aiagents4pharma 1.20.0__tar.gz → 1.21.0__tar.gz

{aiagents4pharma-1.20.0 → aiagents4pharma-1.21.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.20.0
+Version: 1.21.0
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
@@ -110,7 +110,7 @@ free credits [here](https://build.nvidia.com/explore/discover)._
    ```
 2. **Install dependencies:**
    ```bash
-   pip install .
+   pip install -r requirements.txt
    ```
 3. **Initialize OPENAI_API_KEY and NVIDIA_API_KEY**
    ```bash

{aiagents4pharma-1.20.0 → aiagents4pharma-1.21.0}/README.md

@@ -58,7 +58,7 @@ free credits [here](https://build.nvidia.com/explore/discover)._
    ```
 2. **Install dependencies:**
    ```bash
-   pip install .
+   pip install -r requirements.txt
    ```
 3. **Initialize OPENAI_API_KEY and NVIDIA_API_KEY**
    ```bash

aiagents4pharma-1.21.0/aiagents4pharma/talk2biomodels/configs/config.yaml

@@ -0,0 +1,5 @@
+defaults:
+  - _self_
+  - agents/t2b_agent: default
+  - tools/ask_question: default
+  - tools/get_annotation: default

aiagents4pharma-1.21.0/aiagents4pharma/talk2scholars/agents/main_agent.py

@@ -0,0 +1,206 @@
+#!/usr/bin/env python3
+
+"""
+Main agent for the talk2scholars app using ReAct pattern.
+
+This module implements a hierarchical agent system where a supervisor agent
+routes queries to specialized sub-agents. It follows the LangGraph patterns
+for multi-agent systems and implements proper state management.
+"""
+
+import logging
+from typing import Literal, Callable
+from pydantic import BaseModel
+import hydra
+from langchain_core.language_models.chat_models import BaseChatModel
+from langchain_core.messages import SystemMessage, HumanMessage, AIMessage
+from langchain_openai import ChatOpenAI
+from langgraph.checkpoint.memory import MemorySaver
+from langgraph.graph import END, START, StateGraph
+from langgraph.types import Command
+from ..agents import s2_agent
+from ..state.state_talk2scholars import Talk2Scholars
+
+# Configure logging
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+
+def get_hydra_config():
+    """
+    Loads the Hydra configuration for the main agent.
+
+    This function initializes the Hydra configuration system and retrieves the settings
+    for the `Talk2Scholars` agent, ensuring that all required parameters are loaded.
+
+    Returns:
+        DictConfig: The configuration object containing parameters for the main agent.
+    """
+    with hydra.initialize(version_base=None, config_path="../configs"):
+        cfg = hydra.compose(
+            config_name="config", overrides=["agents/talk2scholars/main_agent=default"]
+        )
+    return cfg.agents.talk2scholars.main_agent
+
+
+def make_supervisor_node(llm_model: BaseChatModel, thread_id: str) -> Callable:
+    """
+    Creates the supervisor node responsible for routing user queries to the appropriate sub-agents.
+
+    This function initializes the routing logic by leveraging the system and router prompts defined
+    in the Hydra configuration. The supervisor determines whether to
+    call a sub-agent (like `s2_agent`)
+    or directly generate a response using the language model.
+
+    Args:
+        llm_model (BaseChatModel): The language model used for decision-making.
+        thread_id (str): Unique identifier for the current conversation session.
+
+    Returns:
+        Callable: The supervisor node function that processes user queries and
+        decides the next step.
+    """
+    cfg = get_hydra_config()
+    logger.info("Hydra configuration for Talk2Scholars main agent loaded: %s", cfg)
+    members = ["s2_agent"]
+    options = ["FINISH"] + members
+    # Define system prompt for general interactions
+    system_prompt = cfg.system_prompt
+    # Define router prompt for routing to sub-agents
+    router_prompt = cfg.router_prompt
+
+    class Router(BaseModel):
+        """Worker to route to next. If no workers needed, route to FINISH."""
+
+        next: Literal[*options]
+
+    def supervisor_node(
+        state: Talk2Scholars,
+    ) -> Command:
+        """
+        Handles the routing logic for the supervisor agent.
+
+        This function determines the next agent to invoke based on the router prompt response.
+        If no further processing is required, it generates an AI response using the system prompt.
+
+        Args:
+            state (Talk2Scholars): The current conversation state, including messages
+            exchanged so far.
+
+        Returns:
+            Command: A command dictating whether to invoke a sub-agent or generate a final response.
+        """
+        messages = [SystemMessage(content=router_prompt)] + state["messages"]
+        structured_llm = llm_model.with_structured_output(Router)
+        response = structured_llm.invoke(messages)
+        goto = response.next
+        logger.info("Routing to: %s, Thread ID: %s", goto, thread_id)
+        if goto == "FINISH":
+            goto = END  # Using END from langgraph.graph
+            # If no agents were called, and the last message was
+            # from the user, call the LLM to respond to the user
+            # with a slightly different system prompt.
+            if isinstance(messages[-1], HumanMessage):
+                response = llm_model.invoke(
+                    [
+                        SystemMessage(content=system_prompt),
+                    ]
+                    + messages[1:]
+                )
+                return Command(
+                    goto=goto, update={"messages": AIMessage(content=response.content)}
+                )
+        # Go to the requested agent
+        return Command(goto=goto)
+
+    return supervisor_node
+
+
+def get_app(
+    thread_id: str,
+    llm_model: BaseChatModel = ChatOpenAI(model="gpt-4o-mini", temperature=0),
+):
+    """
+    Initializes and returns the LangGraph-based hierarchical agent system.
+
+    This function constructs the agent workflow by defining nodes for the supervisor
+    and sub-agents. It compiles the graph using `StateGraph` to enable structured
+    conversational workflows.
+
+    Args:
+        thread_id (str): A unique session identifier for tracking conversation state.
+        llm_model (BaseChatModel, optional): The language model used for query processing.
+            Defaults to `ChatOpenAI(model="gpt-4o-mini", temperature=0)`.
+
+    Returns:
+        StateGraph: A compiled LangGraph application that can process user queries.
+
+    Example:
+        >>> app = get_app("thread_123")
+        >>> result = app.invoke(initial_state)
+    """
+    cfg = get_hydra_config()
+
+    def call_s2_agent(
+        state: Talk2Scholars,
+    ) -> Command[Literal["supervisor"]]:
+        """
+        Invokes the Semantic Scholar (S2) agent to retrieve relevant research papers.
+
+        This function calls the `s2_agent` and updates the conversation state with retrieved
+        academic papers. The agent uses Semantic Scholar's API to find papers based on
+        user queries.
+
+        Args:
+            state (Talk2Scholars): The current state of the conversation, containing messages
+                and any previous search results.
+
+        Returns:
+            Command: A command to update the conversation state with the retrieved papers
+                and return control to the supervisor node.
+
+        Example:
+            >>> result = call_s2_agent(current_state)
+            >>> next_step = result.goto
+        """
+        logger.info("Calling S2 agent")
+        app = s2_agent.get_app(thread_id, llm_model)
+
+        # Invoke the S2 agent, passing state,
+        # Pass both config_id and thread_id
+        response = app.invoke(
+            state,
+            {
+                "configurable": {
+                    "config_id": thread_id,
+                    "thread_id": thread_id,
+                }
+            },
+        )
+        logger.info("S2 agent completed with response")
+        return Command(
+            update={
+                "messages": response["messages"],
+                "papers": response.get("papers", {}),
+                "multi_papers": response.get("multi_papers", {}),
+                "last_displayed_papers": response.get("last_displayed_papers", {}),
+            },
+            # Always return to supervisor
+            goto="supervisor",
+        )
+
+    # Initialize LLM
+    logger.info("Using model %s with temperature %s", llm_model, cfg.temperature)
+
+    # Build the graph
+    workflow = StateGraph(Talk2Scholars)
+    supervisor = make_supervisor_node(llm_model, thread_id)
+    # Add nodes
+    workflow.add_node("supervisor", supervisor)
+    workflow.add_node("s2_agent", call_s2_agent)
+    # Add edges
+    workflow.add_edge(START, "supervisor")
+    # Compile the workflow
+    app = workflow.compile(checkpointer=MemorySaver())
+    logger.info("Main agent workflow compiled")
+    return app

aiagents4pharma-1.21.0/aiagents4pharma/talk2scholars/agents/s2_agent.py

@@ -0,0 +1,129 @@
+# /usr/bin/env python3
+
+"""
+Agent for interacting with Semantic Scholar
+"""
+
+import logging
+from typing import Any, Dict
+import hydra
+from langchain_openai import ChatOpenAI
+from langchain_core.language_models.chat_models import BaseChatModel
+from langgraph.graph import START, StateGraph
+from langgraph.prebuilt import create_react_agent, ToolNode
+from langgraph.checkpoint.memory import MemorySaver
+from ..state.state_talk2scholars import Talk2Scholars
+from ..tools.s2.search import search_tool as s2_search
+from ..tools.s2.display_results import display_results as s2_display
+from ..tools.s2.query_results import query_results as s2_query_results
+from ..tools.s2.retrieve_semantic_scholar_paper_id import (
+    retrieve_semantic_scholar_paper_id as s2_retrieve_id,
+)
+from ..tools.s2.single_paper_rec import (
+    get_single_paper_recommendations as s2_single_rec,
+)
+from ..tools.s2.multi_paper_rec import get_multi_paper_recommendations as s2_multi_rec
+
+# Initialize logger
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+
+def get_app(
+    uniq_id, llm_model: BaseChatModel = ChatOpenAI(model="gpt-4o-mini", temperature=0)
+):
+    """
+    Initializes and returns the LangGraph application for the Semantic Scholar (S2) agent.
+
+    This function sets up the S2 agent, which integrates various tools to search, retrieve,
+    and display research papers from Semantic Scholar. The agent follows the ReAct pattern
+    for structured interaction.
+
+    Args:
+        uniq_id (str): Unique identifier for the current conversation session.
+        llm_model (BaseChatModel, optional): The language model to be used by the agent.
+            Defaults to `ChatOpenAI(model="gpt-4o-mini", temperature=0)`.
+
+    Returns:
+        StateGraph: A compiled LangGraph application that enables the S2 agent to process
+            user queries and retrieve research papers.
+
+    Example:
+        >>> app = get_app("thread_123")
+        >>> result = app.invoke(initial_state)
+    """
+
+    # def agent_s2_node(state: Talk2Scholars) -> Command[Literal["supervisor"]]:
+    def agent_s2_node(state: Talk2Scholars) -> Dict[str, Any]:
+        """
+        Processes the user query and retrieves relevant research papers.
+
+        This function calls the language model using the configured `ReAct` agent to analyze
+        the state and generate an appropriate response. The function then returns control
+        to the main supervisor.
+
+        Args:
+            state (Talk2Scholars): The current conversation state, including messages exchanged
+                and any previously retrieved research papers.
+
+        Returns:
+            Dict[str, Any]: A dictionary containing the updated conversation state.
+
+        Example:
+            >>> result = agent_s2_node(current_state)
+            >>> papers = result.get("papers", [])
+        """
+        logger.log(logging.INFO, "Creating Agent_S2 node with thread_id %s", uniq_id)
+        result = model.invoke(state, {"configurable": {"thread_id": uniq_id}})
+
+        return result
+
+    logger.log(logging.INFO, "thread_id, llm_model: %s, %s", uniq_id, llm_model)
+
+    # Load hydra configuration
+    logger.log(logging.INFO, "Load Hydra configuration for Talk2Scholars S2 agent.")
+    with hydra.initialize(version_base=None, config_path="../configs"):
+        cfg = hydra.compose(
+            config_name="config", overrides=["agents/talk2scholars/s2_agent=default"]
+        )
+        cfg = cfg.agents.talk2scholars.s2_agent
+
+    # Define the tools
+    tools = ToolNode(
+        [
+            s2_search,
+            s2_display,
+            s2_query_results,
+            s2_retrieve_id,
+            s2_single_rec,
+            s2_multi_rec,
+        ]
+    )
+
+    # Define the model
+    logger.log(logging.INFO, "Using OpenAI model %s", llm_model)
+
+    # Create the agent
+    model = create_react_agent(
+        llm_model,
+        tools=tools,
+        state_schema=Talk2Scholars,
+        state_modifier=cfg.s2_agent,
+        checkpointer=MemorySaver(),
+    )
+
+    workflow = StateGraph(Talk2Scholars)
+    workflow.add_node("agent_s2", agent_s2_node)
+    workflow.add_edge(START, "agent_s2")
+
+    # Initialize memory to persist state between graph runs
+    checkpointer = MemorySaver()
+
+    # Finally, we compile it!
+    # This compiles it into a LangChain Runnable,
+    # meaning you can use it as you would any other runnable.
+    # Note that we're (optionally) passing the memory when compiling the graph
+    app = workflow.compile(checkpointer=checkpointer)
+    logger.log(logging.INFO, "Compiled the graph")
+
+    return app

aiagents4pharma-1.21.0/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/default.yaml

@@ -0,0 +1,39 @@
+_target_: agents.main_agent.get_app
+openai_api_key: ${oc.env:OPENAI_API_KEY}
+openai_llms:
+  - "gpt-4o-mini"
+  - "gpt-4-turbo"
+  - "gpt-3.5-turbo"
+temperature: 0
+system_prompt: >
+  You are the Talk2Scholars agent coordinating academic paper discovery and analysis.
+
+  You have access to the following agents:
+  1. S2_agent: This agent can be used to search and recommend papers
+    from Semantic Scholar. Use this agent when the user asks for
+    general paper searches and recommendations. This agent can also
+    retrieve the Semantic Scholar ID of a paper.
+router_prompt: >
+  You are a supervisor tasked with managing a conversation between the
+  following workers: {members}. Given the user request, respond with the
+  worker to act next. Each worker will perform a task and respond with
+  their results and status. When finished, respond with FINISH.
+
+  Here is a description of the workers:
+  1. S2_agent: This agent can be used to search and recommend papers
+    from Semantic Scholar. Use this agent when the user asks for
+    general paper searches and recommendations. This agent can also
+    retrieve the Semantic Scholar ID of a paper. It can also be used to
+    provide more information about a paper.
+
+  Here are some instructions for the workers:
+  1. Call the S2 agent for general paper searches and recommendations.
+  2. The S2 agent has access to tools for querying and displaying papers.
+  3. If the user wants suggestions for papers and you don’t have 
+    a Semantic Scholar ID for it but do have the title from
+    the last displayed results, use the S2 agent to retrieve the
+    Semantic Scholar ID of the paper. Then, use the S2 agent again to display
+    recommendations for the paper.
+  4. You can call the S2 agent to get more information about a paper based
+    on the context of the conversation.
+  5. Respond with FINISH when all tasks are completed.

aiagents4pharma-1.21.0/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/default.yaml

@@ -0,0 +1,16 @@
+_target_: agents.s2_agent.get_app
+openai_api_key: ${oc.env:OPENAI_API_KEY}
+openai_llms:
+  - "gpt-4o-mini"
+  - "gpt-4-turbo"
+  - "gpt-3.5-turbo"
+temperature: 0
+s2_agent: >
+  You are an academic research assistant with access to the
+  Semantic Scholar API for paper discovery and analysis.
+  You also have tools to gain more insights on the papers and
+  display them.
+  You must strictly rely on retrieved information and avoid
+  generating unsupported content. Do not generate hallucinations
+  or fabricate details of any article. Stay focused on accurate,
+  sourced academic insights.

{aiagents4pharma-1.20.0 → aiagents4pharma-1.21.0}/aiagents4pharma/talk2scholars/configs/app/frontend/default.yaml

@@ -1,14 +1,13 @@
-# # Page configuration
-# page:
-#   title: "Talk2Scholars"
-#   icon: "🤖"
-#   layout: "wide"
+# Page configuration
+page:
+  title: "Talk2Scholars"
+  icon: "🤖"
+  layout: "wide"
 
 # Available LLM models
-llm_models:
-  - "gpt-4o-mini"
-  - "gpt-4-turbo"
-  - "gpt-3.5-turbo"
+llms:
+  available_models:
+    - "OpenAI/gpt-4o-mini"
 # # Chat UI configuration
 # chat:
 #   assistant_avatar: "🤖"
@@ -16,6 +15,9 @@ llm_models:
 #   input_placeholder: "Say something ..."
 #   spinner_text: "Fetching response ..."
 
+api_keys:
+  openai_key: "OPENAI_API_KEY"
+  nvidia_key: "NVIDIA_API_KEY"
 # # Feedback configuration
 # feedback:
 #   type: "thumbs"

{aiagents4pharma-1.20.0 → aiagents4pharma-1.21.0}/aiagents4pharma/talk2scholars/configs/config.yaml

@@ -5,4 +5,5 @@ defaults:
   - tools/search: default
   - tools/single_paper_recommendation: default
   - tools/multi_paper_recommendation: default
+  - tools/retrieve_semantic_scholar_paper_id: default
   - app/frontend: default

{aiagents4pharma-1.20.0 → aiagents4pharma-1.21.0}/aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/default.yaml

@@ -9,6 +9,8 @@ api_fields:
   - "authors"
   - "citationCount"
   - "url"
+# Commented fields that could be added later if needed
+# - "externalIds"
 
 # Default headers and params
 headers:

{aiagents4pharma-1.20.0 → aiagents4pharma-1.21.0}/aiagents4pharma/talk2scholars/configs/tools/search/default.yaml

@@ -10,6 +10,7 @@ api_fields:
   - "citationCount"
   - "url"
 # Commented fields that could be added later if needed
+# - "externalIds"
 #  - "publicationTypes"
 #  - "openAccessPdf"
 

aiagents4pharma-1.21.0/aiagents4pharma/talk2scholars/configs/tools/single_paper_recommendation/__init__.py

@@ -0,0 +1,3 @@
+"""
+Import all the modules in the package
+"""

{aiagents4pharma-1.20.0 → aiagents4pharma-1.21.0}/aiagents4pharma/talk2scholars/configs/tools/single_paper_recommendation/default.yaml

@@ -10,6 +10,7 @@ api_fields:
   - "citationCount"
   - "url"
 # Commented fields that could be added later if needed
+# - "externalIds"
 #  - "publicationTypes"
 #  - "openAccessPdf"
 

aiagents4pharma-1.21.0/aiagents4pharma/talk2scholars/state/state_talk2scholars.py

@@ -0,0 +1,62 @@
+"""
+State management for the Talk2Scholars agent.
+
+This module defines the state class `Talk2Scholars`, which maintains the conversation
+context, retrieved papers, and other relevant metadata. The state ensures consistency
+across agent interactions.
+"""
+
+import logging
+from typing import Annotated, Any, Dict
+from langchain_core.language_models import BaseChatModel
+from langgraph.prebuilt.chat_agent_executor import AgentState
+
+# Configure logging
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+
+def replace_dict(existing: Dict[str, Any], new: Dict[str, Any]) -> Dict[str, Any]:
+    """
+    Replaces the existing dictionary with a new dictionary.
+
+    This function logs the state update and ensures that the old state is replaced
+    with the new one.
+
+    Args:
+        existing (Dict[str, Any]): The current dictionary state.
+        new (Dict[str, Any]): The new dictionary state to replace the existing one.
+
+    Returns:
+        Dict[str, Any]: The updated dictionary state.
+
+    Example:
+        >>> old_state = {"papers": {"id1": "Paper 1"}}
+        >>> new_state = {"papers": {"id2": "Paper 2"}}
+        >>> updated_state = replace_dict(old_state, new_state)
+        >>> print(updated_state)
+        {"papers": {"id2": "Paper 2"}}
+    """
+    logger.info("Updating existing state %s with the state dict: %s", existing, new)
+    return new
+
+
+class Talk2Scholars(AgentState):
+    """
+    Represents the state of the Talk2Scholars agent.
+
+    This class extends `AgentState` to maintain conversation history, retrieved papers,
+    and interactions with the language model.
+
+    Attributes:
+        last_displayed_papers (Dict[str, Any]): Stores the most recently displayed papers.
+        papers (Dict[str, Any]): Stores the research papers retrieved from the agent's queries.
+        multi_papers (Dict[str, Any]): Stores multiple recommended papers from various sources.
+        llm_model (BaseChatModel): The language model instance used for generating responses.
+    """
+
+    # Agent state fields
+    last_displayed_papers: Annotated[Dict[str, Any], replace_dict]
+    papers: Annotated[Dict[str, Any], replace_dict]
+    multi_papers: Annotated[Dict[str, Any], replace_dict]
+    llm_model: BaseChatModel

aiagents4pharma-1.21.0/aiagents4pharma/talk2scholars/tests/test_llm_main_integration.py

@@ -0,0 +1,58 @@
+"""
+Integration tests for talk2scholars system with OpenAI.
+"""
+
+import os
+import pytest
+import hydra
+from langchain_openai import ChatOpenAI
+from langchain_core.messages import HumanMessage, AIMessage
+from ..agents.main_agent import get_app
+from ..state.state_talk2scholars import Talk2Scholars
+
+# pylint: disable=redefined-outer-name
+
+
+@pytest.mark.skipif(
+    not os.getenv("OPENAI_API_KEY"), reason="Requires OpenAI API key to run"
+)
+def test_main_agent_real_llm():
+    """
+    Test that the main agent invokes S2 agent correctly
+    and updates the state with real LLM execution.
+    """
+
+    # Load Hydra Configuration EXACTLY like in main_agent.py
+    with hydra.initialize(version_base=None, config_path="../configs"):
+        cfg = hydra.compose(
+            config_name="config", overrides=["agents/talk2scholars/main_agent=default"]
+        )
+    hydra_cfg = cfg.agents.talk2scholars.main_agent
+
+    assert hydra_cfg is not None, "Hydra config failed to load"
+
+    # Use the real OpenAI API (ensure env variable is set)
+    llm = ChatOpenAI(model="gpt-4o-mini", temperature=hydra_cfg.temperature)
+
+    # Initialize main agent workflow (WITH real Hydra config)
+    thread_id = "test_thread"
+    app = get_app(thread_id, llm)
+
+    # Provide an actual user query
+    initial_state = Talk2Scholars(
+        messages=[HumanMessage(content="Find AI papers on transformers")]
+    )
+
+    # Invoke the agent (triggers supervisor → s2_agent)
+    result = app.invoke(
+        initial_state,
+        {"configurable": {"config_id": thread_id, "thread_id": thread_id}},
+    )
+
+    # Assert that the supervisor routed correctly
+    assert "messages" in result, "Expected messages in response"
+
+    # Fix: Accept AIMessage as a valid response type
+    assert isinstance(
+        result["messages"][-1], (HumanMessage, AIMessage, str)
+    ), "Last message should be a valid response"