CI checks that can be automatically repaired (#119)

* fix isort & black & toml-sort & sphinx error

* fix ci error

* fix ci error

* add comments

* Update Makefile

* change sphinx build command

* add auto-lint

* add black args

* format with black

* Auto Linting document

* fix ci error

---------

Co-authored-by: you-n-g <you-n-g@users.noreply.github.com>
Co-authored-by: Young <afe.young@gmail.com>

rdagent/log/base.py

@@ -2,19 +2,22 @@ from __future__ import annotations
 
 from abc import abstractmethod
 from collections.abc import Generator
+from dataclasses import dataclass
 from datetime import datetime
 from pathlib import Path
-from typing import Literal, Optional, Union, Literal
-from dataclasses import dataclass
+from typing import Literal, Optional, Union
 
 
 @dataclass
 class Message:
     """The info unit of the storage"""
+
     tag: str  # namespace like like a.b.c
     level: Literal["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]  # The level of the logging
     timestamp: datetime  # The time when the message is generated
-    caller: Optional[str] # The caller of the logging like `rdagent.oai.llm_utils:_create_chat_completion_inner_function:55`(file:func:line)
+    caller: Optional[
+        str
+    ]  # The caller of the logging like `rdagent.oai.llm_utils:_create_chat_completion_inner_function:55`(file:func:line)
     pid_trace: Optional[str]  # The process id trace;  A-B-C represents A create B, B create C
     content: object  # The content
 
@@ -39,7 +42,8 @@ class Storage:
     @abstractmethod
     def log(
         self,
-        obj: object, name: str = "",
+        obj: object,
+        name: str = "",
         save_type: Literal["json", "text", "pkl"] = "text",
         timestamp: datetime | None = None,
         **kwargs: dict,