PR #2584)
 #
 # NOTE: When both `checkpointer` and `database` are configured,
-# `checkpointer` takes precedence for LangGraph state persistence.
+# `checkpointer` takes precedence for the LangGraph checkpointer and Store;
+# `database` still controls DeerFlow application data.
 # If you use `database`, you can remove the `checkpointer` section.
 # database:
 #   backend: sqlite