From 8d58c2ae084509e93116322993ec239c13dc0996 Mon Sep 17 00:00:00 2001
From: Mustafa Kerem Kurban <kurban@bb-g306hl04xd.epfl.ch>
Date: Tue, 24 Sep 2024 13:57:21 +0200
Subject: [PATCH] ruff

---
 src/neuroagent/app/dependencies.py           | 2 +-
 src/neuroagent/tools/__init__.py             | 2 +-
 tests/agents/test_simple_agent.py            | 1 +
 tests/agents/test_simple_chat_agent.py       | 1 +
 tests/app/database/test_threads.py           | 7 ++++---
 tests/app/database/test_tools.py             | 1 +
 tests/app/test_config.py                     | 3 ++-
 tests/app/test_dependencies.py               | 5 +++--
 tests/app/test_main.py                       | 1 +
 tests/app/test_middleware.py                 | 1 +
 tests/conftest.py                            | 7 ++++---
 tests/test_cell_types.py                     | 1 +
 tests/test_resolving.py                      | 1 +
 tests/test_utils.py                          | 1 +
 tests/tools/test_basic_tool.py               | 3 ++-
 tests/tools/test_electrophys_tool.py         | 1 +
 tests/tools/test_get_me_model_tool.py        | 1 +
 tests/tools/test_get_morpho_tool.py          | 1 +
 tests/tools/test_kg_morpho_features_tool.py  | 1 +
 tests/tools/test_literature_search_tool.py   | 1 +
 tests/tools/test_morphology_features_tool.py | 1 +
 tests/tools/test_resolve_br_tool.py          | 1 +
 tests/tools/test_traces_tool.py              | 1 +
 23 files changed, 33 insertions(+), 12 deletions(-)

diff --git a/src/neuroagent/app/dependencies.py b/src/neuroagent/app/dependencies.py
index fcdec92..dfcd9f2 100644
--- a/src/neuroagent/app/dependencies.py
+++ b/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
 
diff --git a/src/neuroagent/tools/__init__.py b/src/neuroagent/tools/__init__.py
index 56779e9..af6761e 100644
--- a/src/neuroagent/tools/__init__.py
+++ b/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",
diff --git a/tests/agents/test_simple_agent.py b/tests/agents/test_simple_agent.py
index a31cf91..0f0ca1d 100644
--- a/tests/agents/test_simple_agent.py
+++ b/tests/agents/test_simple_agent.py
@@ -4,6 +4,7 @@
 from pathlib import Path
 
 import pytest
+
 from neuroagent.agents import AgentOutput, AgentStep, SimpleAgent
 
 
diff --git a/tests/agents/test_simple_chat_agent.py b/tests/agents/test_simple_chat_agent.py
index 6ec5474..e580574 100644
--- a/tests/agents/test_simple_chat_agent.py
+++ b/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
 
 
diff --git a/tests/app/database/test_threads.py b/tests/app/database/test_threads.py
index 7807826..dfc3313 100644
--- a/tests/app/database/test_threads.py
+++ b/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):
diff --git a/tests/app/database/test_tools.py b/tests/app/database/test_tools.py
index a5f55e0..03f2cf0 100644
--- a/tests/app/database/test_tools.py
+++ b/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
diff --git a/tests/app/test_config.py b/tests/app/test_config.py
index 459d457..38191f8 100644
--- a/tests/app/test_config.py
+++ b/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()
diff --git a/tests/app/test_dependencies.py b/tests/app/test_dependencies.py
index 7b3ad21..cde38e3 100644
--- a/tests/app/test_dependencies.py
+++ b/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,
 )
 
 
diff --git a/tests/app/test_main.py b/tests/app/test_main.py
index 79fe9a8..3827ad8 100644
--- a/tests/app/test_main.py
+++ b/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
 
diff --git a/tests/app/test_middleware.py b/tests/app/test_middleware.py
index 2707d4d..5a9bdcf 100644
--- a/tests/app/test_middleware.py
+++ b/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
 
diff --git a/tests/conftest.py b/tests/conftest.py
index d4c5f6d..c49e3a9 100644
--- a/tests/conftest.py
+++ b/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")
diff --git a/tests/test_cell_types.py b/tests/test_cell_types.py
index 0596534..930ec71 100644
--- a/tests/test_cell_types.py
+++ b/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"
diff --git a/tests/test_resolving.py b/tests/test_resolving.py
index eeafbad..2e794ce 100644
--- a/tests/test_resolving.py
+++ b/tests/test_resolving.py
@@ -1,5 +1,6 @@
 import pytest
 from httpx import AsyncClient
+
 from neuroagent.resolving import (
     es_resolve,
     escape_punctuation,
diff --git a/tests/test_utils.py b/tests/test_utils.py
index 742388b..7f30bc3 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -5,6 +5,7 @@
 
 import pytest
 from httpx import AsyncClient
+
 from neuroagent.schemas import KGMetadata
 from neuroagent.utils import (
     RegionMeta,
diff --git a/tests/tools/test_basic_tool.py b/tests/tools/test_basic_tool.py
index fb9ab17..c29bc6c 100644
--- a/tests/tools/test_basic_tool.py
+++ b/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
diff --git a/tests/tools/test_electrophys_tool.py b/tests/tools/test_electrophys_tool.py
index e7729fc..59e8763 100644
--- a/tests/tools/test_electrophys_tool.py
+++ b/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,
diff --git a/tests/tools/test_get_me_model_tool.py b/tests/tools/test_get_me_model_tool.py
index 0627d5f..2366b59 100644
--- a/tests/tools/test_get_me_model_tool.py
+++ b/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
 
 
diff --git a/tests/tools/test_get_morpho_tool.py b/tests/tools/test_get_morpho_tool.py
index d3ef4ab..87fdcbb 100644
--- a/tests/tools/test_get_morpho_tool.py
+++ b/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
 
diff --git a/tests/tools/test_kg_morpho_features_tool.py b/tests/tools/test_kg_morpho_features_tool.py
index 2f5473c..b346e26 100644
--- a/tests/tools/test_kg_morpho_features_tool.py
+++ b/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,
diff --git a/tests/tools/test_literature_search_tool.py b/tests/tools/test_literature_search_tool.py
index 0f58728..93adf4f 100644
--- a/tests/tools/test_literature_search_tool.py
+++ b/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
 
diff --git a/tests/tools/test_morphology_features_tool.py b/tests/tools/test_morphology_features_tool.py
index 22943e6..92a311f 100644
--- a/tests/tools/test_morphology_features_tool.py
+++ b/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
 
diff --git a/tests/tools/test_resolve_br_tool.py b/tests/tools/test_resolve_br_tool.py
index 697a6ef..31f893d 100644
--- a/tests/tools/test_resolve_br_tool.py
+++ b/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,
diff --git a/tests/tools/test_traces_tool.py b/tests/tools/test_traces_tool.py
index 0bae056..ad26bf4 100644
--- a/tests/tools/test_traces_tool.py
+++ b/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