aiagents4pharma 1.16.0__tar.gz → 1.17.1__tar.gz

aiagents4pharma-1.17.1/PKG-INFO

@@ -0,0 +1,150 @@
+Metadata-Version: 2.2
+Name: aiagents4pharma
+Version: 1.17.1
+Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: copasi_basico==0.78
+Requires-Dist: coverage==7.6.4
+Requires-Dist: einops==0.8.0
+Requires-Dist: gdown==5.2.0
+Requires-Dist: huggingface_hub==0.26.5
+Requires-Dist: hydra-core==1.3.2
+Requires-Dist: joblib==1.4.2
+Requires-Dist: langchain==0.3.7
+Requires-Dist: langchain-community==0.3.5
+Requires-Dist: langchain-core==0.3.31
+Requires-Dist: langchain-experimental==0.3.3
+Requires-Dist: langchain-openai==0.2.5
+Requires-Dist: langchain_ollama==0.2.2
+Requires-Dist: langgraph==0.2.66
+Requires-Dist: matplotlib==3.9.2
+Requires-Dist: openai==1.59.4
+Requires-Dist: ollama==0.4.6
+Requires-Dist: pandas==2.2.3
+Requires-Dist: plotly==5.24.1
+Requires-Dist: pydantic==2.9.2
+Requires-Dist: pylint==3.3.1
+Requires-Dist: pypdf==5.2.0
+Requires-Dist: pytest==8.3.3
+Requires-Dist: pytest-asyncio==0.25.2
+Requires-Dist: streamlit==1.39.0
+Requires-Dist: sentence_transformers==3.3.1
+Requires-Dist: tabulate==0.9.0
+Requires-Dist: torch==2.2.2
+Requires-Dist: torch_geometric==2.6.1
+Requires-Dist: tqdm==4.66.6
+Requires-Dist: transformers==4.48.0
+Requires-Dist: mkdocs==1.6.1
+Requires-Dist: mkdocs-jupyter==0.25.1
+Requires-Dist: mkdocs-material==9.5.47
+Requires-Dist: mkdocstrings-python==1.12.2
+Requires-Dist: mkdocs-include-markdown-plugin==7.1.2
+Requires-Dist: mkdocstrings==0.27.0
+Requires-Dist: streamlit-feedback
+
+[![Talk2BioModels](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml)
+[![Talk2Cells](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml)
+[![Talk2KnowledgeGraphs](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml)
+[![TESTS Talk2Scholars](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2scholars.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2scholars.yml)
+![GitHub Release](https://img.shields.io/github/v/release/VirtualPatientEngine/AIAgents4Pharma)
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
+
+
+## Introduction
+
+Welcome to **AIAgents4Pharma** – an open-source project by [Team VPE](https://github.com/VirtualPatientEngine) that brings together AI-driven tools to help researchers and pharma interact seamlessly with complex biological data.
+
+Our toolkit currently consists of the following agents:
+
+- **Talk2BioModels** _(v1 released; v2 in progress)_: Engage directly with mathematical models in systems biology.
+- **Talk2KnowledgeGraphs** _(v1 in progress)_: Access and explore complex biological knowledge graphs for insightful data connections.
+- **Talk2Scholars** _(v1 in progress)_: Get recommendations for articles related to your choice. Download, query, and write/retrieve them to your reference manager (currently supporting Zotero).
+- **Talk2Cells** _(v1 in progress)_: Query and analyze sequencing data with ease.
+
+![AIAgents4Pharma](docs/assets/AIAgents4Pharma.png)
+
+## Getting Started
+
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
+
+### Installation
+
+#### Option 1: PyPI
+
+```bash
+pip install aiagents4pharma
+```
+
+Check out the tutorials on each agent for detailed instrcutions.
+
+#### Option 2: git
+
+1. **Clone the repository:**
+   ```bash
+   git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma
+   cd AIAgents4Pharma
+   ```
+2. **Install dependencies:**
+   ```bash
+   pip install .
+   ```
+3. **Initialize OPENAI_API_KEY**
+   ```bash
+   export OPENAI_API_KEY=....
+   ```
+4. **[Optional] Initialize LANGSMITH_API_KEY**
+   ```bash
+   export LANGCHAIN_TRACING_V2=true
+   export LANGCHAIN_API_KEY=<your-api-key>
+   ```
+_Please note that this will create a new tracing project in your Langsmith
+account with the name `T2X-xxxx`, where `X` can be `B` (Biomodels), `S` (Scholars),
+`KG` (KnowledgeGraphs), or `C` (Cells). If you skip the previous step, it will
+default to the name `default`. `xxxx` will be the 4-digit ID created for the
+session._
+
+5. **Launch the app:**
+   ```bash
+   streamlit run app/frontend/streamlit_app_<agent>.py
+   ```
+_Replace <agent> with the agent name you are interested to launch._
+
+For detailed instructions on each agent, please refer to their respective modules.
+
+---
+
+## Contributing
+
+We welcome contributions to AIAgents4Pharma! Here’s how you can help:
+
+1. **Fork the repository**
+2. **Create a new branch** for your feature (`git checkout -b feat/feature-name`)
+3. **Commit your changes** (`git commit -m 'feat: Add new feature'`)
+4. **Push to the branch** (`git push origin feat/feature-name`)
+5. **Open a pull request** and reach out to any one of us below via Discussions:
+
+   _Note: We welcome all contributions, not just programming-related ones. Feel free to open bug reports, suggest new features, or participate as a beta tester. Your support is greatly appreciated!_
+
+- **Talk2Biomodels/Talk2Cells**: [@gurdeep330](https://github.com/gurdeep330) [@lilijap](https://github.com/lilijap) [@dmccloskey](https://github.com/dmccloskey)
+- **Talk2KnowledgeGraphs**: [@awmulyadi](https://github.com/awmulyadi) [@dmccloskey](https://github.com/dmccloskey)
+- **Talk2Scholars**: [@ansh-info](https://github.com/ansh-info) [@gurdeep330](https://github.com/gurdeep330) [@dmccloskey](https://github.com/dmccloskey)
+
+### Current Needs
+
+- **Beta testers** for Talk2BioModels and Talk2Scholars.
+- **Developers** with experience in Python and Bioinformatics and/or knowledge graphs for contributions to AIAgents4Pharma.
+
+Feel free to reach out to us via Discussions.
+
+Check out our [CONTRIBUTING.md](CONTRIBUTING.md) for more information.
+
+---
+
+## Feedback
+
+Questions/Bug reports/Feature requests/Comments/Suggestions? We welcome all. Please use `Isssues` or `Discussions` 😀

aiagents4pharma-1.17.1/README.md

@@ -0,0 +1,101 @@
+[![Talk2BioModels](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml)
+[![Talk2Cells](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml)
+[![Talk2KnowledgeGraphs](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml)
+[![TESTS Talk2Scholars](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2scholars.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2scholars.yml)
+![GitHub Release](https://img.shields.io/github/v/release/VirtualPatientEngine/AIAgents4Pharma)
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
+
+
+## Introduction
+
+Welcome to **AIAgents4Pharma** – an open-source project by [Team VPE](https://github.com/VirtualPatientEngine) that brings together AI-driven tools to help researchers and pharma interact seamlessly with complex biological data.
+
+Our toolkit currently consists of the following agents:
+
+- **Talk2BioModels** _(v1 released; v2 in progress)_: Engage directly with mathematical models in systems biology.
+- **Talk2KnowledgeGraphs** _(v1 in progress)_: Access and explore complex biological knowledge graphs for insightful data connections.
+- **Talk2Scholars** _(v1 in progress)_: Get recommendations for articles related to your choice. Download, query, and write/retrieve them to your reference manager (currently supporting Zotero).
+- **Talk2Cells** _(v1 in progress)_: Query and analyze sequencing data with ease.
+
+![AIAgents4Pharma](docs/assets/AIAgents4Pharma.png)
+
+## Getting Started
+
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
+
+### Installation
+
+#### Option 1: PyPI
+
+```bash
+pip install aiagents4pharma
+```
+
+Check out the tutorials on each agent for detailed instrcutions.
+
+#### Option 2: git
+
+1. **Clone the repository:**
+   ```bash
+   git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma
+   cd AIAgents4Pharma
+   ```
+2. **Install dependencies:**
+   ```bash
+   pip install .
+   ```
+3. **Initialize OPENAI_API_KEY**
+   ```bash
+   export OPENAI_API_KEY=....
+   ```
+4. **[Optional] Initialize LANGSMITH_API_KEY**
+   ```bash
+   export LANGCHAIN_TRACING_V2=true
+   export LANGCHAIN_API_KEY=<your-api-key>
+   ```
+_Please note that this will create a new tracing project in your Langsmith
+account with the name `T2X-xxxx`, where `X` can be `B` (Biomodels), `S` (Scholars),
+`KG` (KnowledgeGraphs), or `C` (Cells). If you skip the previous step, it will
+default to the name `default`. `xxxx` will be the 4-digit ID created for the
+session._
+
+5. **Launch the app:**
+   ```bash
+   streamlit run app/frontend/streamlit_app_<agent>.py
+   ```
+_Replace <agent> with the agent name you are interested to launch._
+
+For detailed instructions on each agent, please refer to their respective modules.
+
+---
+
+## Contributing
+
+We welcome contributions to AIAgents4Pharma! Here’s how you can help:
+
+1. **Fork the repository**
+2. **Create a new branch** for your feature (`git checkout -b feat/feature-name`)
+3. **Commit your changes** (`git commit -m 'feat: Add new feature'`)
+4. **Push to the branch** (`git push origin feat/feature-name`)
+5. **Open a pull request** and reach out to any one of us below via Discussions:
+
+   _Note: We welcome all contributions, not just programming-related ones. Feel free to open bug reports, suggest new features, or participate as a beta tester. Your support is greatly appreciated!_
+
+- **Talk2Biomodels/Talk2Cells**: [@gurdeep330](https://github.com/gurdeep330) [@lilijap](https://github.com/lilijap) [@dmccloskey](https://github.com/dmccloskey)
+- **Talk2KnowledgeGraphs**: [@awmulyadi](https://github.com/awmulyadi) [@dmccloskey](https://github.com/dmccloskey)
+- **Talk2Scholars**: [@ansh-info](https://github.com/ansh-info) [@gurdeep330](https://github.com/gurdeep330) [@dmccloskey](https://github.com/dmccloskey)
+
+### Current Needs
+
+- **Beta testers** for Talk2BioModels and Talk2Scholars.
+- **Developers** with experience in Python and Bioinformatics and/or knowledge graphs for contributions to AIAgents4Pharma.
+
+Feel free to reach out to us via Discussions.
+
+Check out our [CONTRIBUTING.md](CONTRIBUTING.md) for more information.
+
+---
+
+## Feedback
+
+Questions/Bug reports/Feature requests/Comments/Suggestions? We welcome all. Please use `Isssues` or `Discussions` 😀

{aiagents4pharma-1.16.0 → aiagents4pharma-1.17.1}/aiagents4pharma/__init__.py

@@ -3,7 +3,6 @@ This file is used to import aiagents4pharma modules.
 """
 
 from . import (
-    configs,
     talk2biomodels,
     talk2cells,
     talk2scholars,

{aiagents4pharma-1.16.0 → aiagents4pharma-1.17.1}/aiagents4pharma/talk2biomodels/__init__.py

@@ -6,3 +6,4 @@ from . import tools
 from . import agents
 from . import states
 from . import api
+from . import configs

{aiagents4pharma-1.16.0 → aiagents4pharma-1.17.1}/aiagents4pharma/talk2biomodels/agents/t2b_agent.py

@@ -55,10 +55,10 @@ def get_app(uniq_id, llm_model='gpt-4o-mini'):
     llm = ChatOpenAI(model=llm_model, temperature=0)
     # Load hydra configuration
     logger.log(logging.INFO, "Load Hydra configuration for Talk2BioModels agent.")
-    with hydra.initialize(version_base=None, config_path="../../configs"):
+    with hydra.initialize(version_base=None, config_path="../configs"):
         cfg = hydra.compose(config_name='config',
-                            overrides=['talk2biomodels/agents/t2b_agent=default'])
-        cfg = cfg.talk2biomodels.agents.t2b_agent
+                            overrides=['agents/t2b_agent=default'])
+        cfg = cfg.agents.t2b_agent
     logger.log(logging.INFO, "state_modifier: %s", cfg.state_modifier)
     # Create the agent
     model = create_react_agent(

{aiagents4pharma-1.16.0/aiagents4pharma/configs/talk2biomodels → aiagents4pharma-1.17.1/aiagents4pharma/talk2biomodels/configs}/agents/t2b_agent/default.yaml

@@ -1,4 +1,4 @@
-_target_: talk2biomodels.agents.t2b_agent.get_app
+_target_: agents.t2b_agent.get_app
 state_modifier: >
   You are Talk2BioModels agent.
   If the user asks for the uploaded model, 

{aiagents4pharma-1.16.0/aiagents4pharma/configs/talk2biomodels → aiagents4pharma-1.17.1/aiagents4pharma/talk2biomodels/configs}/tools/ask_question/default.yaml

@@ -1,4 +1,4 @@
-_target_: talk2biomodels.tools.ask_question.AskQuestionTool
+_target_: tools.ask_question.AskQuestionTool
 steady_state_prompt: >
   Following are header columns of the data:
   `species_name`: Name of the species,

{aiagents4pharma-1.16.0/aiagents4pharma/configs/talk2biomodels → aiagents4pharma-1.17.1/aiagents4pharma/talk2biomodels/configs}/tools/get_annotation/default.yaml

@@ -1,4 +1,4 @@
-_target_: talk2biomodels.tools.get_annotation.GetAnnotationTool
+_target_: tools.get_annotation.GetAnnotationTool
 prompt: >
   Given the user question, extract the relevant species names.
   If the user aks for a specific species, extract that species.

{aiagents4pharma-1.16.0 → aiagents4pharma-1.17.1}/aiagents4pharma/talk2biomodels/tools/ask_question.py

@@ -66,10 +66,10 @@ class AskQuestionTool(BaseTool):
                    question_context,
                    experiment_name)
         # Load hydra configuration
-        with hydra.initialize(version_base=None, config_path="../../configs"):
+        with hydra.initialize(version_base=None, config_path="../configs"):
             cfg = hydra.compose(config_name='config',
-                                overrides=['talk2biomodels/tools/ask_question=default'])
-            cfg = cfg.talk2biomodels.tools.ask_question
+                                overrides=['tools/ask_question=default'])
+            cfg = cfg.tools.ask_question
         # Get the context of the question
         # and based on the context, get the data
         # and prompt content to ask the question
@@ -111,5 +111,6 @@ class AskQuestionTool(BaseTool):
                         verbose=True,
                         prefix=prompt_content)
         # Invoke the agent with the question
-        llm_result = df_agent.invoke(question)
+        llm_result = df_agent.invoke(question, stream_mode=None)
+        # print (llm_result)
         return llm_result["output"]

{aiagents4pharma-1.16.0 → aiagents4pharma-1.17.1}/aiagents4pharma/talk2biomodels/tools/get_annotation.py

@@ -34,10 +34,10 @@ def extract_relevant_species_names(model_object, arg_data, state):
     Extract relevant species names based on the user question.
     """
     # Load hydra configuration
-    with hydra.initialize(version_base=None, config_path="../../configs"):
+    with hydra.initialize(version_base=None, config_path="../configs"):
         cfg = hydra.compose(config_name='config',
-                            overrides=['talk2biomodels/tools/get_annotation=default'])
-        cfg = cfg.talk2biomodels.tools.get_annotation
+                            overrides=['tools/get_annotation=default'])
+        cfg = cfg.tools.get_annotation
     logger.info("Loaded the following system prompt for the LLM"
                 " to get a structured output: %s", cfg.prompt)
 

{aiagents4pharma-1.16.0 → aiagents4pharma-1.17.1}/aiagents4pharma/talk2biomodels/tools/search_models.py

@@ -29,7 +29,7 @@ class SearchModelsTool(BaseTool):
     name: str = "search_models"
     description: str = "Search models in the BioMmodels database based on keywords."
     args_schema: Type[BaseModel] = SearchModelsInput
-    return_direct: bool = True
+    return_direct: bool = False
 
     def _run(self,
              query: str,

{aiagents4pharma-1.16.0 → aiagents4pharma-1.17.1}/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-1.17.1}/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-1.17.1}/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-1.17.1/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-1.16.0/aiagents4pharma/configs → aiagents4pharma-1.17.1/aiagents4pharma/talk2scholars/configs/agents}/__init__.py

@@ -1,5 +1,5 @@
-'''
+"""
 Import all the modules in the package
-'''
+"""
 
-from . import talk2biomodels
+from . import talk2scholars

aiagents4pharma-1.17.1/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-1.17.1/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/__init__.py

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

aiagents4pharma-1.17.1/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-1.17.1/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/__init__.py

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