aiagents4pharma 1.16.0__py3-none-any.whl → 1.17.0__py3-none-any.whl

aiagents4pharma/talk2scholars/__init__.py

@@ -2,4 +2,4 @@
 This file is used to import all the modules in the package.
 """
 
-from . import agents, config, state, tests, tools
+from . import agents, configs, state, tests, tools

aiagents4pharma/talk2scholars/agents/main_agent.py

@@ -5,8 +5,8 @@ Main agent for the talk2scholars app.
 """
 
 import logging
-from typing import Literal
-from dotenv import load_dotenv
+from typing import Literal, Any
+import hydra
 from langchain_core.language_models.chat_models import BaseChatModel
 from langchain_core.messages import AIMessage
 from langchain_openai import ChatOpenAI
@@ -14,27 +14,26 @@ from langgraph.checkpoint.memory import MemorySaver
 from langgraph.graph import END, START, StateGraph
 from langgraph.types import Command
 from ..agents import s2_agent
-from ..config.config import config
 from ..state.state_talk2scholars import Talk2Scholars
 
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
-load_dotenv()
 
-def make_supervisor_node(llm: BaseChatModel) -> str:
+def make_supervisor_node(llm: BaseChatModel, cfg: Any) -> str:
     """
     Creates a supervisor node following LangGraph patterns.
 
     Args:
         llm (BaseChatModel): The language model to use for generating responses.
+        cfg (Any): The configuration object.
 
     Returns:
         str: The supervisor node function.
     """
-    # options = ["FINISH", "s2_agent"]
-
-    def supervisor_node(state: Talk2Scholars) -> Command[Literal["s2_agent", "__end__"]]:
+    def supervisor_node(
+        state: Talk2Scholars,
+    ) -> Command[Literal["s2_agent", "__end__"]]:
         """
         Supervisor node that routes to appropriate sub-agents.
 
@@ -44,9 +43,13 @@ def make_supervisor_node(llm: BaseChatModel) -> str:
         Returns:
             Command[Literal["s2_agent", "__end__"]]: The command to execute next.
         """
-        logger.info("Supervisor node called")
+        logger.info(
+            "Supervisor node called - Messages count: %d, Current Agent: %s",
+            len(state["messages"]),
+            state.get("current_agent", "None"),
+        )
 
-        messages = [{"role": "system", "content": config.MAIN_AGENT_PROMPT}] + state[
+        messages = [{"role": "system", "content": cfg.state_modifier}] + state[
             "messages"
         ]
         response = llm.invoke(messages)
@@ -81,7 +84,8 @@ def make_supervisor_node(llm: BaseChatModel) -> str:
 
     return supervisor_node
 
-def get_app(thread_id: str, llm_model ='gpt-4o-mini') -> StateGraph:
+
+def get_app(thread_id: str, llm_model="gpt-4o-mini") -> StateGraph:
     """
     Returns the langraph app with hierarchical structure.
 
@@ -91,6 +95,16 @@ def get_app(thread_id: str, llm_model ='gpt-4o-mini') -> StateGraph:
     Returns:
         The compiled langraph app.
     """
+
+    # Load hydra configuration
+    logger.log(logging.INFO, "Load Hydra configuration for Talk2Scholars main agent.")
+    with hydra.initialize(version_base=None, config_path="../../configs"):
+        cfg = hydra.compose(
+            config_name="config", overrides=["agents/talk2scholars/main_agent=default"]
+        )
+        cfg = cfg.agents.talk2scholars.main_agent
+        logger.info("Hydra configuration loaded with values: %s", cfg)
+
     def call_s2_agent(state: Talk2Scholars) -> Command[Literal["__end__"]]:
         """
         Node for calling the S2 agent.
@@ -101,10 +115,10 @@ def get_app(thread_id: str, llm_model ='gpt-4o-mini') -> StateGraph:
         Returns:
             Command[Literal["__end__"]]: The command to execute next.
         """
-        logger.info("Calling S2 agent")
+        logger.info("Calling S2 agent with state: %s", state)
         app = s2_agent.get_app(thread_id, llm_model)
         response = app.invoke(state)
-        logger.info("S2 agent completed")
+        logger.info("S2 agent completed with response: %s", response)
         return Command(
             goto=END,
             update={
@@ -114,10 +128,17 @@ def get_app(thread_id: str, llm_model ='gpt-4o-mini') -> StateGraph:
                 "current_agent": "s2_agent",
             },
         )
-    llm = ChatOpenAI(model=llm_model, temperature=0)
+
+    logger.log(
+        logging.INFO,
+        "Using OpenAI model %s with temperature %s",
+        llm_model,
+        cfg.temperature
+    )
+    llm = ChatOpenAI(model=llm_model, temperature=cfg.temperature)
     workflow = StateGraph(Talk2Scholars)
 
-    supervisor = make_supervisor_node(llm)
+    supervisor = make_supervisor_node(llm, cfg)
     workflow.add_node("supervisor", supervisor)
     workflow.add_node("s2_agent", call_s2_agent)
 

aiagents4pharma/talk2scholars/agents/s2_agent.py

@@ -1,56 +1,65 @@
-#/usr/bin/env python3
+# /usr/bin/env python3
 
-'''
+"""
 Agent for interacting with Semantic Scholar
-'''
+"""
 
 import logging
-from dotenv import load_dotenv
+import hydra
 from langchain_openai import ChatOpenAI
 from langgraph.graph import START, StateGraph
-from langgraph.prebuilt import create_react_agent
+from langgraph.prebuilt import create_react_agent, ToolNode
 from langgraph.checkpoint.memory import MemorySaver
-from ..config.config import config
 from ..state.state_talk2scholars import Talk2Scholars
-# from ..tools.s2 import s2_tools
-from ..tools.s2.search import search_tool
-from ..tools.s2.display_results import display_results
-from ..tools.s2.single_paper_rec import get_single_paper_recommendations
-from ..tools.s2.multi_paper_rec import get_multi_paper_recommendations
+from ..tools.s2.search import search_tool as s2_search
+from ..tools.s2.display_results import display_results as s2_display
+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
 
-load_dotenv()
 
 # Initialize logger
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
-def get_app(uniq_id, llm_model='gpt-4o-mini'):
-    '''
+
+def get_app(uniq_id, llm_model="gpt-4o-mini"):
+    """
     This function returns the langraph app.
-    '''
+    """
+
     def agent_s2_node(state: Talk2Scholars):
-        '''
+        """
         This function calls the model.
-        '''
+        """
         logger.log(logging.INFO, "Creating Agent_S2 node with thread_id %s", uniq_id)
         response = model.invoke(state, {"configurable": {"thread_id": uniq_id}})
         return response
 
+    # 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 = [search_tool,
-            display_results,
-            get_single_paper_recommendations,
-            get_multi_paper_recommendations]
+    tools = ToolNode([s2_search, s2_display, s2_single_rec, s2_multi_rec])
+
+    # Define the model
+    logger.log(logging.INFO, "Using OpenAI model %s", llm_model)
+    llm = ChatOpenAI(model=llm_model, temperature=cfg.temperature)
 
-    # Create the LLM
-    llm = ChatOpenAI(model=llm_model, temperature=0)
+    # Create the agent
     model = create_react_agent(
-                            llm,
-                            tools=tools,
-                            state_schema=Talk2Scholars,
-                            state_modifier=config.S2_AGENT_PROMPT,
-                            checkpointer=MemorySaver()
-                        )
+        llm,
+        tools=tools,
+        state_schema=Talk2Scholars,
+        state_modifier=cfg.s2_agent,
+        checkpointer=MemorySaver(),
+    )
 
     # Define a new graph
     workflow = StateGraph(Talk2Scholars)

aiagents4pharma/talk2scholars/{config → configs}/__init__.py

@@ -2,4 +2,6 @@
 This package contains configuration settings and prompts used by various AI agents
 """
 
-from . import config
+from . import agents
+from . import tools
+from . import app

aiagents4pharma/talk2scholars/configs/agents/__init__.py

@@ -0,0 +1,5 @@
+"""
+Import all the modules in the package
+"""
+
+from . import talk2scholars

aiagents4pharma/talk2scholars/configs/agents/talk2scholars/__init__.py

@@ -0,0 +1,6 @@
+"""
+Import all the modules in the package
+"""
+
+from . import s2_agent
+from . import main_agent

aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/__init__.py

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

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
+main_agent: >
+  "You are a supervisory AI agent that routes user queries to specialized tools.\n"
+  "Your task is to select the most appropriate tool based on the user's request.\n\n"
+  "Available tools and their capabilities:\n\n"
+  "1. semantic_scholar_agent:\n"
+  "   - Search for academic papers and research\n"
+  "   - Get paper recommendations\n"
+  "   - Find similar papers\n"
+  "   USE FOR: Any queries about finding papers, academic research, "
+  "or getting paper recommendations\n\n"
+  "ROUTING GUIDELINES:\n\n"
+  "ALWAYS route to semantic_scholar_agent for:\n"
+  "- Finding academic papers\n"
+  "- Searching research topics\n"
+  "- Getting paper recommendations\n"
+  "- Finding similar papers\n"
+  "- Any query about academic literature\n\n"
+  "Approach:\n"
+  "1. Identify the core need in the user's query\n"
+  "2. Select the most appropriate tool based on the guidelines above\n"
+  "3. If unclear, ask for clarification\n"
+  "4. For multi-step tasks, focus on the immediate next step\n\n"
+  "Remember:\n"
+  "- Be decisive in your tool selection\n"
+  "- Focus on the immediate task\n"
+  "- Default to semantic_scholar_agent for any paper-finding tasks\n"
+  "- Ask for clarification if the request is ambiguous\n\n"
+  "When presenting paper search results, always use this exact format:\n\n"
+  "Remember to:\n"
+  "- To always add the url\n"
+  "- Put URLs on the title line itself as markdown\n"
+  "- Maintain consistent spacing and formatting"

aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/__init__.py

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

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

@@ -0,0 +1,68 @@
+_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 a specialized academic research assistant with access to the following tools:\n\n"
+  "1. search_papers:\n"
+  "   USE FOR: General paper searches\n"
+  "   - Enhances search terms automatically\n"
+  "   - Adds relevant academic keywords\n"
+  "   - Focuses on recent research when appropriate\n\n"
+  "2. get_single_paper_recommendations:\n"
+  "   USE FOR: Finding papers similar to a specific paper\n"
+  "   - Takes a single paper ID\n"
+  "   - Returns related papers\n\n"
+  "3. get_multi_paper_recommendations:\n"
+  "   USE FOR: Finding papers similar to multiple papers\n"
+  "   - Takes multiple paper IDs\n"
+  "   - Finds papers related to all inputs\n\n"
+  "GUIDELINES:\n\n"
+  "For paper searches:\n"
+  "- Enhance search terms with academic language\n"
+  "- Include field-specific terminology\n"
+  '- Add "recent" or "latest" when appropriate\n'
+  "- Keep queries focused and relevant\n\n"
+  "For paper recommendations:\n"
+  "- Identify paper IDs (40-character hexadecimal strings)\n"
+  "- Use single_paper_recommendations for one ID\n"
+  "- Use multi_paper_recommendations for multiple IDs\n\n"
+  "Best practices:\n"
+  "1. Start with a broad search if no paper IDs are provided\n"
+  "2. Look for paper IDs in user input\n"
+  "3. Enhance search terms for better results\n"
+  "4. Consider the academic context\n"
+  "5. Be prepared to refine searches based on feedback\n\n"
+  "Remember:\n"
+  "- Always select the most appropriate tool\n"
+  "- Enhance search queries naturally\n"
+  "- Consider academic context\n"
+  "- Focus on delivering relevant results\n\n"
+  "IMPORTANT GUIDELINES FOR PAPER RECOMMENDATIONS:\n\n"
+  "For Multiple Papers:\n"
+  "- When getting recommendations for multiple papers, always use "
+  "get_multi_paper_recommendations tool\n"
+  "- DO NOT call get_single_paper_recommendations multiple times\n"
+  "- Always pass all paper IDs in a single call to get_multi_paper_recommendations\n"
+  '- Use for queries like "find papers related to both/all papers" or '
+  '"find similar papers to these papers"\n\n'
+  "For Single Paper:\n"
+  "- Use get_single_paper_recommendations when focusing on one specific paper\n"
+  "- Pass only one paper ID at a time\n"
+  '- Use for queries like "find papers similar to this paper" or '
+  '"get recommendations for paper X"\n'
+  "- Do not use for multiple papers\n\n"
+  "Examples:\n"
+  '- For "find related papers for both papers":\n'
+  "  ✓ Use get_multi_paper_recommendations with both paper IDs\n"
+  "  × Don't make multiple calls to get_single_paper_recommendations\n\n"
+  '- For "find papers related to the first paper":\n'
+  "  ✓ Use get_single_paper_recommendations with just that paper's ID\n"
+  "  × Don't use get_multi_paper_recommendations\n\n"
+  "Remember:\n"
+  "- Be precise in identifying which paper ID to use for single recommendations\n"
+  "- Don't reuse previous paper IDs unless specifically requested\n"
+  "- For fresh paper recommendations, always use the original paper ID"

aiagents4pharma/talk2scholars/configs/app/__init__.py

@@ -0,0 +1,5 @@
+"""
+Import all the modules in the package
+"""
+
+from . import frontend

aiagents4pharma/talk2scholars/configs/app/frontend/__init__.py

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

aiagents4pharma/talk2scholars/configs/app/frontend/default.yaml

@@ -0,0 +1,33 @@
+# # Page configuration
+# page:
+#   title: "Talk2Scholars"
+#   icon: "🤖"
+#   layout: "wide"
+
+# Available LLM models
+llm_models:
+  - "gpt-4o-mini"
+  - "gpt-4-turbo"
+  - "gpt-3.5-turbo"
+# # Chat UI configuration
+# chat:
+#   assistant_avatar: "🤖"
+#   user_avatar: "👩🏻‍💻"
+#   input_placeholder: "Say something ..."
+#   spinner_text: "Fetching response ..."
+
+# # Feedback configuration
+# feedback:
+#   type: "thumbs"
+#   text_label: "[Optional] Please provide an explanation"
+#   success_message: "Your feedback is on its way to the developers. Thank you!"
+#   success_icon: "🚀"
+
+# # Layout configuration
+# layout:
+#   column_ratio: [3, 7] # Ratio for main_col1 and main_col2
+#   chat_container_height: 575
+#   sidebar_container_height: 500
+#
+# # Project name prefix
+# project_name_prefix: "Talk2Scholars-"

aiagents4pharma/talk2scholars/configs/config.yaml

@@ -0,0 +1,8 @@
+defaults:
+  - _self_
+  - agents/talk2scholars/main_agent: default
+  - agents/talk2scholars/s2_agent: default
+  - tools/search: default
+  - tools/single_paper_recommendation: default
+  - tools/multi_paper_recommendation: default
+  - app/frontend: default

aiagents4pharma/talk2scholars/configs/tools/__init__.py

@@ -0,0 +1,7 @@
+"""
+Import all the modules in the package
+"""
+
+from . import search
+from . import single_paper_recommendation
+from . import multi_paper_recommendation

aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/__init__.py

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

aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/default.yaml

@@ -0,0 +1,19 @@
+api_endpoint: "https://api.semanticscholar.org/recommendations/v1/papers"
+default_limit: 2
+request_timeout: 10
+api_fields:
+  - "paperId"
+  - "title"
+  - "abstract"
+  - "year"
+  - "authors"
+  - "citationCount"
+  - "url"
+
+# Default headers and params
+headers:
+  Content-Type: "application/json"
+
+recommendation_params:
+  limit: ${.default_limit}
+  fields: ${.api_fields}

aiagents4pharma/talk2scholars/configs/tools/search/__init__.py

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

aiagents4pharma/talk2scholars/configs/tools/search/default.yaml

@@ -0,0 +1,19 @@
+api_endpoint: "https://api.semanticscholar.org/graph/v1/paper/search"
+default_limit: 2
+request_timeout: 10
+api_fields:
+  - "paperId"
+  - "title"
+  - "abstract"
+  - "year"
+  - "authors"
+  - "citationCount"
+  - "url"
+# Commented fields that could be added later if needed
+#  - "publicationTypes"
+#  - "openAccessPdf"
+
+# Default search parameters
+search_params:
+  limit: ${.default_limit} # Reference to the default_limit above
+  fields: ${.api_fields} # Reference to the api_fields above

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

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

aiagents4pharma/talk2scholars/configs/tools/single_paper_recommendation/default.yaml

@@ -0,0 +1,20 @@
+api_endpoint: "https://api.semanticscholar.org/recommendations/v1/papers/forpaper"
+default_limit: 2
+request_timeout: 10
+api_fields:
+  - "paperId"
+  - "title"
+  - "abstract"
+  - "year"
+  - "authors"
+  - "citationCount"
+  - "url"
+# Commented fields that could be added later if needed
+#  - "publicationTypes"
+#  - "openAccessPdf"
+
+# Default recommendation parameters
+recommendation_params:
+  limit: ${.default_limit} # Reference to the default_limit above
+  fields: ${.api_fields} # Reference to the api_fields above
+  from_pool: "all-cs" # Using all-cs pool as specified in docs

aiagents4pharma/talk2scholars/tests/test_langgraph.py

@@ -5,12 +5,14 @@ Tests are deterministic and independent of each other.
 """
 
 from unittest.mock import Mock, patch
-
 import pytest
 from langchain_core.messages import AIMessage, HumanMessage
+import hydra
+from hydra.core.global_hydra import GlobalHydra
+from omegaconf import DictConfig, OmegaConf
 
 from ..agents.main_agent import get_app, make_supervisor_node
-from ..state.state_talk2scholars import replace_dict
+from ..state.state_talk2scholars import replace_dict, Talk2Scholars
 from ..tools.s2.display_results import display_results
 from ..tools.s2.multi_paper_rec import get_multi_paper_recommendations
 from ..tools.s2.search import search_tool
@@ -18,6 +20,42 @@ from ..tools.s2.single_paper_rec import get_single_paper_recommendations
 
 # pylint: disable=redefined-outer-name
 
+
+@pytest.fixture(autouse=True)
+def hydra_setup():
+    """Setup and cleanup Hydra for tests."""
+    GlobalHydra.instance().clear()
+    with hydra.initialize(version_base=None, config_path="../configs"):
+        yield
+
+
+@pytest.fixture
+def mock_cfg() -> DictConfig:
+    """Create a mock configuration for testing."""
+    config = {
+        "agents": {
+            "talk2scholars": {
+                "main_agent": {
+                    "state_modifier": "Test prompt for main agent",
+                    "temperature": 0,
+                },
+                "s2_agent": {
+                    "temperature": 0,
+                    "s2_agent": "Test prompt for s2 agent",
+                },
+            }
+        },
+        "tools": {
+            "search": {
+                "api_endpoint": "https://api.semanticscholar.org/graph/v1/paper/search",
+                "default_limit": 2,
+                "api_fields": ["paperId", "title", "abstract", "year", "authors"],
+            }
+        },
+    }
+    return OmegaConf.create(config)
+
+
 # Fixed test data for deterministic results
 MOCK_SEARCH_RESPONSE = {
     "data": [
@@ -45,27 +83,33 @@ MOCK_STATE_PAPER = {
 
 
 @pytest.fixture
-def initial_state():
+def initial_state() -> Talk2Scholars:
     """Create a base state for tests"""
-    return {
-        "messages": [],
-        "papers": {},
-        "is_last_step": False,
-        "current_agent": None,
-        "llm_model": "gpt-4o-mini",
-    }
+    return Talk2Scholars(
+        messages=[],
+        papers={},
+        is_last_step=False,
+        current_agent=None,
+        llm_model="gpt-4o-mini",
+        next="",
+    )
 
 
 class TestMainAgent:
     """Unit tests for main agent functionality"""
 
-    def test_supervisor_routes_search_to_s2(self, initial_state):
+    def test_supervisor_routes_search_to_s2(
+        self, initial_state: Talk2Scholars, mock_cfg
+    ):
         """Verifies that search-related queries are routed to S2 agent"""
         llm_mock = Mock()
         llm_mock.invoke.return_value = AIMessage(content="Search initiated")
 
-        supervisor = make_supervisor_node(llm_mock)
-        state = initial_state.copy()
+        # Extract the main_agent config
+        supervisor = make_supervisor_node(
+            llm_mock, mock_cfg.agents.talk2scholars.main_agent
+        )
+        state = initial_state
         state["messages"] = [HumanMessage(content="search for papers")]
 
         result = supervisor(state)
@@ -73,13 +117,18 @@ class TestMainAgent:
         assert not result.update["is_last_step"]
         assert result.update["current_agent"] == "s2_agent"
 
-    def test_supervisor_routes_general_to_end(self, initial_state):
+    def test_supervisor_routes_general_to_end(
+        self, initial_state: Talk2Scholars, mock_cfg
+    ):
         """Verifies that non-search queries end the conversation"""
         llm_mock = Mock()
         llm_mock.invoke.return_value = AIMessage(content="General response")
 
-        supervisor = make_supervisor_node(llm_mock)
-        state = initial_state.copy()
+        # Extract the main_agent config
+        supervisor = make_supervisor_node(
+            llm_mock, mock_cfg.agents.talk2scholars.main_agent
+        )
+        state = initial_state
         state["messages"] = [HumanMessage(content="What is ML?")]
 
         result = supervisor(state)
@@ -90,9 +139,9 @@ class TestMainAgent:
 class TestS2Tools:
     """Unit tests for individual S2 tools"""
 
-    def test_display_results_shows_papers(self, initial_state):
+    def test_display_results_shows_papers(self, initial_state: Talk2Scholars):
         """Verifies display_results tool correctly returns papers from state"""
-        state = initial_state.copy()
+        state = initial_state
         state["papers"] = MOCK_STATE_PAPER
         result = display_results.invoke(input={"state": state})
         assert result == MOCK_STATE_PAPER
@@ -199,40 +248,6 @@ class TestS2Tools:
         assert "papers" in result.update
         assert len(result.update["messages"]) == 1
 
-    @patch("requests.get")
-    def test_single_paper_rec_empty_response(self, mock_get):
-        """Tests single paper recommendations with empty response"""
-        mock_get.return_value.json.return_value = {"recommendedPapers": []}
-        mock_get.return_value.status_code = 200
-
-        result = get_single_paper_recommendations.invoke(
-            input={
-                "paper_id": "123",
-                "limit": 1,
-                "tool_call_id": "test123",
-                "id": "test123",
-            }
-        )
-        assert "papers" in result.update
-        assert len(result.update["papers"]) == 0
-
-    @patch("requests.post")
-    def test_multi_paper_rec_empty_response(self, mock_post):
-        """Tests multi-paper recommendations with empty response"""
-        mock_post.return_value.json.return_value = {"recommendedPapers": []}
-        mock_post.return_value.status_code = 200
-
-        result = get_multi_paper_recommendations.invoke(
-            input={
-                "paper_ids": ["123", "456"],
-                "limit": 1,
-                "tool_call_id": "test123",
-                "id": "test123",
-            }
-        )
-        assert "papers" in result.update
-        assert len(result.update["papers"]) == 0
-
 
 def test_state_replace_dict():
     """Verifies state dictionary replacement works correctly"""
@@ -244,11 +259,13 @@ def test_state_replace_dict():
 
 
 @pytest.mark.integration
-def test_end_to_end_search_workflow(initial_state):
+def test_end_to_end_search_workflow(initial_state: Talk2Scholars, mock_cfg):
     """Integration test: Complete search workflow"""
     with (
         patch("requests.get") as mock_get,
         patch("langchain_openai.ChatOpenAI") as mock_llm,
+        patch("hydra.compose", return_value=mock_cfg),
+        patch("hydra.initialize"),
     ):
         mock_get.return_value.json.return_value = MOCK_SEARCH_RESPONSE
         mock_get.return_value.status_code = 200
@@ -258,7 +275,7 @@ def test_end_to_end_search_workflow(initial_state):
         mock_llm.return_value = llm_instance
 
         app = get_app("test_integration")
-        test_state = initial_state.copy()
+        test_state = initial_state
         test_state["messages"] = [HumanMessage(content="search for ML papers")]
 
         config = {

aiagents4pharma/talk2scholars/tools/s2/multi_paper_rec.py

@@ -8,7 +8,7 @@ multi_paper_rec: Tool for getting recommendations
 import json
 import logging
 from typing import Annotated, Any, Dict, List, Optional
-
+import hydra
 import pandas as pd
 import requests
 from langchain_core.messages import ToolMessage
@@ -40,6 +40,14 @@ class MultiPaperRecInput(BaseModel):
     model_config = {"arbitrary_types_allowed": True}
 
 
+# Load hydra configuration
+with hydra.initialize(version_base=None, config_path="../../configs"):
+    cfg = hydra.compose(
+        config_name="config", overrides=["tools/multi_paper_recommendation=default"]
+    )
+    cfg = cfg.tools.multi_paper_recommendation
+
+
 @tool(args_schema=MultiPaperRecInput)
 def get_multi_paper_recommendations(
     paper_ids: List[str],
@@ -62,12 +70,12 @@ def get_multi_paper_recommendations(
     """
     logging.info("Starting multi-paper recommendations search.")
 
-    endpoint = "https://api.semanticscholar.org/recommendations/v1/papers"
-    headers = {"Content-Type": "application/json"}
+    endpoint = cfg.api_endpoint
+    headers = cfg.headers
     payload = {"positivePaperIds": paper_ids, "negativePaperIds": []}
     params = {
         "limit": min(limit, 500),
-        "fields": "paperId,title,abstract,year,authors,citationCount,url",
+        "fields": ",".join(cfg.api_fields),
     }
 
     # Add year parameter if provided
@@ -80,7 +88,7 @@ def get_multi_paper_recommendations(
         headers=headers,
         params=params,
         data=json.dumps(payload),
-        timeout=10,
+        timeout=cfg.request_timeout,
     )
     logging.info(
         "API Response Status for multi-paper recommendations: %s", response.status_code

aiagents4pharma/talk2scholars/tools/s2/search.py

@@ -6,7 +6,7 @@ This tool is used to search for academic papers on Semantic Scholar.
 
 import logging
 from typing import Annotated, Any, Dict, Optional
-
+import hydra
 import pandas as pd
 import requests
 from langchain_core.messages import ToolMessage
@@ -34,6 +34,12 @@ class SearchInput(BaseModel):
     tool_call_id: Annotated[str, InjectedToolCallId]
 
 
+# Load hydra configuration
+with hydra.initialize(version_base=None, config_path="../../configs"):
+    cfg = hydra.compose(config_name="config", overrides=["tools/search=default"])
+    cfg = cfg.tools.search
+
+
 @tool(args_schema=SearchInput)
 def search_tool(
     query: str,
@@ -55,13 +61,13 @@ def search_tool(
         Dict[str, Any]: The search results and related information.
     """
     print("Starting paper search...")
-    endpoint = "https://api.semanticscholar.org/graph/v1/paper/search"
+    endpoint = cfg.api_endpoint
     params = {
         "query": query,
         "limit": min(limit, 100),
         # "fields": "paperId,title,abstract,year,authors,
         # citationCount,url,publicationTypes,openAccessPdf",
-        "fields": "paperId,title,abstract,year,authors,citationCount,url",
+        "fields": ",".join(cfg.api_fields),
     }
 
     # Add year parameter if provided

aiagents4pharma/talk2scholars/tools/s2/single_paper_rec.py

@@ -6,7 +6,7 @@ This tool is used to return recommendations for a single paper.
 
 import logging
 from typing import Annotated, Any, Dict, Optional
-
+import hydra
 import pandas as pd
 import requests
 from langchain_core.messages import ToolMessage
@@ -41,6 +41,14 @@ class SinglePaperRecInput(BaseModel):
     model_config = {"arbitrary_types_allowed": True}
 
 
+# Load hydra configuration
+with hydra.initialize(version_base=None, config_path="../../configs"):
+    cfg = hydra.compose(
+        config_name="config", overrides=["tools/single_paper_recommendation=default"]
+    )
+    cfg = cfg.tools.single_paper_recommendation
+
+
 @tool(args_schema=SinglePaperRecInput)
 def get_single_paper_recommendations(
     paper_id: str,
@@ -63,20 +71,18 @@ def get_single_paper_recommendations(
     """
     logger.info("Starting single paper recommendations search.")
 
-    endpoint = (
-        f"https://api.semanticscholar.org/recommendations/v1/papers/forpaper/{paper_id}"
-    )
+    endpoint = f"{cfg.api_endpoint}/{paper_id}"
     params = {
         "limit": min(limit, 500),  # Max 500 per API docs
-        "fields": "paperId,title,abstract,year,authors,citationCount,url",
-        "from": "all-cs",  # Using all-cs pool as specified in docs
+        "fields": ",".join(cfg.api_fields),
+        "from": cfg.recommendation_params.from_pool,
     }
 
     # Add year parameter if provided
     if year:
         params["year"] = year
 
-    response = requests.get(endpoint, params=params, timeout=10)
+    response = requests.get(endpoint, params=params, timeout=cfg.request_timeout)
     data = response.json()
     papers = data.get("data", [])
     response = requests.get(endpoint, params=params, timeout=10)

{aiagents4pharma-1.16.0.dist-info → aiagents4pharma-1.17.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.16.0
+Version: 1.17.0
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License

{aiagents4pharma-1.16.0.dist-info → aiagents4pharma-1.17.0.dist-info}/RECORD

@@ -82,24 +82,40 @@ aiagents4pharma/talk2knowledgegraphs/utils/embeddings/sentence_transformer.py,sh
 aiagents4pharma/talk2knowledgegraphs/utils/enrichments/__init__.py,sha256=tW426knki2DBIHcWyF_K04iMMdbpIn_e_TpPmTgz2dI,113
 aiagents4pharma/talk2knowledgegraphs/utils/enrichments/enrichments.py,sha256=Bx8x6zzk5614ApWB90N_iv4_Y_Uq0-KwUeBwYSdQMU4,924
 aiagents4pharma/talk2knowledgegraphs/utils/enrichments/ollama.py,sha256=8eoxR-VHo0G7ReQIwje7xEhE-SJlHdef7_wJRpnvFIc,4116
-aiagents4pharma/talk2scholars/__init__.py,sha256=haaikzND3c0Euqq86ndA4fl9q42aOop5rYG_8Zh1D-o,119
+aiagents4pharma/talk2scholars/__init__.py,sha256=gphERyVKZHvOnMQsml7TIHlaIshHJ75R1J3FKExkfuY,120
 aiagents4pharma/talk2scholars/agents/__init__.py,sha256=ykszlVGxz3egLHZAttlNoTPxIrnQJZYva_ssR8fwIFk,117
-aiagents4pharma/talk2scholars/agents/main_agent.py,sha256=HN3MkfHSDDlfzCKP79yAkpf3uyz3ZOCDGNRQ4gRL5RI,3854
-aiagents4pharma/talk2scholars/agents/s2_agent.py,sha256=HI037q-bq-bGf5DqtraSCWO493fAzUZ81lOEOCbMAaM,2486
-aiagents4pharma/talk2scholars/config/__init__.py,sha256=HyM6paOpKZ5_tZnyVheSAFmxjT6Mb3PxvWKfP0rz-dE,113
-aiagents4pharma/talk2scholars/config/config.py,sha256=jd4ltMBJyTztm9wT7j3ujOyYxL2SXRgxQJ4OZUBmCG4,5387
+aiagents4pharma/talk2scholars/agents/main_agent.py,sha256=etPQUCjHtD-in-kD7Wg_UD6jRtCHj-mj41y03PYbAQM,4616
+aiagents4pharma/talk2scholars/agents/s2_agent.py,sha256=0OlxNb8IEhd7JJNL8rRlr_U67iPgtGjbbAiJo9HFPdY,2737
+aiagents4pharma/talk2scholars/configs/__init__.py,sha256=tf2gz8n7M4ko6xLdX_C925ELVIxoP6SgkPcbeh59ad4,151
+aiagents4pharma/talk2scholars/configs/config.yaml,sha256=a3_jCFAmsVL6gZuvzoRe4jL94mQaSbp0CUXZDUtqhZA,254
+aiagents4pharma/talk2scholars/configs/agents/__init__.py,sha256=yyh7PB2oY_JulnpSQCWS4wwCH_uzIdt47O2Ay48x_oU,75
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/__init__.py,sha256=Tj4urOkjpu2cTlpJl0Fmr_18RZCR88vns-Gt-XquDzs,95
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/default.yaml,sha256=77DLch0YDiGslm3HerBaEDqKj1jLqI_jusHFbCchJDU,1617
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/default.yaml,sha256=6mgBvjifpHJ20kLwuwWr56UoZqmyf1luZnNWlYR6gnc,3135
+aiagents4pharma/talk2scholars/configs/app/__init__.py,sha256=JoSZV6N669kGMv5zLDszwf0ZjcRHx9TJfIqGhIIdPXE,70
+aiagents4pharma/talk2scholars/configs/app/frontend/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
+aiagents4pharma/talk2scholars/configs/app/frontend/default.yaml,sha256=BX-J1zQyb0QJ7hcOFOnkJ8aWoWbjK4WE2VG7OZTOyKU,821
+aiagents4pharma/talk2scholars/configs/tools/__init__.py,sha256=w0BJK0MR6Et8Pw1htP8JV0Lr9F_N68CqvbpV14KBy_8,151
+aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
+aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/default.yaml,sha256=70HSJ8WbS2Qbhur5FpuOPBjrea9g3TioM0gjGn6U1bE,369
+aiagents4pharma/talk2scholars/configs/tools/search/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
+aiagents4pharma/talk2scholars/configs/tools/search/default.yaml,sha256=NznRVqB6EamMfsFc5hj5s9ygzl6rPuFPiy9ikcpqp68,486
+aiagents4pharma/talk2scholars/configs/tools/single_paper_recommendation/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
+aiagents4pharma/talk2scholars/configs/tools/single_paper_recommendation/default.yaml,sha256=4_gTvdVc-hf9GNxBKMGQd72s5h53Zy09j9qeZ9Fys04,578
 aiagents4pharma/talk2scholars/state/__init__.py,sha256=S6SxlszIMZSIMJehjevPF9sKyR-PAwWb5TEdo6xWXE8,103
 aiagents4pharma/talk2scholars/state/state_talk2scholars.py,sha256=nwNRKdhoTXAtBGMMp6coMyUCaQVOnoGNqyjpKKw_FVM,998
 aiagents4pharma/talk2scholars/tests/__init__.py,sha256=U3PsTiUZaUBD1IZanFGkDIOdFieDVJtGKQ5-woYUo8c,45
-aiagents4pharma/talk2scholars/tests/test_langgraph.py,sha256=HcnahbazwaLaZg71OyCho2FLZ0ePedmv3XGvARFNe0g,9277
+aiagents4pharma/talk2scholars/tests/test_langgraph.py,sha256=36tWBmdewCZC8Yw1CCIpJxusGLCy21SVHhG1tR5C3TU,9605
 aiagents4pharma/talk2scholars/tools/__init__.py,sha256=YudBDRwaEzDnAcpxGZvEOfyh5-6xd51CTvTKTkywgXw,68
 aiagents4pharma/talk2scholars/tools/s2/__init__.py,sha256=9RQH3efTj6qkXk0ICKSc7Mzpkitt4gRGsQ1pGPrrREU,181
 aiagents4pharma/talk2scholars/tools/s2/display_results.py,sha256=B8JJGohi1Eyx8C3MhO_SiyQP3R6hPyUKJOAzcHmq3FU,584
-aiagents4pharma/talk2scholars/tools/s2/multi_paper_rec.py,sha256=FYLt47DAk6WOKfEk1Gj9zVvJGNyxA283PCp8IKW9U5M,4262
-aiagents4pharma/talk2scholars/tools/s2/search.py,sha256=pppjrQv5-8ep4fnqgTSBNgnbSnQsVIcNrRrH0p2TP1o,4025
-aiagents4pharma/talk2scholars/tools/s2/single_paper_rec.py,sha256=dAfUQxI7T5eu0eDxK8VAl7-JH0Wnw24CVkOQqwj-hXc,4810
-aiagents4pharma-1.16.0.dist-info/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
-aiagents4pharma-1.16.0.dist-info/METADATA,sha256=XH5jLQYNhAKOc4ixt5KovsExcjX14eEBrzTp40YluKY,8906
-aiagents4pharma-1.16.0.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-aiagents4pharma-1.16.0.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
-aiagents4pharma-1.16.0.dist-info/RECORD,,
+aiagents4pharma/talk2scholars/tools/s2/multi_paper_rec.py,sha256=0Y3q8TkF_Phng9L7g1kk9Fhyit9UNitWurp03H0GZv8,4455
+aiagents4pharma/talk2scholars/tools/s2/search.py,sha256=CcgFN7YuuQ9Vl1DJcldnnvPrswABKjNxeauK1rABps8,4176
+aiagents4pharma/talk2scholars/tools/s2/single_paper_rec.py,sha256=irS-igdG8BZbVb0Z4VlIjzsyBlUfREd0v0_RlUM-0_U,4994
+aiagents4pharma-1.17.0.dist-info/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
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+aiagents4pharma-1.17.0.dist-info/RECORD,,

aiagents4pharma/talk2scholars/config/config.py

@@ -1,110 +0,0 @@
-"""Configuration module for AI agents handling paper searches and recommendations."""
-
-
-# pylint: disable=R0903
-class Config:
-    """Configuration class containing prompts for AI agents.
-
-    This class stores prompt templates used by various AI agents in the system,
-    particularly for academic paper searches and recommendations.
-    """
-
-    MAIN_AGENT_PROMPT = (
-        "You are a supervisory AI agent that routes user queries to specialized tools.\n"
-        "Your task is to select the most appropriate tool based on the user's request.\n\n"
-        "Available tools and their capabilities:\n\n"
-        "1. semantic_scholar_agent:\n"
-        "   - Search for academic papers and research\n"
-        "   - Get paper recommendations\n"
-        "   - Find similar papers\n"
-        "   USE FOR: Any queries about finding papers, academic research, "
-        "or getting paper recommendations\n\n"
-        "ROUTING GUIDELINES:\n\n"
-        "ALWAYS route to semantic_scholar_agent for:\n"
-        "- Finding academic papers\n"
-        "- Searching research topics\n"
-        "- Getting paper recommendations\n"
-        "- Finding similar papers\n"
-        "- Any query about academic literature\n\n"
-        "Approach:\n"
-        "1. Identify the core need in the user's query\n"
-        "2. Select the most appropriate tool based on the guidelines above\n"
-        "3. If unclear, ask for clarification\n"
-        "4. For multi-step tasks, focus on the immediate next step\n\n"
-        "Remember:\n"
-        "- Be decisive in your tool selection\n"
-        "- Focus on the immediate task\n"
-        "- Default to semantic_scholar_agent for any paper-finding tasks\n"
-        "- Ask for clarification if the request is ambiguous\n\n"
-        "When presenting paper search results, always use this exact format:\n\n"
-        "Remember to:\n"
-        "- Always remember to add the url\n"
-        "- Put URLs on the title line itself as markdown\n"
-        "- Maintain consistent spacing and formatting"
-    )
-
-    S2_AGENT_PROMPT = (
-        "You are a specialized academic research assistant with access to the following tools:\n\n"
-        "1. search_papers:\n"
-        "   USE FOR: General paper searches\n"
-        "   - Enhances search terms automatically\n"
-        "   - Adds relevant academic keywords\n"
-        "   - Focuses on recent research when appropriate\n\n"
-        "2. get_single_paper_recommendations:\n"
-        "   USE FOR: Finding papers similar to a specific paper\n"
-        "   - Takes a single paper ID\n"
-        "   - Returns related papers\n\n"
-        "3. get_multi_paper_recommendations:\n"
-        "   USE FOR: Finding papers similar to multiple papers\n"
-        "   - Takes multiple paper IDs\n"
-        "   - Finds papers related to all inputs\n\n"
-        "GUIDELINES:\n\n"
-        "For paper searches:\n"
-        "- Enhance search terms with academic language\n"
-        "- Include field-specific terminology\n"
-        '- Add "recent" or "latest" when appropriate\n'
-        "- Keep queries focused and relevant\n\n"
-        "For paper recommendations:\n"
-        "- Identify paper IDs (40-character hexadecimal strings)\n"
-        "- Use single_paper_recommendations for one ID\n"
-        "- Use multi_paper_recommendations for multiple IDs\n\n"
-        "Best practices:\n"
-        "1. Start with a broad search if no paper IDs are provided\n"
-        "2. Look for paper IDs in user input\n"
-        "3. Enhance search terms for better results\n"
-        "4. Consider the academic context\n"
-        "5. Be prepared to refine searches based on feedback\n\n"
-        "Remember:\n"
-        "- Always select the most appropriate tool\n"
-        "- Enhance search queries naturally\n"
-        "- Consider academic context\n"
-        "- Focus on delivering relevant results\n\n"
-        "IMPORTANT GUIDELINES FOR PAPER RECOMMENDATIONS:\n\n"
-        "For Multiple Papers:\n"
-        "- When getting recommendations for multiple papers, always use "
-        "get_multi_paper_recommendations tool\n"
-        "- DO NOT call get_single_paper_recommendations multiple times\n"
-        "- Always pass all paper IDs in a single call to get_multi_paper_recommendations\n"
-        '- Use for queries like "find papers related to both/all papers" or '
-        '"find similar papers to these papers"\n\n'
-        "For Single Paper:\n"
-        "- Use get_single_paper_recommendations when focusing on one specific paper\n"
-        "- Pass only one paper ID at a time\n"
-        '- Use for queries like "find papers similar to this paper" or '
-        '"get recommendations for paper X"\n'
-        "- Do not use for multiple papers\n\n"
-        "Examples:\n"
-        '- For "find related papers for both papers":\n'
-        "  ✓ Use get_multi_paper_recommendations with both paper IDs\n"
-        "  × Don't make multiple calls to get_single_paper_recommendations\n\n"
-        '- For "find papers related to the first paper":\n'
-        "  ✓ Use get_single_paper_recommendations with just that paper's ID\n"
-        "  × Don't use get_multi_paper_recommendations\n\n"
-        "Remember:\n"
-        "- Be precise in identifying which paper ID to use for single recommendations\n"
-        "- Don't reuse previous paper IDs unless specifically requested\n"
-        "- For fresh paper recommendations, always use the original paper ID"
-    )
-
-
-config = Config()