ruff

src/neuroagent/app/dependencies.py

@@ -28,13 +28,13 @@
 from neuroagent.multi_agents import BaseMultiAgent, SupervisorMultiAgent
 from neuroagent.tools import (
     ElectrophysFeatureTool,
+    GetMEModelTool,
     GetMorphoTool,
     GetTracesTool,
     KGMorphoFeatureTool,
     LiteratureSearchTool,
     MorphologyFeatureTool,
     ResolveBrainRegionTool,
-    GetMEModelTool,
 )
 from neuroagent.utils import RegionMeta, get_file_from_KG
 

src/neuroagent/tools/__init__.py

@@ -1,6 +1,7 @@
 """Tools folder."""
 
 from neuroagent.tools.electrophys_tool import ElectrophysFeatureTool, FeaturesOutput
+from neuroagent.tools.get_me_model_tool import GetMEModelTool
 from neuroagent.tools.get_morpho_tool import GetMorphoTool, KnowledgeGraphOutput
 from neuroagent.tools.kg_morpho_features_tool import (
     KGMorphoFeatureOutput,
@@ -19,7 +20,6 @@
     ResolveBrainRegionTool,
 )
 from neuroagent.tools.traces_tool import GetTracesTool, TracesOutput
-from neuroagent.tools.get_me_model_tool import GetMEModelTool
 
 __all__ = [
     "BRResolveOutput",

tests/agents/test_simple_agent.py

@@ -4,6 +4,7 @@
 from pathlib import Path
 
 import pytest
+
 from neuroagent.agents import AgentOutput, AgentStep, SimpleAgent
 
 

tests/agents/test_simple_chat_agent.py

@@ -6,6 +6,7 @@
 import pytest
 from langchain_core.messages import HumanMessage, ToolMessage
 from langgraph.checkpoint.sqlite.aio import AsyncSqliteSaver
+
 from neuroagent.agents import AgentOutput, AgentStep, SimpleChatAgent
 
 

tests/app/database/test_threads.py

@@ -1,13 +1,14 @@
 """Test of the thread router."""
 
 import pytest
+from sqlalchemy import MetaData, create_engine
+from sqlalchemy.orm import Session
+from sqlalchemy.sql.expression import Select
+
 from neuroagent.app.config import Settings
 from neuroagent.app.dependencies import get_language_model, get_settings
 from neuroagent.app.main import app
 from neuroagent.app.routers.database.schemas import GetThreadsOutput
-from sqlalchemy import MetaData, create_engine
-from sqlalchemy.orm import Session
-from sqlalchemy.sql.expression import Select
 
 
 def test_create_thread(patch_required_env, app_client, db_connection):

tests/app/database/test_tools.py

@@ -1,6 +1,7 @@
 """Test of the tool router."""
 
 import pytest
+
 from neuroagent.app.config import Settings
 from neuroagent.app.dependencies import get_language_model, get_settings
 from neuroagent.app.main import app

tests/app/test_config.py

@@ -1,9 +1,10 @@
 """Test config"""
 
 import pytest
-from neuroagent.app.config import Settings
 from pydantic import ValidationError
 
+from neuroagent.app.config import Settings
+
 
 def test_required(monkeypatch, patch_required_env):
     settings = Settings()

tests/app/test_dependencies.py

@@ -11,6 +11,7 @@
 from langchain_openai import ChatOpenAI
 from langgraph.checkpoint.postgres.aio import AsyncPostgresSaver
 from langgraph.checkpoint.sqlite.aio import AsyncSqliteSaver
+
 from neuroagent.agents import SimpleAgent, SimpleChatAgent
 from neuroagent.app.dependencies import (
     Settings,
@@ -24,21 +25,21 @@
     get_kg_morpho_feature_tool,
     get_language_model,
     get_literature_tool,
+    get_me_model_tool,
     get_morpho_tool,
     get_morphology_feature_tool,
     get_traces_tool,
     get_update_kg_hierarchy,
     get_user_id,
-    get_me_model_tool,
 )
 from neuroagent.tools import (
     ElectrophysFeatureTool,
+    GetMEModelTool,
     GetMorphoTool,
     GetTracesTool,
     KGMorphoFeatureTool,
     LiteratureSearchTool,
     MorphologyFeatureTool,
-    GetMEModelTool,
 )
 
 

tests/app/test_main.py

@@ -2,6 +2,7 @@
 from unittest.mock import patch
 
 from fastapi.testclient import TestClient
+
 from neuroagent.app.dependencies import get_settings
 from neuroagent.app.main import app
 

tests/app/test_middleware.py

@@ -5,6 +5,7 @@
 import pytest
 from fastapi.requests import Request
 from fastapi.responses import Response
+
 from neuroagent.app.config import Settings
 from neuroagent.app.middleware import strip_path_prefix
 

tests/conftest.py

@@ -8,13 +8,14 @@
 from httpx import AsyncClient
 from langchain_core.language_models.fake_chat_models import GenericFakeChatModel
 from langchain_core.messages import AIMessage
+from sqlalchemy import MetaData, create_engine
+from sqlalchemy.exc import OperationalError
+from sqlalchemy.orm import Session
+
 from neuroagent.app.config import Settings
 from neuroagent.app.dependencies import get_kg_token, get_settings
 from neuroagent.app.main import app
 from neuroagent.tools import GetMorphoTool
-from sqlalchemy import MetaData, create_engine
-from sqlalchemy.exc import OperationalError
-from sqlalchemy.orm import Session
 
 
 @pytest.fixture(name="app_client")

tests/test_cell_types.py

@@ -3,6 +3,7 @@
 from pathlib import Path
 
 import pytest
+
 from neuroagent.cell_types import CellTypesMeta, get_celltypes_descendants
 
 CELL_TYPES_FILE = Path(__file__).parent / "data" / "kg_cell_types_hierarchy_test.json"

tests/test_resolving.py

@@ -1,5 +1,6 @@
 import pytest
 from httpx import AsyncClient
+
 from neuroagent.resolving import (
     es_resolve,
     escape_punctuation,

tests/test_utils.py

@@ -5,6 +5,7 @@
 
 import pytest
 from httpx import AsyncClient
+
 from neuroagent.schemas import KGMetadata
 from neuroagent.utils import (
     RegionMeta,

tests/tools/test_basic_tool.py

@@ -4,9 +4,10 @@
 from langchain_core.messages import AIMessage, HumanMessage
 from langchain_core.tools import ToolException
 from langgraph.prebuilt import create_react_agent
-from neuroagent.tools.base_tool import BasicTool
 from pydantic import BaseModel
 
+from neuroagent.tools.base_tool import BasicTool
+
 
 class input_for_test(BaseModel):
     test_str: str

tests/tools/test_electrophys_tool.py

@@ -6,6 +6,7 @@
 import httpx
 import pytest
 from langchain_core.tools import ToolException
+
 from neuroagent.tools import ElectrophysFeatureTool
 from neuroagent.tools.electrophys_tool import (
     CALCULATED_FEATURES,

tests/tools/test_get_me_model_tool.py

@@ -6,6 +6,7 @@
 import httpx
 import pytest
 from langchain_core.tools import ToolException
+
 from neuroagent.tools.get_me_model_tool import GetMEModelTool, MEModelOutput
 
 

tests/tools/test_get_morpho_tool.py

@@ -6,6 +6,7 @@
 import httpx
 import pytest
 from langchain_core.tools import ToolException
+
 from neuroagent.tools import GetMorphoTool
 from neuroagent.tools.get_morpho_tool import KnowledgeGraphOutput
 

tests/tools/test_kg_morpho_features_tool.py

@@ -6,6 +6,7 @@
 import httpx
 import pytest
 from langchain_core.tools import ToolException
+
 from neuroagent.tools import KGMorphoFeatureTool
 from neuroagent.tools.kg_morpho_features_tool import (
     FeatRangeInput,

tests/tools/test_literature_search_tool.py

@@ -4,6 +4,7 @@
 
 import httpx
 import pytest
+
 from neuroagent.tools import LiteratureSearchTool
 from neuroagent.tools.literature_search_tool import ParagraphMetadata
 

tests/tools/test_morphology_features_tool.py

@@ -6,6 +6,7 @@
 import httpx
 import pytest
 from langchain_core.tools import ToolException
+
 from neuroagent.tools import MorphologyFeatureTool
 from neuroagent.tools.morphology_features_tool import MorphologyFeatureOutput
 

tests/tools/test_resolve_br_tool.py

@@ -2,6 +2,7 @@
 
 import pytest
 from httpx import AsyncClient
+
 from neuroagent.tools import ResolveBrainRegionTool
 from neuroagent.tools.resolve_brain_region_tool import (
     BRResolveOutput,

tests/tools/test_traces_tool.py

@@ -6,6 +6,7 @@
 import httpx
 import pytest
 from langchain_core.tools import ToolException
+
 from neuroagent.tools import GetTracesTool
 from neuroagent.tools.traces_tool import TracesOutput