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/components/workflow/conf.py

@@ -1,5 +1,6 @@
 from pydantic_settings import BaseSettings
 
+
 class BasePropSetting(BaseSettings):
     """
     The common part of the config for RD Loop to propose and developement
@@ -11,6 +12,7 @@ class BasePropSetting(BaseSettings):
             env_prefix = "DM_MODEL_"  # Use MODEL_CODER_ as prefix for environment variables
             protected_namespaces = ()  # Add 'model_' to the protected namespaces
     """
+
     scen: str = ""
     hypothesis_gen: str = ""
     hypothesis2experiment: str = ""

rdagent/components/workflow/rd_loop.py

@@ -4,6 +4,7 @@ It is from `rdagent/app/qlib_rd_loop/model.py` and try to replace `rdagent/app/q
 """
 
 from typing import Any
+
 from rdagent.components.workflow.conf import BasePropSetting
 from rdagent.core.developer import Developer
 from rdagent.core.proposal import (
@@ -15,11 +16,10 @@ from rdagent.core.proposal import (
 from rdagent.core.scenario import Scenario
 from rdagent.core.utils import import_class
 from rdagent.log import rdagent_logger as logger
+from rdagent.utils.workflow import LoopBase, LoopMeta
 
-from rdagent.utils.workflow import LoopMeta, LoopBase
 
 class RDLoop(LoopBase, metaclass=LoopMeta):
-
     def __init__(self, PROP_SETTING: BasePropSetting):
         scen: Scenario = import_class(PROP_SETTING.scen)()
 
@@ -62,4 +62,4 @@ class RDLoop(LoopBase, metaclass=LoopMeta):
         feedback = self.summarizer.generate_feedback(prev_out["running"], prev_out["propose"], self.trace)
         with logger.tag("ef"):  # evaluate and feedback
             logger.log_object(feedback, tag="feedback")
-        self.trace.hist.append((prev_out["propose"],prev_out["running"] , feedback))
+        self.trace.hist.append((prev_out["propose"], prev_out["running"], feedback))