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/utils/agent/ret.py

@@ -3,8 +3,8 @@ The output of a agent is very important.
 
 We think this part can be shared.
 """
-from abc import abstractclassmethod
 import re
+from abc import abstractclassmethod
 from typing import Any
 
 from rdagent.utils.agent.tpl import T

rdagent/utils/agent/tpl.py

@@ -4,13 +4,12 @@ Here are some infrastruture to build a agent
 The motivation of tempalte and AgentOutput Design
 """
 
-from typing import Any
-from jinja2 import Environment, StrictUndefined
-
+import inspect
 from pathlib import Path
+from typing import Any
 
 import yaml
-import inspect
+from jinja2 import Environment, StrictUndefined
 
 from rdagent.core.utils import SingletonBaseClass
 
@@ -21,9 +20,10 @@ PROJ_PATH = DIRNAME.parent.parent
 # class T(SingletonBaseClass): TODO: singleton does not support args now.
 class T:
     """Use the simplest way to (C)reate a Template and (r)ender it!!"""
+
     def __init__(self, uri: str):
         """
-        here are some uri usages 
+        here are some uri usages
             case 1) "a.b.c:x.y.z"
                 It will load DIRNAME/a/b/c.yaml as `yaml` and load yaml[x][y][z]
             case 2) ".c:x.y.z"
@@ -38,16 +38,16 @@ class T:
         caller_dir = Path(caller_module.__file__).parent
 
         # Parse the URI
-        path_part, yaml_path = uri.split(':')
-        yaml_keys = yaml_path.split('.')
+        path_part, yaml_path = uri.split(":")
+        yaml_keys = yaml_path.split(".")
 
-        if path_part.startswith('.'):
+        if path_part.startswith("."):
             yaml_file_path = caller_dir / f"{path_part[1:].replace('.', '/')}.yaml"
         else:
-            yaml_file_path = (PROJ_PATH / path_part.replace('.', '/')).with_suffix('.yaml')
+            yaml_file_path = (PROJ_PATH / path_part.replace(".", "/")).with_suffix(".yaml")
 
         # Load the YAML file
-        with open(yaml_file_path, 'r') as file:
+        with open(yaml_file_path, "r") as file:
             yaml_content = yaml.safe_load(file)
 
         # Traverse the YAML content to get the desired template