fix(tools): introduce Runtime type alias to eliminate Pydantic serialization warning (#2774)

* fix(tools): introduce Runtime type alias to eliminate Pydantic serialization warning

Add deerflow/tools/types.py with:

    Runtime = ToolRuntime[dict[str, Any], ThreadState]

Replace every runtime: ToolRuntime[ContextT, ThreadState] and
runtime: ToolRuntime[dict[str, Any], ThreadState] annotation in
sandbox/tools.py, present_file_tool.py, task_tool.py, view_image_tool.py,
and skill_manage_tool.py with the new Runtime alias.

The unbound ContextT TypeVar (default None) caused
PydanticSerializationUnexpectedValue warnings on every tool call because
LangChain's BaseTool._parse_input calls model_dump() on the auto-generated
args_schema while DeerFlow passes a dict as runtime context.
Binding the context to dict[str, Any] aligns Pydantic's serialization
expectations with reality and removes the noise from all run modes.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-authored-by: Cursor <cursoragent@cursor.com>

* fix(tools): extend Runtime alias to setup_agent and update_agent tools

Replace bare ToolRuntime annotations in setup_agent_tool.py and
update_agent_tool.py with the shared Runtime alias introduced in the
previous commit, and add both tools to the Pydantic serialization
warning regression test (13 cases total).

Co-authored-by: Cursor <cursoragent@cursor.com>

* test(tools): loosen Pydantic warning filter to avoid version-specific format

Replace the brittle "field_name='context'" substring check with a looser
"context" match so the assertion stays valid if Pydantic changes its
internal warning format across versions.

Co-authored-by: Cursor <cursoragent@cursor.com>

* test(tools): simplify warning filter and clean up docstring

Remove the "context" substring condition from the Pydantic warning
filter — asserting that no PydanticSerializationUnexpectedValue fires
at all is both simpler and more comprehensive, since the test payload
contains only the tool's own args plus runtime.

Also update the module docstring to remove the version-specific warning
format example that was inconsistent with the looser filter.

Co-authored-by: Cursor <cursoragent@cursor.com>

---------

Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-authored-by: Cursor <cursoragent@cursor.com>

backend/packages/harness/deerflow/sandbox/tools.py

@@ -3,10 +3,9 @@ import re
 import shlex
 from pathlib import Path
 
-from langchain.tools import ToolRuntime, tool
-from langgraph.typing import ContextT
+from langchain.tools import tool
 
-from deerflow.agents.thread_state import ThreadDataState, ThreadState
+from deerflow.agents.thread_state import ThreadDataState
 from deerflow.config import get_app_config
 from deerflow.config.paths import VIRTUAL_PATH_PREFIX
 from deerflow.sandbox.exceptions import (
@@ -19,6 +18,7 @@ from deerflow.sandbox.sandbox import Sandbox
 from deerflow.sandbox.sandbox_provider import get_sandbox_provider
 from deerflow.sandbox.search import GrepMatch
 from deerflow.sandbox.security import LOCAL_HOST_BASH_DISABLED_MESSAGE, is_host_bash_allowed
+from deerflow.tools.types import Runtime
 
 _ABSOLUTE_PATH_PATTERN = re.compile(r"(?<![:\w])(?<!:/)/(?:[^\s\"'`;&|<>()]+)")
 _FILE_URL_PATTERN = re.compile(r"\bfile://\S+", re.IGNORECASE)
@@ -419,7 +419,7 @@ def _join_path_preserving_style(base: str, relative: str) -> str:
     return f"{stripped_base}{separator}{normalized_relative}"
 
 
-def _sanitize_error(error: Exception, runtime: "ToolRuntime[ContextT, ThreadState] | None" = None) -> str:
+def _sanitize_error(error: Exception, runtime: Runtime | None = None) -> str:
     """Sanitize an error message to avoid leaking host filesystem paths.
 
     In local-sandbox mode, resolved host paths in the error string are masked
@@ -994,7 +994,7 @@ def _apply_cwd_prefix(command: str, thread_data: ThreadDataState | None) -> str:
     return command
 
 
-def get_thread_data(runtime: ToolRuntime[ContextT, ThreadState] | None) -> ThreadDataState | None:
+def get_thread_data(runtime: Runtime | None) -> ThreadDataState | None:
     """Extract thread_data from runtime state."""
     if runtime is None:
         return None
@@ -1003,7 +1003,7 @@ def get_thread_data(runtime: ToolRuntime[ContextT, ThreadState] | None) -> Threa
     return runtime.state.get("thread_data")
 
 
-def is_local_sandbox(runtime: ToolRuntime[ContextT, ThreadState] | None) -> bool:
+def is_local_sandbox(runtime: Runtime | None) -> bool:
     """Check if the current sandbox is a local sandbox.
 
     Path replacement is only needed for local sandbox since aio sandbox
@@ -1019,7 +1019,7 @@ def is_local_sandbox(runtime: ToolRuntime[ContextT, ThreadState] | None) -> bool
     return sandbox_state.get("sandbox_id") == "local"
 
 
-def sandbox_from_runtime(runtime: ToolRuntime[ContextT, ThreadState] | None = None) -> Sandbox:
+def sandbox_from_runtime(runtime: Runtime | None = None) -> Sandbox:
     """Extract sandbox instance from tool runtime.
 
     DEPRECATED: Use ensure_sandbox_initialized() for lazy initialization support.
@@ -1048,7 +1048,7 @@ def sandbox_from_runtime(runtime: ToolRuntime[ContextT, ThreadState] | None = No
     return sandbox
 
 
-def ensure_sandbox_initialized(runtime: ToolRuntime[ContextT, ThreadState] | None = None) -> Sandbox:
+def ensure_sandbox_initialized(runtime: Runtime | None = None) -> Sandbox:
     """Ensure sandbox is initialized, acquiring lazily if needed.
 
     On first call, acquires a sandbox from the provider and stores it in runtime state.
@@ -1107,7 +1107,7 @@ def ensure_sandbox_initialized(runtime: ToolRuntime[ContextT, ThreadState] | Non
     return sandbox
 
 
-def ensure_thread_directories_exist(runtime: ToolRuntime[ContextT, ThreadState] | None) -> None:
+def ensure_thread_directories_exist(runtime: Runtime | None) -> None:
     """Ensure thread data directories (workspace, uploads, outputs) exist.
 
     This function is called lazily when any sandbox tool is first used.
@@ -1221,7 +1221,7 @@ def _truncate_ls_output(output: str, max_chars: int) -> str:
 
 
 @tool("bash", parse_docstring=True)
-def bash_tool(runtime: ToolRuntime[ContextT, ThreadState], description: str, command: str) -> str:
+def bash_tool(runtime: Runtime, description: str, command: str) -> str:
     """Execute a bash command in a Linux environment.
 
 
@@ -1270,7 +1270,7 @@ def bash_tool(runtime: ToolRuntime[ContextT, ThreadState], description: str, com
 
 
 @tool("ls", parse_docstring=True)
-def ls_tool(runtime: ToolRuntime[ContextT, ThreadState], description: str, path: str) -> str:
+def ls_tool(runtime: Runtime, description: str, path: str) -> str:
     """List the contents of a directory up to 2 levels deep in tree format.
 
     Args:
@@ -1318,7 +1318,7 @@ def ls_tool(runtime: ToolRuntime[ContextT, ThreadState], description: str, path:
 
 @tool("glob", parse_docstring=True)
 def glob_tool(
-    runtime: ToolRuntime[ContextT, ThreadState],
+    runtime: Runtime,
     description: str,
     pattern: str,
     path: str,
@@ -1368,7 +1368,7 @@ def glob_tool(
 
 @tool("grep", parse_docstring=True)
 def grep_tool(
-    runtime: ToolRuntime[ContextT, ThreadState],
+    runtime: Runtime,
     description: str,
     pattern: str,
     path: str,
@@ -1438,7 +1438,7 @@ def grep_tool(
 
 @tool("read_file", parse_docstring=True)
 def read_file_tool(
-    runtime: ToolRuntime[ContextT, ThreadState],
+    runtime: Runtime,
     description: str,
     path: str,
     start_line: int | None = None,
@@ -1493,7 +1493,7 @@ def read_file_tool(
 
 @tool("write_file", parse_docstring=True)
 def write_file_tool(
-    runtime: ToolRuntime[ContextT, ThreadState],
+    runtime: Runtime,
     description: str,
     path: str,
     content: str,
@@ -1533,7 +1533,7 @@ def write_file_tool(
 
 @tool("str_replace", parse_docstring=True)
 def str_replace_tool(
-    runtime: ToolRuntime[ContextT, ThreadState],
+    runtime: Runtime,
     description: str,
     path: str,
     old_str: str,

backend/packages/harness/deerflow/tools/builtins/present_file_tool.py

@@ -1,20 +1,19 @@
 from pathlib import Path
 from typing import Annotated
 
-from langchain.tools import InjectedToolCallId, ToolRuntime, tool
+from langchain.tools import InjectedToolCallId, tool
 from langchain_core.messages import ToolMessage
 from langgraph.config import get_config
 from langgraph.types import Command
-from langgraph.typing import ContextT
 
-from deerflow.agents.thread_state import ThreadState
 from deerflow.config.paths import VIRTUAL_PATH_PREFIX, get_paths
 from deerflow.runtime.user_context import get_effective_user_id
+from deerflow.tools.types import Runtime
 
 OUTPUTS_VIRTUAL_PREFIX = f"{VIRTUAL_PATH_PREFIX}/outputs"
 
 
-def _get_thread_id(runtime: ToolRuntime[ContextT, ThreadState]) -> str | None:
+def _get_thread_id(runtime: Runtime) -> str | None:
     """Resolve the current thread id from runtime context or RunnableConfig."""
     thread_id = runtime.context.get("thread_id") if runtime.context else None
     if thread_id:
@@ -32,7 +31,7 @@ def _get_thread_id(runtime: ToolRuntime[ContextT, ThreadState]) -> str | None:
 
 
 def _normalize_presented_filepath(
-    runtime: ToolRuntime[ContextT, ThreadState],
+    runtime: Runtime,
     filepath: str,
 ) -> str:
     """Normalize a presented file path to the `/mnt/user-data/outputs/*` contract.
@@ -83,7 +82,7 @@ def _normalize_presented_filepath(
 
 @tool("present_files", parse_docstring=True)
 def present_file_tool(
-    runtime: ToolRuntime[ContextT, ThreadState],
+    runtime: Runtime,
     filepaths: list[str],
     tool_call_id: Annotated[str, InjectedToolCallId],
 ) -> Command:

backend/packages/harness/deerflow/tools/builtins/setup_agent_tool.py

@@ -3,12 +3,12 @@ import logging
 import yaml
 from langchain_core.messages import ToolMessage
 from langchain_core.tools import tool
-from langgraph.prebuilt import ToolRuntime
 from langgraph.types import Command
 
 from deerflow.config.agents_config import validate_agent_name
 from deerflow.config.paths import get_paths
 from deerflow.runtime.user_context import get_effective_user_id
+from deerflow.tools.types import Runtime
 
 logger = logging.getLogger(__name__)
 
@@ -17,7 +17,7 @@ logger = logging.getLogger(__name__)
 def setup_agent(
     soul: str,
     description: str,
-    runtime: ToolRuntime,
+    runtime: Runtime,
     skills: list[str] | None = None,
 ) -> Command:
     """Setup the custom DeerFlow agent.

backend/packages/harness/deerflow/tools/builtins/task_tool.py

@@ -6,11 +6,9 @@ import uuid
 from dataclasses import replace
 from typing import TYPE_CHECKING, Annotated, Any, cast
 
-from langchain.tools import InjectedToolCallId, ToolRuntime, tool
+from langchain.tools import InjectedToolCallId, tool
 from langgraph.config import get_stream_writer
-from langgraph.typing import ContextT
 
-from deerflow.agents.thread_state import ThreadState
 from deerflow.config import get_app_config
 from deerflow.sandbox.security import LOCAL_BASH_SUBAGENT_DISABLED_MESSAGE, is_host_bash_allowed
 from deerflow.subagents import SubagentExecutor, get_available_subagent_names, get_subagent_config
@@ -21,6 +19,7 @@ from deerflow.subagents.executor import (
     get_background_task_result,
     request_cancel_background_task,
 )
+from deerflow.tools.types import Runtime
 
 if TYPE_CHECKING:
     from deerflow.config.app_config import AppConfig
@@ -50,7 +49,7 @@ def _merge_skill_allowlists(parent: list[str] | None, child: list[str] | None) -
 
 @tool("task", parse_docstring=True)
 async def task_tool(
-    runtime: ToolRuntime[ContextT, ThreadState],
+    runtime: Runtime,
     description: str,
     prompt: str,
     subagent_type: str,

backend/packages/harness/deerflow/tools/builtins/update_agent_tool.py

@@ -22,13 +22,13 @@ from typing import Any
 import yaml
 from langchain_core.messages import ToolMessage
 from langchain_core.tools import tool
-from langgraph.prebuilt import ToolRuntime
 from langgraph.types import Command
 
 from deerflow.config.agents_config import load_agent_config, validate_agent_name
 from deerflow.config.app_config import get_app_config
 from deerflow.config.paths import get_paths
 from deerflow.runtime.user_context import get_effective_user_id
+from deerflow.tools.types import Runtime
 
 logger = logging.getLogger(__name__)
 
@@ -69,7 +69,7 @@ def _cleanup_temps(temps: list[Path]) -> None:
 
 @tool
 def update_agent(
-    runtime: ToolRuntime,
+    runtime: Runtime,
     soul: str | None = None,
     description: str | None = None,
     skills: list[str] | None = None,

backend/packages/harness/deerflow/tools/builtins/view_image_tool.py

@@ -3,13 +3,13 @@ import mimetypes
 from pathlib import Path
 from typing import Annotated
 
-from langchain.tools import InjectedToolCallId, ToolRuntime, tool
+from langchain.tools import InjectedToolCallId, tool
 from langchain_core.messages import ToolMessage
 from langgraph.types import Command
-from langgraph.typing import ContextT
 
-from deerflow.agents.thread_state import ThreadDataState, ThreadState
+from deerflow.agents.thread_state import ThreadDataState
 from deerflow.config.paths import VIRTUAL_PATH_PREFIX
+from deerflow.tools.types import Runtime
 
 _ALLOWED_IMAGE_VIRTUAL_ROOTS = (
     f"{VIRTUAL_PATH_PREFIX}/workspace",
@@ -48,7 +48,7 @@ def _sanitize_image_error(error: Exception, thread_data: ThreadDataState | None)
 
 @tool("view_image", parse_docstring=True)
 def view_image_tool(
-    runtime: ToolRuntime[ContextT, ThreadState],
+    runtime: Runtime,
     image_path: str,
     tool_call_id: Annotated[str, InjectedToolCallId],
 ) -> Command:

backend/packages/harness/deerflow/tools/skill_manage_tool.py

@@ -7,16 +7,15 @@ import logging
 from typing import Any
 from weakref import WeakValueDictionary
 
-from langchain.tools import ToolRuntime, tool
-from langgraph.typing import ContextT
+from langchain.tools import tool
 
 from deerflow.agents.lead_agent.prompt import refresh_skills_system_prompt_cache_async
-from deerflow.agents.thread_state import ThreadState
 from deerflow.mcp.tools import _make_sync_tool_wrapper
 from deerflow.skills.security_scanner import scan_skill_content
 from deerflow.skills.storage import get_or_new_skill_storage
 from deerflow.skills.storage.skill_storage import SkillStorage
 from deerflow.skills.types import SKILL_MD_FILE
+from deerflow.tools.types import Runtime
 
 logger = logging.getLogger(__name__)
 
@@ -31,7 +30,7 @@ def _get_lock(name: str) -> asyncio.Lock:
     return lock
 
 
-def _get_thread_id(runtime: ToolRuntime[ContextT, ThreadState] | None) -> str | None:
+def _get_thread_id(runtime: Runtime | None) -> str | None:
     if runtime is None:
         return None
     if runtime.context and runtime.context.get("thread_id"):
@@ -65,7 +64,7 @@ async def _to_thread(func, /, *args, **kwargs):
 
 
 async def _skill_manage_impl(
-    runtime: ToolRuntime[ContextT, ThreadState],
+    runtime: Runtime,
     action: str,
     name: str,
     content: str | None = None,
@@ -204,7 +203,7 @@ async def _skill_manage_impl(
 
 @tool("skill_manage", parse_docstring=True)
 async def skill_manage_tool(
-    runtime: ToolRuntime[ContextT, ThreadState],
+    runtime: Runtime,
     action: str,
     name: str,
     content: str | None = None,

backend/packages/harness/deerflow/tools/types.py

@@ -0,0 +1,11 @@
+from typing import Any
+
+from langchain.tools import ToolRuntime
+
+from deerflow.agents.thread_state import ThreadState
+
+# Concrete runtime type used by all DeerFlow tools.
+# Using dict[str, Any] for the context parameter instead of the unbound ContextT
+# TypeVar prevents PydanticSerializationUnexpectedValue warnings when LangChain
+# calls model_dump() on a tool's auto-generated args_schema.
+Runtime = ToolRuntime[dict[str, Any], ThreadState]

backend/tests/test_tool_args_schema_no_pydantic_warning.py

@@ -0,0 +1,91 @@
+"""Regression test: tool args schemas must not emit Pydantic serialization warnings.
+
+DeerFlow tools annotate their runtime parameter as ``Runtime``
+(``deerflow.tools.types.Runtime`` = ``ToolRuntime[dict[str, Any], ThreadState]``)
+so the LangChain tool framework injects the runtime automatically.
+When the inner ``Runtime.context`` field is left as the unbound ``ContextT``
+TypeVar (default ``None``), Pydantic's ``model_dump()`` on the auto-generated
+args schema emits a ``PydanticSerializationUnexpectedValue`` warning on every
+tool call because the actual context DeerFlow installs is a dict. Using the
+``Runtime`` alias (which binds the context to ``dict[str, Any]``) keeps
+Pydantic's serialization expectations aligned with reality.
+"""
+
+from __future__ import annotations
+
+import warnings
+
+import pytest
+from langchain.tools import ToolRuntime
+
+from deerflow.sandbox.tools import (
+    bash_tool,
+    glob_tool,
+    grep_tool,
+    ls_tool,
+    read_file_tool,
+    str_replace_tool,
+    write_file_tool,
+)
+from deerflow.tools.builtins.present_file_tool import present_file_tool
+from deerflow.tools.builtins.setup_agent_tool import setup_agent
+from deerflow.tools.builtins.task_tool import task_tool
+from deerflow.tools.builtins.update_agent_tool import update_agent
+from deerflow.tools.builtins.view_image_tool import view_image_tool
+from deerflow.tools.skill_manage_tool import skill_manage_tool
+
+
+def _make_runtime(context: dict) -> ToolRuntime:
+    return ToolRuntime(
+        state={"sandbox": {"sandbox_id": "local"}, "thread_data": {}},
+        context=context,
+        config={"configurable": {"thread_id": context.get("thread_id", "thread-1")}},
+        stream_writer=lambda _: None,
+        tools=[],
+        tool_call_id="call-1",
+        store=None,
+    )
+
+
+_TOOL_CASES = [
+    (bash_tool, {"description": "list", "command": "ls"}),
+    (ls_tool, {"description": "list", "path": "/tmp"}),
+    (glob_tool, {"description": "find", "pattern": "*.py", "path": "/tmp"}),
+    (grep_tool, {"description": "search", "pattern": "x", "path": "/tmp"}),
+    (read_file_tool, {"description": "read", "path": "/tmp/x"}),
+    (write_file_tool, {"description": "write", "path": "/tmp/x", "content": "hi"}),
+    (str_replace_tool, {"description": "replace", "path": "/tmp/x", "old_str": "a", "new_str": "b"}),
+    (present_file_tool, {"filepaths": ["/tmp/x"], "tool_call_id": "call-1"}),
+    (view_image_tool, {"image_path": "/tmp/img.png", "tool_call_id": "call-1"}),
+    (task_tool, {"description": "do", "prompt": "go", "subagent_type": "general-purpose", "tool_call_id": "call-1"}),
+    (skill_manage_tool, {"action": "list", "name": "demo"}),
+    (setup_agent, {"soul": "s", "description": "d"}),
+    (update_agent, {}),
+]
+
+
+@pytest.mark.parametrize(
+    ("tool_obj", "extra_args"),
+    _TOOL_CASES,
+    ids=[case[0].name for case in _TOOL_CASES],
+)
+def test_tool_args_schema_does_not_emit_pydantic_context_warning(tool_obj, extra_args) -> None:
+    """``model_dump()`` of the auto-generated args_schema must not warn about ``context``.
+
+    The model_dump path is hit by LangChain's ``BaseTool._parse_input`` on every tool
+    invocation (see langchain_core/tools/base.py:712), so any warning here would fire
+    once per tool call and pollute production logs.
+    """
+    schema = tool_obj.args_schema
+    assert schema is not None, f"{tool_obj.name} has no args_schema"
+
+    runtime_obj = _make_runtime({"thread_id": "thread-1", "sandbox_id": "local"})
+    payload = {**extra_args, "runtime": runtime_obj}
+
+    with warnings.catch_warnings(record=True) as caught:
+        warnings.simplefilter("always")
+        validated = schema.model_validate(payload)
+        validated.model_dump()
+
+    pydantic_warnings = [w for w in caught if "PydanticSerializationUnexpectedValue" in str(w.message)]
+    assert not pydantic_warnings, f"{tool_obj.name} args_schema.model_dump() emitted Pydantic context serialization warnings: {[str(w.message) for w in pydantic_warnings]}"