aiagents4pharma 1.16.0__tar.gz → 1.17.0__tar.gz

{aiagents4pharma-1.16.0 → aiagents4pharma-1.17.0}/PKG-INFO

@@ -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 → aiagents4pharma-1.17.0}/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-1.16.0 → aiagents4pharma-1.17.0}/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-1.16.0 → aiagents4pharma-1.17.0}/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-1.16.0/aiagents4pharma/talk2scholars/config → aiagents4pharma-1.17.0/aiagents4pharma/talk2scholars/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-1.17.0/aiagents4pharma/talk2scholars/configs/agents/__init__.py

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

aiagents4pharma-1.17.0/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-1.17.0/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/__init__.py

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

aiagents4pharma-1.17.0/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
+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-1.17.0/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/__init__.py

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

aiagents4pharma-1.17.0/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-1.17.0/aiagents4pharma/talk2scholars/configs/app/__init__.py

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

aiagents4pharma-1.17.0/aiagents4pharma/talk2scholars/configs/app/frontend/__init__.py

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

aiagents4pharma-1.17.0/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-1.17.0/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-1.17.0/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-1.17.0/aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/__init__.py

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

aiagents4pharma-1.17.0/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-1.17.0/aiagents4pharma/talk2scholars/configs/tools/search/__init__.py

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

aiagents4pharma-1.17.0/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-1.17.0/aiagents4pharma/talk2scholars/configs/tools/single_paper_recommendation/__init__.py

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

aiagents4pharma-1.17.0/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