Refactor iteration 2

.env.example

@@ -5,7 +5,7 @@ NEUROAGENT_GENERATIVE__OPENAI__TOKEN=
 
 # Important but not required
 NEUROAGENT_AGENT__MODEL=
-NEUROAGENT_AGENT__CHAT=
+
 NEUROAGENT_KNOWLEDGE_GRAPH__USE_TOKEN=
 NEUROAGENT_KNOWLEDGE_GRAPH__TOKEN=
 NEUROAGENT_KNOWLEDGE_GRAPH__DOWNLOAD_HIERARCHY=
@@ -27,12 +27,9 @@ NEUROAGENT_TOOLS__TRACE__SEARCH_SIZE=
 
 NEUROAGENT_TOOLS__KG_MORPHO__SEARCH_SIZE=
 
-NEUROAGENT_GENERATIVE__LLM_TYPE= # can only be openai for now
-NEUROAGENT_GENERATIVE__OPENAI__MODEL=
-NEUROAGENT_GENERATIVE__OPENAI__TEMPERATURE=
-NEUROAGENT_GENERATIVE__OPENAI__MAX_TOKENS=
-
-NEUROAGENT_COHERE__TOKEN=
+NEUROAGENT_OPENAI__MODEL=
+NEUROAGENT_OPENAI__TEMPERATURE=
+NEUROAGENT_OPENAI__MAX_TOKENS=
 
 NEUROAGENT_LOGGING__LEVEL=
 NEUROAGENT_LOGGING__EXTERNAL_PACKAGES=

CHANGELOG.md

@@ -12,3 +12,4 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 - Migration to pydantic V2.
+- Deleted some legacy code.

src/neuroagent/agents/base_agent.py

@@ -4,61 +4,9 @@
 from typing import Any, AsyncIterator
 
 from langchain.chat_models.base import BaseChatModel
-from langchain_core.messages import (
-    AIMessage,
-    ChatMessage,
-    FunctionMessage,
-    HumanMessage,
-    SystemMessage,
-    ToolMessage,
-)
-from langchain_core.prompts import (
-    ChatPromptTemplate,
-    HumanMessagePromptTemplate,
-    MessagesPlaceholder,
-    PromptTemplate,
-    SystemMessagePromptTemplate,
-)
 from langchain_core.tools import BaseTool
 from pydantic import BaseModel, ConfigDict
 
-BASE_PROMPT = ChatPromptTemplate(
-    input_variables=["agent_scratchpad", "input"],
-    input_types={
-        "chat_history": list[
-            AIMessage
-            | HumanMessage
-            | ChatMessage
-            | SystemMessage
-            | FunctionMessage
-            | ToolMessage
-        ],
-        "agent_scratchpad": list[
-            AIMessage
-            | HumanMessage
-            | ChatMessage
-            | SystemMessage
-            | FunctionMessage
-            | ToolMessage
-        ],
-    },
-    messages=[
-        SystemMessagePromptTemplate(
-            prompt=PromptTemplate(
-                input_variables=[],
-                template="""You are a helpful assistant helping scientists with neuro-scientific questions.
-                You must always specify in your answers from which brain regions the information is extracted.
-                Do no blindly repeat the brain region requested by the user, use the output of the tools instead.""",
-            )
-        ),
-        MessagesPlaceholder(variable_name="chat_history", optional=True),
-        HumanMessagePromptTemplate(
-            prompt=PromptTemplate(input_variables=["input"], template="{input}")
-        ),
-        MessagesPlaceholder(variable_name="agent_scratchpad"),
-    ],
-)
-
 
 class AgentStep(BaseModel):
     """Class for agent decision steps."""
@@ -72,7 +20,6 @@ class AgentOutput(BaseModel):
 
     response: str
     steps: list[AgentStep]
-    plan: str | None = None
 
 
 class BaseAgent(BaseModel, ABC):

src/neuroagent/app/config.py

@@ -13,8 +13,7 @@
 class SettingsAgent(BaseModel):
     """Agent setting."""
 
-    model: str = "simple"
-    chat: str = "simple"
+    model: Literal["simple", "multi"] = "simple"
 
     model_config = ConfigDict(frozen=True)
 
@@ -84,9 +83,9 @@ class SettingsLiterature(BaseModel):
     """Literature search API settings."""
 
     url: str
-    retriever_k: int = 700
+    retriever_k: int = 500
     use_reranker: bool = True
-    reranker_k: int = 5
+    reranker_k: int = 8
 
     model_config = ConfigDict(frozen=True)
 
@@ -173,23 +172,6 @@ class SettingsOpenAI(BaseModel):
     model_config = ConfigDict(frozen=True)
 
 
-class SettingsGenerative(BaseModel):
-    """Generative QA settings."""
-
-    llm_type: Literal["fake", "openai"] = "openai"
-    openai: SettingsOpenAI = SettingsOpenAI()
-
-    model_config = ConfigDict(frozen=True)
-
-
-class SettingsCohere(BaseModel):
-    """Settings cohere reranker."""
-
-    token: Optional[SecretStr] = None
-
-    model_config = ConfigDict(frozen=True)
-
-
 class SettingsLogging(BaseModel):
     """Metadata settings."""
 
@@ -219,8 +201,7 @@ class Settings(BaseSettings):
     knowledge_graph: SettingsKnowledgeGraph
     agent: SettingsAgent = SettingsAgent()  # has no required
     db: SettingsDB = SettingsDB()  # has no required
-    generative: SettingsGenerative = SettingsGenerative()  # has no required
-    cohere: SettingsCohere = SettingsCohere()  # has no required
+    openai: SettingsOpenAI = SettingsOpenAI()  # has no required
     logging: SettingsLogging = SettingsLogging()  # has no required
     keycloak: SettingsKeycloak = SettingsKeycloak()  # has no required
     misc: SettingsMisc = SettingsMisc()  # has no required
@@ -240,10 +221,6 @@ def check_consistency(self) -> "Settings":
         model validator is run during instantiation.
 
         """
-        # generative
-        if self.generative.llm_type == "openai":
-            if self.generative.openai.token is None:
-                raise ValueError("OpenAI token not provided")
         if not self.keycloak.password and not self.keycloak.validate_token:
             if not self.knowledge_graph.use_token:
                 raise ValueError("if no password is provided, please use token auth.")

src/neuroagent/app/dependencies.py

@@ -308,12 +308,12 @@ def get_language_model(
     settings: Annotated[Settings, Depends(get_settings)],
 ) -> ChatOpenAI:
     """Get the language model."""
-    logger.info(f"OpenAI selected. Loading model {settings.generative.openai.model}.")
+    logger.info(f"OpenAI selected. Loading model {settings.openai.model}.")
     return ChatOpenAI(
-        model_name=settings.generative.openai.model,
-        temperature=settings.generative.openai.temperature,
-        openai_api_key=settings.generative.openai.token.get_secret_value(),  # type: ignore
-        max_tokens=settings.generative.openai.max_tokens,
+        model_name=settings.openai.model,
+        temperature=settings.openai.temperature,
+        openai_api_key=settings.openai.token.get_secret_value(),  # type: ignore
+        max_tokens=settings.openai.max_tokens,
         seed=78,
         streaming=True,
     )
@@ -369,43 +369,10 @@ def get_agent(
         ElectrophysFeatureTool, Depends(get_electrophys_feature_tool)
     ],
     traces_tool: Annotated[GetTracesTool, Depends(get_traces_tool)],
-) -> BaseAgent | BaseMultiAgent:
-    """Get the generative question answering service."""
-    tools = [
-        literature_tool,
-        br_resolver_tool,
-        morpho_tool,
-        morphology_feature_tool,
-        kg_morpho_feature_tool,
-        electrophys_feature_tool,
-        traces_tool,
-    ]
-    logger.info("Load simple agent")
-    return SimpleAgent(llm=llm, tools=tools)  # type: ignore
-
-
-def get_chat_agent(
-    llm: Annotated[ChatOpenAI, Depends(get_language_model)],
-    memory: Annotated[BaseCheckpointSaver, Depends(get_agent_memory)],
-    literature_tool: Annotated[LiteratureSearchTool, Depends(get_literature_tool)],
-    br_resolver_tool: Annotated[
-        ResolveBrainRegionTool, Depends(get_brain_region_resolver_tool)
-    ],
-    morpho_tool: Annotated[GetMorphoTool, Depends(get_morpho_tool)],
-    morphology_feature_tool: Annotated[
-        MorphologyFeatureTool, Depends(get_morphology_feature_tool)
-    ],
-    kg_morpho_feature_tool: Annotated[
-        KGMorphoFeatureTool, Depends(get_kg_morpho_feature_tool)
-    ],
-    electrophys_feature_tool: Annotated[
-        ElectrophysFeatureTool, Depends(get_electrophys_feature_tool)
-    ],
-    traces_tool: Annotated[GetTracesTool, Depends(get_traces_tool)],
     settings: Annotated[Settings, Depends(get_settings)],
-) -> BaseAgent:
+) -> BaseAgent | BaseMultiAgent:
     """Get the generative question answering service."""
-    if settings.agent.chat == "multi":
+    if settings.agent.model == "multi":
         logger.info("Load multi-agent chat")
         tools_list = [
             ("literature", [literature_tool]),
@@ -422,7 +389,6 @@ def get_chat_agent(
         ]
         return SupervisorMultiAgent(llm=llm, agents=tools_list)  # type: ignore
     else:
-        logger.info("Load simple chat")
         tools = [
             literature_tool,
             br_resolver_tool,
@@ -432,7 +398,41 @@ def get_chat_agent(
             electrophys_feature_tool,
             traces_tool,
         ]
-        return SimpleChatAgent(llm=llm, tools=tools, memory=memory)  # type: ignore
+        logger.info("Load simple agent")
+        return SimpleAgent(llm=llm, tools=tools)  # type: ignore
+
+
+def get_chat_agent(
+    llm: Annotated[ChatOpenAI, Depends(get_language_model)],
+    memory: Annotated[BaseCheckpointSaver, Depends(get_agent_memory)],
+    literature_tool: Annotated[LiteratureSearchTool, Depends(get_literature_tool)],
+    br_resolver_tool: Annotated[
+        ResolveBrainRegionTool, Depends(get_brain_region_resolver_tool)
+    ],
+    morpho_tool: Annotated[GetMorphoTool, Depends(get_morpho_tool)],
+    morphology_feature_tool: Annotated[
+        MorphologyFeatureTool, Depends(get_morphology_feature_tool)
+    ],
+    kg_morpho_feature_tool: Annotated[
+        KGMorphoFeatureTool, Depends(get_kg_morpho_feature_tool)
+    ],
+    electrophys_feature_tool: Annotated[
+        ElectrophysFeatureTool, Depends(get_electrophys_feature_tool)
+    ],
+    traces_tool: Annotated[GetTracesTool, Depends(get_traces_tool)],
+) -> BaseAgent:
+    """Get the generative question answering service."""
+    logger.info("Load simple chat")
+    tools = [
+        literature_tool,
+        br_resolver_tool,
+        morpho_tool,
+        morphology_feature_tool,
+        kg_morpho_feature_tool,
+        electrophys_feature_tool,
+        traces_tool,
+    ]
+    return SimpleChatAgent(llm=llm, tools=tools, memory=memory)  # type: ignore
 
 
 async def get_update_kg_hierarchy(

src/neuroagent/app/routers/qa.py

@@ -34,8 +34,8 @@ async def run_agent(
 ) -> AgentOutput:
     """Run agent."""
     logger.info("Running agent query.")
-    logger.info(f"User's query: {request.inputs}")
-    return await agent.arun(request.inputs)
+    logger.info(f"User's query: {request.query}")
+    return await agent.arun(request.query)
 
 
 @router.post("/chat/{thread_id}", response_model=AgentOutput)
@@ -47,8 +47,8 @@ async def run_chat_agent(
 ) -> AgentOutput:
     """Run chat agent."""
     logger.info("Running agent query.")
-    logger.info(f"User's query: {request.inputs}")
-    return await agent.arun(query=request.inputs, thread_id=thread_id)
+    logger.info(f"User's query: {request.query}")
+    return await agent.arun(query=request.query, thread_id=thread_id)
 
 
 @router.post("/chat_streamed/{thread_id}")
@@ -60,5 +60,5 @@ async def run_streamed_chat_agent(
 ) -> StreamingResponse:
     """Run agent in streaming mode."""
     logger.info("Running agent query.")
-    logger.info(f"User's query: {request.inputs}")
-    return StreamingResponse(agent.astream(query=request.inputs, thread_id=thread_id))  # type: ignore
+    logger.info(f"User's query: {request.query}")
+    return StreamingResponse(agent.astream(query=request.query, thread_id=thread_id))  # type: ignore

src/neuroagent/app/schemas.py

@@ -1,12 +1,9 @@
 """Schemas."""
 
-from typing import Any
-
 from pydantic import BaseModel
 
 
 class AgentRequest(BaseModel):
     """Class for agent request."""
 
-    inputs: str
-    parameters: dict[str, Any]
+    query: str

tests/app/database/test_threads.py

@@ -65,7 +65,7 @@ async def test_get_thread(
         # Fill the thread
         app_client.post(
             f"/qa/chat/{thread_id}",
-            json={"inputs": "This is my query", "parameters": {}},
+            json={"query": "This is my query"},
         )
 
         create_output = app_client.post("/threads/").json()
@@ -131,7 +131,7 @@ async def test_delete_thread(
         # Fill the thread
         app_client.post(
             f"/qa/chat/{thread_id}",
-            json={"inputs": "This is my query", "parameters": {}},
+            json={"query": "This is my query"},
             params={"thread_id": thread_id},
         )
         # Get the messages of the thread

tests/app/database/test_tools.py

@@ -30,7 +30,7 @@ async def test_get_tool_calls(
         # Fill the thread
         app_client.post(
             f"/qa/chat/{thread_id}",
-            json={"inputs": "This is my query", "parameters": {}},
+            json={"query": "This is my query"},
             params={"thread_id": thread_id},
         )
 
@@ -121,7 +121,7 @@ async def test_get_tool_output(
         # Fill the thread
         app_client.post(
             f"/qa/chat/{thread_id}",
-            json={"inputs": "This is my query", "parameters": {}},
+            json={"query": "This is my query"},
             params={"thread_id": thread_id},
         )
 

tests/app/test_config.py

@@ -10,7 +10,7 @@ def test_required(monkeypatch, patch_required_env):
 
     assert settings.tools.literature.url == "https://fake_url"
     assert settings.knowledge_graph.base_url == "https://fake_url/api/nexus/v1"
-    assert settings.generative.openai.token.get_secret_value() == "dummy"
+    assert settings.openai.token.get_secret_value() == "dummy"
     assert settings.knowledge_graph.use_token
     assert settings.knowledge_graph.token.get_secret_value() == "token"