aiagents4pharma 1.15.2__tar.gz → 1.16.0__tar.gz

{aiagents4pharma-1.15.2 → aiagents4pharma-1.16.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.15.2
+Version: 1.16.0
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
@@ -50,11 +50,10 @@ 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)
-[![Talk2Competitors](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2competitors.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2competitors.yml)
+[![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)
 
-
 <h1 align="center" style="border-bottom: none;">🤖 AIAgents4Pharma</h1>
 
 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.
@@ -64,7 +63,7 @@ Our toolkit currently consists of three intelligent agents, each designed to sim
 - **Talk2BioModels**: Engage directly with mathematical models in systems biology.
 - **Talk2Cells** _(Work in progress)_: Query and analyze sequencing data with ease.
 - **Talk2KnowledgeGraphs** _(Work in progress)_: Access and explore complex biological knowledge graphs for insightful data connections.
-- **Talk2Competitors** _(Coming soon)_: Get recommendations for articles related to your choice. Download, query, and write/retrieve them to your reference manager (currently supporting Zotero).
+- **Talk2Scholars** _(Coming soon)_: Get recommendations for articles related to your choice. Download, query, and write/retrieve them to your reference manager (currently supporting Zotero).
 
 ---
 
@@ -87,7 +86,9 @@ Our toolkit currently consists of three intelligent agents, each designed to sim
 
 **Talk2KnowledgeGraphs** is an agent designed to enable interaction with biological knowledge graphs (KGs). KGs integrate vast amounts of structured biological data into a format that highlights relationships between entities, such as proteins, genes, and diseases.
 
-### 4. Talk2Competitors _(Coming soon)_
+### 4. Talk2Scholars _(Work in Progress)_
+
+Talk2Scholars is an AI-powered hierarchical agent system designed to revolutionize academic paper search and analysis. Through intelligent conversation, users can discover, analyze, and receive recommendations for academic papers using state-of-the-art natural language processing.
 
 ## Getting Started
 
@@ -198,7 +199,7 @@ Check out our [CONTRIBUTING.md](CONTRIBUTING.md) for more information.
 - **User Interface**: Interactive web UI for all agents.
 - **Talk2Cells**: Integration of sequencing data analysis tools.
 - **Talk2KnowledgeGraphs**: Interface for biological knowledge graph interaction.
-- **Talk2Competitors**: Interface for exploring articles
+- **Talk2Scholars**: Interface for exploring articles
 
 We’re excited to bring AIAgents4Pharma to the bioinformatics and pharmaceutical research community. Together, let’s make data-driven biological research more accessible and insightful.
 

{aiagents4pharma-1.15.2 → aiagents4pharma-1.16.0}/README.md

@@ -1,11 +1,10 @@
 [![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)
-[![Talk2Competitors](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2competitors.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2competitors.yml)
+[![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)
 
-
 <h1 align="center" style="border-bottom: none;">🤖 AIAgents4Pharma</h1>
 
 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.
@@ -15,7 +14,7 @@ Our toolkit currently consists of three intelligent agents, each designed to sim
 - **Talk2BioModels**: Engage directly with mathematical models in systems biology.
 - **Talk2Cells** _(Work in progress)_: Query and analyze sequencing data with ease.
 - **Talk2KnowledgeGraphs** _(Work in progress)_: Access and explore complex biological knowledge graphs for insightful data connections.
-- **Talk2Competitors** _(Coming soon)_: Get recommendations for articles related to your choice. Download, query, and write/retrieve them to your reference manager (currently supporting Zotero).
+- **Talk2Scholars** _(Coming soon)_: Get recommendations for articles related to your choice. Download, query, and write/retrieve them to your reference manager (currently supporting Zotero).
 
 ---
 
@@ -38,7 +37,9 @@ Our toolkit currently consists of three intelligent agents, each designed to sim
 
 **Talk2KnowledgeGraphs** is an agent designed to enable interaction with biological knowledge graphs (KGs). KGs integrate vast amounts of structured biological data into a format that highlights relationships between entities, such as proteins, genes, and diseases.
 
-### 4. Talk2Competitors _(Coming soon)_
+### 4. Talk2Scholars _(Work in Progress)_
+
+Talk2Scholars is an AI-powered hierarchical agent system designed to revolutionize academic paper search and analysis. Through intelligent conversation, users can discover, analyze, and receive recommendations for academic papers using state-of-the-art natural language processing.
 
 ## Getting Started
 
@@ -149,7 +150,7 @@ Check out our [CONTRIBUTING.md](CONTRIBUTING.md) for more information.
 - **User Interface**: Interactive web UI for all agents.
 - **Talk2Cells**: Integration of sequencing data analysis tools.
 - **Talk2KnowledgeGraphs**: Interface for biological knowledge graph interaction.
-- **Talk2Competitors**: Interface for exploring articles
+- **Talk2Scholars**: Interface for exploring articles
 
 We’re excited to bring AIAgents4Pharma to the bioinformatics and pharmaceutical research community. Together, let’s make data-driven biological research more accessible and insightful.
 

{aiagents4pharma-1.15.2 → aiagents4pharma-1.16.0}/aiagents4pharma/__init__.py

@@ -6,6 +6,6 @@ from . import (
     configs,
     talk2biomodels,
     talk2cells,
-    talk2competitors,
+    talk2scholars,
     talk2knowledgegraphs,
 )

{aiagents4pharma-1.15.2/aiagents4pharma/talk2competitors → aiagents4pharma-1.16.0/aiagents4pharma/talk2scholars}/agents/main_agent.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 
 """
-Main agent for the talk2competitors app.
+Main agent for the talk2scholars app.
 """
 
 import logging
@@ -15,7 +15,7 @@ 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_talk2competitors import Talk2Competitors
+from ..state.state_talk2scholars import Talk2Scholars
 
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
@@ -34,12 +34,12 @@ def make_supervisor_node(llm: BaseChatModel) -> str:
     """
     # options = ["FINISH", "s2_agent"]
 
-    def supervisor_node(state: Talk2Competitors) -> Command[Literal["s2_agent", "__end__"]]:
+    def supervisor_node(state: Talk2Scholars) -> Command[Literal["s2_agent", "__end__"]]:
         """
         Supervisor node that routes to appropriate sub-agents.
 
         Args:
-            state (Talk2Competitors): The current state of the conversation.
+            state (Talk2Scholars): The current state of the conversation.
 
         Returns:
             Command[Literal["s2_agent", "__end__"]]: The command to execute next.
@@ -91,12 +91,12 @@ def get_app(thread_id: str, llm_model ='gpt-4o-mini') -> StateGraph:
     Returns:
         The compiled langraph app.
     """
-    def call_s2_agent(state: Talk2Competitors) -> Command[Literal["__end__"]]:
+    def call_s2_agent(state: Talk2Scholars) -> Command[Literal["__end__"]]:
         """
         Node for calling the S2 agent.
 
         Args:
-            state (Talk2Competitors): The current state of the conversation.
+            state (Talk2Scholars): The current state of the conversation.
 
         Returns:
             Command[Literal["__end__"]]: The command to execute next.
@@ -115,7 +115,7 @@ def get_app(thread_id: str, llm_model ='gpt-4o-mini') -> StateGraph:
             },
         )
     llm = ChatOpenAI(model=llm_model, temperature=0)
-    workflow = StateGraph(Talk2Competitors)
+    workflow = StateGraph(Talk2Scholars)
 
     supervisor = make_supervisor_node(llm)
     workflow.add_node("supervisor", supervisor)

{aiagents4pharma-1.15.2/aiagents4pharma/talk2competitors → aiagents4pharma-1.16.0/aiagents4pharma/talk2scholars}/agents/s2_agent.py

@@ -11,7 +11,7 @@ from langgraph.graph import START, StateGraph
 from langgraph.prebuilt import create_react_agent
 from langgraph.checkpoint.memory import MemorySaver
 from ..config.config import config
-from ..state.state_talk2competitors import Talk2Competitors
+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
@@ -28,7 +28,7 @@ def get_app(uniq_id, llm_model='gpt-4o-mini'):
     '''
     This function returns the langraph app.
     '''
-    def agent_s2_node(state: Talk2Competitors):
+    def agent_s2_node(state: Talk2Scholars):
         '''
         This function calls the model.
         '''
@@ -47,13 +47,13 @@ def get_app(uniq_id, llm_model='gpt-4o-mini'):
     model = create_react_agent(
                             llm,
                             tools=tools,
-                            state_schema=Talk2Competitors,
+                            state_schema=Talk2Scholars,
                             state_modifier=config.S2_AGENT_PROMPT,
                             checkpointer=MemorySaver()
                         )
 
     # Define a new graph
-    workflow = StateGraph(Talk2Competitors)
+    workflow = StateGraph(Talk2Scholars)
 
     # Define the two nodes we will cycle between
     workflow.add_node("agent_s2", agent_s2_node)

{aiagents4pharma-1.15.2/aiagents4pharma/talk2competitors → aiagents4pharma-1.16.0/aiagents4pharma/talk2scholars}/state/__init__.py

@@ -2,4 +2,4 @@
 This file is used to import all the modules in the package.
 '''
 
-from . import state_talk2competitors
+from . import state_talk2scholars

aiagents4pharma-1.15.2/aiagents4pharma/talk2competitors/state/state_talk2competitors.py → aiagents4pharma-1.16.0/aiagents4pharma/talk2scholars/state/state_talk2scholars.py

@@ -1,5 +1,5 @@
 """
-This is the state file for the talk2comp agent.
+This is the state file for the talk2scholars agent.
 """
 
 import logging
@@ -19,9 +19,9 @@ def replace_dict(existing: Dict[str, Any], new: Dict[str, Any]) -> Dict[str, Any
     return new
 
 
-class Talk2Competitors(AgentState):
+class Talk2Scholars(AgentState):
     """
-    The state for the talk2comp agent, inheriting from AgentState.
+    The state for the talk2scholars agent, inheriting from AgentState.
     """
 
     papers: Annotated[Dict[str, Any], replace_dict]  # Changed from List to Dict

{aiagents4pharma-1.15.2/aiagents4pharma/talk2competitors → aiagents4pharma-1.16.0/aiagents4pharma/talk2scholars}/tests/test_langgraph.py

@@ -1,5 +1,5 @@
 """
-Unit and integration tests for Talk2Competitors system.
+Unit and integration tests for Talk2Scholars system.
 Each test focuses on a single, specific functionality.
 Tests are deterministic and independent of each other.
 """
@@ -10,7 +10,7 @@ import pytest
 from langchain_core.messages import AIMessage, HumanMessage
 
 from ..agents.main_agent import get_app, make_supervisor_node
-from ..state.state_talk2competitors import replace_dict
+from ..state.state_talk2scholars import replace_dict
 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

{aiagents4pharma-1.15.2 → aiagents4pharma-1.16.0}/aiagents4pharma.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.15.2
+Version: 1.16.0
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
@@ -50,11 +50,10 @@ 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)
-[![Talk2Competitors](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2competitors.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2competitors.yml)
+[![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)
 
-
 <h1 align="center" style="border-bottom: none;">🤖 AIAgents4Pharma</h1>
 
 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.
@@ -64,7 +63,7 @@ Our toolkit currently consists of three intelligent agents, each designed to sim
 - **Talk2BioModels**: Engage directly with mathematical models in systems biology.
 - **Talk2Cells** _(Work in progress)_: Query and analyze sequencing data with ease.
 - **Talk2KnowledgeGraphs** _(Work in progress)_: Access and explore complex biological knowledge graphs for insightful data connections.
-- **Talk2Competitors** _(Coming soon)_: Get recommendations for articles related to your choice. Download, query, and write/retrieve them to your reference manager (currently supporting Zotero).
+- **Talk2Scholars** _(Coming soon)_: Get recommendations for articles related to your choice. Download, query, and write/retrieve them to your reference manager (currently supporting Zotero).
 
 ---
 
@@ -87,7 +86,9 @@ Our toolkit currently consists of three intelligent agents, each designed to sim
 
 **Talk2KnowledgeGraphs** is an agent designed to enable interaction with biological knowledge graphs (KGs). KGs integrate vast amounts of structured biological data into a format that highlights relationships between entities, such as proteins, genes, and diseases.
 
-### 4. Talk2Competitors _(Coming soon)_
+### 4. Talk2Scholars _(Work in Progress)_
+
+Talk2Scholars is an AI-powered hierarchical agent system designed to revolutionize academic paper search and analysis. Through intelligent conversation, users can discover, analyze, and receive recommendations for academic papers using state-of-the-art natural language processing.
 
 ## Getting Started
 
@@ -198,7 +199,7 @@ Check out our [CONTRIBUTING.md](CONTRIBUTING.md) for more information.
 - **User Interface**: Interactive web UI for all agents.
 - **Talk2Cells**: Integration of sequencing data analysis tools.
 - **Talk2KnowledgeGraphs**: Interface for biological knowledge graph interaction.
-- **Talk2Competitors**: Interface for exploring articles
+- **Talk2Scholars**: Interface for exploring articles
 
 We’re excited to bring AIAgents4Pharma to the bioinformatics and pharmaceutical research community. Together, let’s make data-driven biological research more accessible and insightful.
 

{aiagents4pharma-1.15.2 → aiagents4pharma-1.16.0}/aiagents4pharma.egg-info/SOURCES.txt

@@ -66,22 +66,6 @@ aiagents4pharma/talk2cells/tools/__init__.py
 aiagents4pharma/talk2cells/tools/scp_agent/__init__.py
 aiagents4pharma/talk2cells/tools/scp_agent/display_studies.py
 aiagents4pharma/talk2cells/tools/scp_agent/search_studies.py
-aiagents4pharma/talk2competitors/__init__.py
-aiagents4pharma/talk2competitors/agents/__init__.py
-aiagents4pharma/talk2competitors/agents/main_agent.py
-aiagents4pharma/talk2competitors/agents/s2_agent.py
-aiagents4pharma/talk2competitors/config/__init__.py
-aiagents4pharma/talk2competitors/config/config.py
-aiagents4pharma/talk2competitors/state/__init__.py
-aiagents4pharma/talk2competitors/state/state_talk2competitors.py
-aiagents4pharma/talk2competitors/tests/__init__.py
-aiagents4pharma/talk2competitors/tests/test_langgraph.py
-aiagents4pharma/talk2competitors/tools/__init__.py
-aiagents4pharma/talk2competitors/tools/s2/__init__.py
-aiagents4pharma/talk2competitors/tools/s2/display_results.py
-aiagents4pharma/talk2competitors/tools/s2/multi_paper_rec.py
-aiagents4pharma/talk2competitors/tools/s2/search.py
-aiagents4pharma/talk2competitors/tools/s2/single_paper_rec.py
 aiagents4pharma/talk2knowledgegraphs/__init__.py
 aiagents4pharma/talk2knowledgegraphs/datasets/__init__.py
 aiagents4pharma/talk2knowledgegraphs/datasets/biobridge_primekg.py
@@ -106,4 +90,20 @@ aiagents4pharma/talk2knowledgegraphs/utils/embeddings/huggingface.py
 aiagents4pharma/talk2knowledgegraphs/utils/embeddings/sentence_transformer.py
 aiagents4pharma/talk2knowledgegraphs/utils/enrichments/__init__.py
 aiagents4pharma/talk2knowledgegraphs/utils/enrichments/enrichments.py
-aiagents4pharma/talk2knowledgegraphs/utils/enrichments/ollama.py
+aiagents4pharma/talk2knowledgegraphs/utils/enrichments/ollama.py
+aiagents4pharma/talk2scholars/__init__.py
+aiagents4pharma/talk2scholars/agents/__init__.py
+aiagents4pharma/talk2scholars/agents/main_agent.py
+aiagents4pharma/talk2scholars/agents/s2_agent.py
+aiagents4pharma/talk2scholars/config/__init__.py
+aiagents4pharma/talk2scholars/config/config.py
+aiagents4pharma/talk2scholars/state/__init__.py
+aiagents4pharma/talk2scholars/state/state_talk2scholars.py
+aiagents4pharma/talk2scholars/tests/__init__.py
+aiagents4pharma/talk2scholars/tests/test_langgraph.py
+aiagents4pharma/talk2scholars/tools/__init__.py
+aiagents4pharma/talk2scholars/tools/s2/__init__.py
+aiagents4pharma/talk2scholars/tools/s2/display_results.py
+aiagents4pharma/talk2scholars/tools/s2/multi_paper_rec.py
+aiagents4pharma/talk2scholars/tools/s2/search.py
+aiagents4pharma/talk2scholars/tools/s2/single_paper_rec.py

aiagents4pharma-1.16.0/release_version.txt

@@ -0,0 +1 @@
+v1.16.0

aiagents4pharma-1.15.2/release_version.txt

@@ -1 +0,0 @@
-v1.15.2