aiagents4pharma 1.25.0__py3-none-any.whl → 1.25.1__py3-none-any.whl

aiagents4pharma/talk2aiagents4pharma/agents/main_agent.py

@@ -18,11 +18,14 @@ from ..states.state_talk2aiagents4pharma import Talk2AIAgents4Pharma
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
-def get_app(uniq_id,
-            llm_model: BaseChatModel = ChatOpenAI(model='gpt-4o-mini', temperature=0)):
+def get_app(uniq_id, llm_model: BaseChatModel):
     '''
     This function returns the langraph app.
     '''
+    if llm_model.model_name == 'gpt-4o-mini':
+        llm_model = ChatOpenAI(model='gpt-4o-mini',
+                               temperature=0,
+                               model_kwargs={"parallel_tool_calls": False})
     # Load hydra configuration
     logger.log(logging.INFO, "Launching AIAgents4Pharma_Agent with thread_id %s", uniq_id)
     with hydra.initialize(version_base=None, config_path="../configs"):
@@ -30,6 +33,19 @@ def get_app(uniq_id,
                             overrides=['agents/main_agent=default'])
         cfg = cfg.agents.main_agent
     logger.log(logging.INFO, "System_prompt of T2AA4P: %s", cfg.system_prompt)
+    with hydra.initialize(version_base=None, config_path="../../talk2biomodels/configs"):
+        cfg_t2b = hydra.compose(config_name='config',
+                            overrides=['agents/t2b_agent=default'])
+        cfg_t2b = cfg_t2b.agents.t2b_agent
+    with hydra.initialize(version_base=None, config_path="../../talk2knowledgegraphs/configs"):
+        cfg_t2kg = hydra.compose(config_name='config',
+                            overrides=['agents/t2kg_agent=default'])
+        cfg_t2kg = cfg_t2kg.agents.t2kg_agent
+    system_prompt = cfg.system_prompt
+    system_prompt += "\n\nHere is the system prompt of T2B agent\n"
+    system_prompt += cfg_t2b.state_modifier
+    system_prompt += "\n\nHere is the system prompt of T2KG agent\n"
+    system_prompt += cfg_t2kg.state_modifier
     # Create supervisor workflow
     workflow = create_supervisor(
         [
@@ -42,7 +58,7 @@ def get_app(uniq_id,
         # the tool artifacts
         output_mode="full_history",
         add_handoff_back_messages=False,
-        prompt=cfg.system_prompt
+        prompt=system_prompt
     )
 
     # Compile and run

aiagents4pharma/talk2aiagents4pharma/tests/test_main_agent.py

@@ -9,6 +9,7 @@ from ..agents.main_agent import get_app
 
 # Define the data path for the test files of Talk2KnowledgeGraphs agent
 DATA_PATH = "aiagents4pharma/talk2knowledgegraphs/tests/files"
+LLM_MODEL = ChatOpenAI(model="gpt-4o-mini", temperature=0.0)
 
 @pytest.fixture(name="input_dict")
 def input_dict_fixture():
@@ -44,7 +45,7 @@ def test_main_agent_invokes_t2kg(input_dict):
         input_dict: Input dictionary
     """
     # Prepare LLM and embedding model
-    input_dict["llm_model"] = ChatOpenAI(model="gpt-4o-mini", temperature=0.0)
+    input_dict["llm_model"] = LLM_MODEL
     input_dict["embedding_model"] = OpenAIEmbeddings(model="text-embedding-3-small")
 
     # Setup the app
@@ -88,7 +89,7 @@ def test_main_agent_invokes_t2b():
     Talk2BioModels agent.
     '''
     unique_id = 123
-    app = get_app(unique_id)
+    app = get_app(unique_id, llm_model=LLM_MODEL)
     config = {"configurable": {"thread_id": unique_id}}
     prompt = "Simulate model 64"
     # Invoke the agent

aiagents4pharma/talk2biomodels/agents/t2b_agent.py

@@ -7,7 +7,6 @@ This is the agent file for the Talk2BioModels agent.
 import logging
 from typing import Annotated
 import hydra
-from langchain_openai import ChatOpenAI
 from langchain_core.language_models.chat_models import BaseChatModel
 from langgraph.checkpoint.memory import MemorySaver
 from langgraph.graph import START, StateGraph
@@ -28,7 +27,7 @@ logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
 def get_app(uniq_id,
-            llm_model: BaseChatModel = ChatOpenAI(model='gpt-4o-mini', temperature=0)):
+            llm_model: BaseChatModel):
     '''
     This function returns the langraph app.
     '''
@@ -65,7 +64,8 @@ def get_app(uniq_id,
                 llm_model,
                 tools=tools,
                 state_schema=Talk2Biomodels,
-                state_modifier=cfg.state_modifier,
+                prompt=cfg.state_modifier,
+                version='v2',
                 checkpointer=MemorySaver()
             )
 

aiagents4pharma/talk2biomodels/tests/test_ask_question.py

@@ -11,7 +11,7 @@ def test_ask_question_tool():
     Test the ask_question tool without the simulation results.
     '''
     unique_id = 12345
-    app = get_app(unique_id)
+    app = get_app(unique_id, llm_model=ChatOpenAI(model='gpt-4o-mini', temperature=0))
     config = {"configurable": {"thread_id": unique_id}}
 
     ##########################################
@@ -20,9 +20,6 @@ def test_ask_question_tool():
     # simulation has not been run. In this
     # case, the tool should return an error
     ##########################################
-    # Update state
-    app.update_state(config,
-            {"llm_model": ChatOpenAI(model='gpt-4o-mini', temperature=0)})
     # Define the prompt
     prompt = "Call the ask_question tool to answer the "
     prompt += "question: What is the concentration of CRP "

aiagents4pharma/talk2biomodels/tests/test_get_annotation.py

@@ -9,17 +9,20 @@ from langchain_openai import ChatOpenAI
 from ..agents.t2b_agent import get_app
 from ..tools.get_annotation import prepare_content_msg
 
+LLM_MODEL = ChatOpenAI(model='gpt-4o-mini', temperature=0)
+
 @pytest.fixture(name="make_graph")
 def make_graph_fixture():
     '''
     Create an instance of the talk2biomodels agent.
     '''
     unique_id = random.randint(1000, 9999)
-    graph = get_app(unique_id)
+    graph = get_app(unique_id, llm_model=LLM_MODEL)
     config = {"configurable": {"thread_id": unique_id}}
-    graph.update_state(config, {"llm_model": ChatOpenAI(model='gpt-4o-mini',
-                                    temperature=0)
-                                })
+    graph.update_state(
+            config,
+            {"llm_model": LLM_MODEL}
+        )
     return graph, config
 
 def test_no_model_provided(make_graph):

aiagents4pharma/talk2biomodels/tests/test_getmodelinfo.py

@@ -3,14 +3,17 @@ Test cases for Talk2Biomodels get_modelinfo tool.
 '''
 
 from langchain_core.messages import HumanMessage, ToolMessage
+from langchain_openai import ChatOpenAI
 from ..agents.t2b_agent import get_app
 
+LLM_MODEL = ChatOpenAI(model='gpt-4o-mini',temperature=0)
+
 def test_get_modelinfo_tool():
     '''
     Test the get_modelinfo tool.
     '''
     unique_id = 12345
-    app = get_app(unique_id)
+    app = get_app(unique_id, LLM_MODEL)
     config = {"configurable": {"thread_id": unique_id}}
     # Update state
     app.update_state(config,
@@ -33,7 +36,7 @@ def test_model_with_no_species():
     This should raise a tool error.
     '''
     unique_id = 12345
-    app = get_app(unique_id)
+    app = get_app(unique_id, LLM_MODEL)
     config = {"configurable": {"thread_id": unique_id}}
     prompt = "Extract all species from model 20"
     # Test the tool get_modelinfo
@@ -64,7 +67,7 @@ def test_model_with_no_parameters():
     This should raise a tool error.
     '''
     unique_id = 12345
-    app = get_app(unique_id)
+    app = get_app(unique_id, LLM_MODEL)
     config = {"configurable": {"thread_id": unique_id}}
     prompt = "Extract all parameters from model 10"
     # Test the tool get_modelinfo

aiagents4pharma/talk2biomodels/tests/test_integration.py

@@ -14,9 +14,8 @@ def test_integration():
     Test the integration of the tools.
     '''
     unique_id = 1234567
-    app = get_app(unique_id)
+    app = get_app(unique_id, llm_model=LLM_MODEL)
     config = {"configurable": {"thread_id": unique_id}}
-    app.update_state(config, {"llm_model": LLM_MODEL})
     # ##########################################
     # ## Test simulate_model tool
     # ##########################################

aiagents4pharma/talk2biomodels/tests/test_param_scan.py

@@ -4,8 +4,11 @@ Test cases for Talk2Biomodels parameter scan tool.
 
 import pandas as pd
 from langchain_core.messages import HumanMessage, ToolMessage
+from langchain_openai import ChatOpenAI
 from ..agents.t2b_agent import get_app
 
+LLM_MODEL = ChatOpenAI(model='gpt-4o-mini', temperature=0)
+
 def test_param_scan_tool():
     '''
     In this test, we will test the parameter_scan tool.
@@ -27,9 +30,8 @@ def test_param_scan_tool():
 
     '''
     unique_id = 1234
-    app = get_app(unique_id)
+    app = get_app(unique_id, llm_model=LLM_MODEL)
     config = {"configurable": {"thread_id": unique_id}}
-    app.update_state(config, {"llm_model": "gpt-4o-mini"})
     prompt = """How will the value of Ab in serum in model 537 change
             if the param kIL6Rbind is varied from 1 to 100 in steps of 10?
             Set the initial `DoseQ2W` concentration to 300. Assume

aiagents4pharma/talk2biomodels/tests/test_query_article.py

@@ -8,6 +8,8 @@ from langchain_openai import ChatOpenAI
 from langchain_nvidia_ai_endpoints import NVIDIAEmbeddings
 from ..agents.t2b_agent import get_app
 
+LLM_MODEL = ChatOpenAI(model='gpt-4o-mini', temperature=0)
+
 class Article(BaseModel):
     '''
     Article schema.
@@ -19,7 +21,7 @@ def test_query_article_with_an_article():
     Test the query_article tool by providing an article.
     '''
     unique_id = 12345
-    app = get_app(unique_id)
+    app = get_app(unique_id, llm_model=LLM_MODEL)
     config = {"configurable": {"thread_id": unique_id}}
     # Update state by providing the pdf file name
     # and the text embedding model
@@ -35,7 +37,7 @@ def test_query_article_with_an_article():
     # Get the response from the tool
     assistant_msg = response["messages"][-1].content
     # Prepare a LLM that can be used as a judge
-    llm = ChatOpenAI(model='gpt-4o-mini', temperature=0)
+    llm = LLM_MODEL
     # Make it return a structured output
     structured_llm = llm.with_structured_output(Article)
     # Prepare a prompt for the judge
@@ -55,7 +57,7 @@ def test_query_article_without_an_article():
     The status of the tool should be error.
     '''
     unique_id = 12345
-    app = get_app(unique_id)
+    app = get_app(unique_id, llm_model=LLM_MODEL)
     config = {"configurable": {"thread_id": unique_id}}
     prompt = "What is the title of the uploaded article?"
     # Update state by providing the text embedding model

aiagents4pharma/talk2biomodels/tests/test_search_models.py

@@ -3,20 +3,23 @@ Test cases for Talk2Biomodels search models tool.
 '''
 
 from langchain_core.messages import HumanMessage, ToolMessage
-from langchain_nvidia_ai_endpoints import ChatNVIDIA
+from langchain_openai import ChatOpenAI
 from ..agents.t2b_agent import get_app
 
+LLM_MODEL = ChatOpenAI(model='gpt-4o-mini', temperature=0)
+
 def test_search_models_tool():
     '''
     Test the search_models tool.
     '''
     unique_id = 12345
-    app = get_app(unique_id)
+    app = get_app(unique_id, llm_model=LLM_MODEL)
     config = {"configurable": {"thread_id": unique_id}}
-    # Update state
-    app.update_state(config,
-            {"llm_model": ChatNVIDIA(model="meta/llama-3.3-70b-instruct")})
     prompt = "Search for models on Crohn's disease."
+    app.update_state(
+            config,
+            {"llm_model": LLM_MODEL}
+        )
     # Test the tool get_modelinfo
     response = app.invoke(
                         {"messages": [HumanMessage(content=prompt)]},

aiagents4pharma/talk2biomodels/tests/test_simulate_model.py

@@ -3,17 +3,19 @@ Test cases for Talk2Biomodels.
 '''
 
 from langchain_core.messages import HumanMessage
+from langchain_openai import ChatOpenAI
 from ..agents.t2b_agent import get_app
 
+LLM_MODEL = ChatOpenAI(model='gpt-4o-mini', temperature=0)
+
 def test_simulate_model_tool():
     '''
     Test the simulate_model tool when simulating
     multiple models.
     '''
     unique_id = 123
-    app = get_app(unique_id)
+    app = get_app(unique_id, llm_model=LLM_MODEL)
     config = {"configurable": {"thread_id": unique_id}}
-    app.update_state(config, {"llm_model": "gpt-4o-mini"})
     # Upload a model to the state
     app.update_state(config,
         {"sbml_file_path": ["aiagents4pharma/talk2biomodels/tests/BIOMD0000000449_url.xml"]})

aiagents4pharma/talk2biomodels/tests/test_steady_state.py

@@ -13,9 +13,12 @@ def test_steady_state_tool():
     Test the steady_state tool.
     '''
     unique_id = 123
-    app = get_app(unique_id)
+    app = get_app(unique_id, llm_model=LLM_MODEL)
     config = {"configurable": {"thread_id": unique_id}}
-    app.update_state(config, {"llm_model": LLM_MODEL})
+    app.update_state(
+            config,
+            {"llm_model": LLM_MODEL}
+        )
     #########################################################
     # In this case, we will test if the tool returns an error
     # when the model does not achieve a steady state. The tool

aiagents4pharma/talk2knowledgegraphs/agents/t2kg_agent.py

@@ -5,7 +5,6 @@ This is the agent file for the Talk2KnowledgeGraphs agent.
 import logging
 from typing import Annotated
 import hydra
-from langchain_ollama import ChatOllama
 from langchain_core.language_models.chat_models import BaseChatModel
 from langgraph.checkpoint.memory import MemorySaver
 from langgraph.graph import START, StateGraph
@@ -19,7 +18,7 @@ from ..states.state_talk2knowledgegraphs import Talk2KnowledgeGraphs
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
-def get_app(uniq_id, llm_model: BaseChatModel=ChatOllama(model='llama3.2:1b', temperature=0.0)):
+def get_app(uniq_id, llm_model: BaseChatModel):
     '''
     This function returns the langraph app.
     '''
@@ -54,7 +53,8 @@ def get_app(uniq_id, llm_model: BaseChatModel=ChatOllama(model='llama3.2:1b', te
                 llm_model,
                 tools=tools,
                 state_schema=Talk2KnowledgeGraphs,
-                state_modifier=cfg.state_modifier,
+                prompt=cfg.state_modifier,
+                version='v2',
                 checkpointer=MemorySaver()
             )
 

aiagents4pharma/talk2scholars/agents/main_agent.py

@@ -14,7 +14,6 @@ from pydantic import BaseModel
 import hydra
 from langchain_core.language_models.chat_models import BaseChatModel
 from langchain_core.messages import SystemMessage, HumanMessage, AIMessage
-from langchain_openai import ChatOpenAI
 from langgraph.checkpoint.memory import MemorySaver
 from langgraph.graph import END, START, StateGraph
 from langgraph.types import Command
@@ -119,7 +118,7 @@ def make_supervisor_node(llm_model: BaseChatModel, thread_id: str) -> Callable:
 
 def get_app(
     thread_id: str,
-    llm_model: BaseChatModel = ChatOpenAI(model="gpt-4o-mini", temperature=0),
+    llm_model: BaseChatModel
 ):
     """
     Initializes and returns the LangGraph-based hierarchical agent system.

aiagents4pharma/talk2scholars/agents/s2_agent.py

@@ -7,7 +7,6 @@ Agent for interacting with Semantic Scholar
 import logging
 from typing import Any, Dict
 import hydra
-from langchain_openai import ChatOpenAI
 from langchain_core.language_models.chat_models import BaseChatModel
 from langgraph.graph import START, StateGraph
 from langgraph.prebuilt import create_react_agent, ToolNode
@@ -30,7 +29,7 @@ logger = logging.getLogger(__name__)
 
 
 def get_app(
-    uniq_id, llm_model: BaseChatModel = ChatOpenAI(model="gpt-4o-mini", temperature=0)
+    uniq_id, llm_model: BaseChatModel
 ):
     """
     Initializes and returns the LangGraph application for the Semantic Scholar (S2) agent.

aiagents4pharma/talk2scholars/agents/zotero_agent.py

@@ -7,7 +7,7 @@ Agent for interacting with Zotero
 import logging
 from typing import Any, Dict
 import hydra
-from langchain_openai import ChatOpenAI
+
 from langchain_core.language_models.chat_models import BaseChatModel
 from langgraph.graph import START, StateGraph
 from langgraph.prebuilt import create_react_agent, ToolNode
@@ -26,7 +26,7 @@ logger = logging.getLogger(__name__)
 
 
 def get_app(
-    uniq_id, llm_model: BaseChatModel = ChatOpenAI(model="gpt-4o-mini", temperature=0)
+    uniq_id, llm_model: BaseChatModel
 ):
     """
     Initializes and returns the LangGraph application for the Zotero agent.

aiagents4pharma/talk2scholars/tests/test_call_s2.py

@@ -7,11 +7,12 @@ import pytest
 from langgraph.types import Command
 from langgraph.graph import END
 from langchain_core.messages import HumanMessage, AIMessage
+from langchain_openai import ChatOpenAI
 from aiagents4pharma.talk2scholars.agents.main_agent import get_app
 from aiagents4pharma.talk2scholars.state.state_talk2scholars import Talk2Scholars
 
 # pylint: disable=redefined-outer-name
-
+LLM_MODEL = ChatOpenAI(model='gpt-4o-mini', temperature=0)
 
 @pytest.fixture
 def mock_state():
@@ -68,7 +69,7 @@ def test_call_s2_agent(mock_state, mock_s2_agent, mock_supervisor, monkeypatch):
     )
 
     # Initialize the LangGraph application
-    app = get_app(thread_id="test_thread")
+    app = get_app(thread_id="test_thread", llm_model=LLM_MODEL)
 
     # Simulate running the workflow and provide required `configurable` parameters
     result = app.invoke(

aiagents4pharma/talk2scholars/tests/test_call_zotero.py

@@ -7,11 +7,12 @@ import pytest
 from langgraph.types import Command
 from langgraph.graph import END
 from langchain_core.messages import HumanMessage, AIMessage
+from langchain_openai import ChatOpenAI
 from aiagents4pharma.talk2scholars.agents.main_agent import get_app
 from aiagents4pharma.talk2scholars.state.state_talk2scholars import Talk2Scholars
 
 # pylint: disable=redefined-outer-name
-
+LLM_MODEL = ChatOpenAI(model='gpt-4o-mini', temperature=0)
 
 @pytest.fixture
 def test_state():
@@ -68,7 +69,7 @@ def test_zotero_integration(
     )
 
     # Initialize the LangGraph application
-    app = get_app(thread_id="test_thread")
+    app = get_app(thread_id="test_thread", llm_model=LLM_MODEL)
 
     # Run the full workflow (mocked Zotero agent is called)
     result = app.invoke(

aiagents4pharma/talk2scholars/tests/test_main_agent.py

@@ -63,9 +63,10 @@ def test_get_hydra_config():
 def test_hydra_failure():
     """Test exception handling when Hydra fails to load config."""
     thread_id = "test_thread"
+    llm_mock = Mock()
     with patch("hydra.initialize", side_effect=Exception("Hydra error")):
         with pytest.raises(Exception) as exc_info:
-            get_app(thread_id)
+            get_app(thread_id, llm_model=llm_mock)
         assert "Hydra error" in str(exc_info.value)
 
 

aiagents4pharma/talk2scholars/tests/test_s2_agent.py

@@ -6,9 +6,11 @@ Updated Unit Tests for the S2 agent (Semantic Scholar sub-agent).
 from unittest import mock
 import pytest
 from langchain_core.messages import HumanMessage, AIMessage
+from langchain_openai import ChatOpenAI
 from ..agents.s2_agent import get_app
 from ..state.state_talk2scholars import Talk2Scholars
 
+LLM_MODEL = ChatOpenAI(model='gpt-4o-mini', temperature=0)
 
 @pytest.fixture(autouse=True)
 def mock_hydra_fixture():
@@ -71,7 +73,7 @@ def test_s2_agent_initialization():
         "aiagents4pharma.talk2scholars.agents.s2_agent.create_react_agent"
     ) as mock_create:
         mock_create.return_value = mock.Mock()
-        app = get_app(thread_id)
+        app = get_app(thread_id, llm_model=LLM_MODEL)
         assert app is not None
         assert mock_create.called
 
@@ -89,7 +91,7 @@ def test_s2_agent_invocation():
             "messages": [AIMessage(content="Here are some AI papers")],
             "papers": {"id123": "AI Research Paper"},
         }
-        app = get_app(thread_id)
+        app = get_app(thread_id, llm_model=LLM_MODEL)
         result = app.invoke(
             mock_state,
             config={
@@ -122,7 +124,7 @@ def test_s2_agent_tools_assignment(request):
         mock_tool_instance = mock.Mock()
         mock_tool_instance.tools = mock_tools
         mock_toolnode.return_value = mock_tool_instance
-        get_app(thread_id)
+        get_app(thread_id, llm_model=LLM_MODEL)
         assert mock_toolnode.called
         assert len(mock_tool_instance.tools) == 6
 
@@ -146,7 +148,7 @@ def test_s2_query_results_tool():
             },  # Ensure the expected key is inside 'papers'
             "multi_papers": {},
         }
-        app = get_app(thread_id)
+        app = get_app(thread_id, llm_model=LLM_MODEL)
         result = app.invoke(
             mock_state,
             config={
@@ -180,7 +182,7 @@ def test_s2_retrieve_id_tool():
             },  # Ensure 'paper_id' is inside 'papers'
             "multi_papers": {},
         }
-        app = get_app(thread_id)
+        app = get_app(thread_id, llm_model=LLM_MODEL)
         result = app.invoke(
             mock_state,
             config={
@@ -200,5 +202,5 @@ def test_s2_agent_hydra_failure():
     thread_id = "test_thread"
     with mock.patch("hydra.initialize", side_effect=Exception("Hydra error")):
         with pytest.raises(Exception) as exc_info:
-            get_app(thread_id)
+            get_app(thread_id, llm_model=LLM_MODEL)
         assert "Hydra error" in str(exc_info.value)

aiagents4pharma/talk2scholars/tests/test_zotero_agent.py

@@ -6,9 +6,11 @@ Updated Unit Tests for the Zotero agent (Zotero Library Managent sub-agent).
 from unittest import mock
 import pytest
 from langchain_core.messages import HumanMessage, AIMessage
+from langchain_openai import ChatOpenAI
 from ..agents.zotero_agent import get_app
 from ..state.state_talk2scholars import Talk2Scholars
 
+LLM_MODEL = ChatOpenAI(model='gpt-4o-mini', temperature=0)
 
 @pytest.fixture(autouse=True)
 def mock_hydra_fixture():
@@ -61,7 +63,7 @@ def test_zotero_agent_initialization():
         "aiagents4pharma.talk2scholars.agents.zotero_agent.create_react_agent"
     ) as mock_create:
         mock_create.return_value = mock.Mock()
-        app = get_app(thread_id)
+        app = get_app(thread_id, llm_model=LLM_MODEL)
         assert app is not None
         assert mock_create.called
 
@@ -79,7 +81,7 @@ def test_zotero_agent_invocation():
             "messages": [AIMessage(content="Here are some AI papers")],
             "papers": {"id123": "AI Research Paper"},
         }
-        app = get_app(thread_id)
+        app = get_app(thread_id, llm_model=LLM_MODEL)
         result = app.invoke(
             mock_state,
             config={
@@ -112,7 +114,7 @@ def test_zotero_agent_tools_assignment(request):
         mock_tool_instance = mock.Mock()
         mock_tool_instance.tools = mock_tools
         mock_toolnode.return_value = mock_tool_instance
-        get_app(thread_id)
+        get_app(thread_id, llm_model=LLM_MODEL)
         assert mock_toolnode.called
         assert len(mock_tool_instance.tools) == 4
 
@@ -136,7 +138,7 @@ def test_s2_query_results_tool():
             },  # Ensure the expected key is inside 'papers'
             "multi_papers": {},
         }
-        app = get_app(thread_id)
+        app = get_app(thread_id, llm_model=LLM_MODEL)
         result = app.invoke(
             mock_state,
             config={
@@ -156,5 +158,5 @@ def test_zotero_agent_hydra_failure():
     thread_id = "test_thread"
     with mock.patch("hydra.initialize", side_effect=Exception("Hydra error")):
         with pytest.raises(Exception) as exc_info:
-            get_app(thread_id)
+            get_app(thread_id, llm_model=LLM_MODEL)
         assert "Hydra error" in str(exc_info.value)

{aiagents4pharma-1.25.0.dist-info → aiagents4pharma-1.25.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.25.0
+Version: 1.25.1
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
@@ -42,7 +42,6 @@ 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
@@ -56,7 +55,6 @@ Requires-Dist: h5py==3.13.0
 Requires-Dist: igraph==0.11.8
 Requires-Dist: ipykernel==6.29.5
 Requires-Dist: ipython==8.32.0
-Requires-Dist: numpy==2.1.3
 Requires-Dist: nbformat==5.10.4
 Requires-Dist: scipy==1.15.2
 Requires-Dist: tqdm==4.67.1
@@ -136,7 +134,7 @@ _Both `Talk2Biomodels` and `Talk2Scholars` are now available on Docker Hub._
      virtualpatientengine/talk2scholars
    ```
 
-3. **Access the Web App**  
+3. **Access the Web App**
     Open your browser and go to:
 
    ```
@@ -166,6 +164,33 @@ _Both `Talk2Biomodels` and `Talk2Scholars` are now available on Docker Hub._
    ```bash
    pip install -r requirements.txt
    ```
+   The current version of T2KG requires additional Ollama library to be installed.
+
+   Ollama can be easily downloaded and installed from the following link: [https://ollama.com/download](https://ollama.com/download)
+
+   As an alternative, use the following commands to install the library using terminal and to pull necessary model:
+
+   - Ubuntu:
+      ```
+      curl -fsSL https://ollama.com/install.sh | sh
+      ollama pull nomic-embed-text
+      ```
+   - Windows:
+      ```
+      curl -L https://ollama.com/download/ollama-windows-amd64.zip -o ollama-windows-amd64.zip
+      tar -xzf .\ollama-windows-amd64.zip
+      start ollama serve
+      ollama pull nomic-embed-text
+      ```
+   - macOS:
+      ```
+      brew install ollama
+      ollama pull nomic-embed-text
+      ```
+   A list of pulled Ollama models can be checked using the following command:
+   ```
+   ollama list
+   ```
 3. **Initialize OPENAI_API_KEY and NVIDIA_API_KEY**
 
    ```bash

{aiagents4pharma-1.25.0.dist-info → aiagents4pharma-1.25.1.dist-info}/RECORD

@@ -1,7 +1,7 @@
 aiagents4pharma/__init__.py,sha256=7xnvthMuxYurECWvyb0_yaPJ18SsqvmkKPTCxgbQlNQ,186
 aiagents4pharma/talk2aiagents4pharma/__init__.py,sha256=KOPe8cZ-ROQ6EGn8FeejRFUPokayKRMTgiXFyOpZGoA,122
 aiagents4pharma/talk2aiagents4pharma/agents/__init__.py,sha256=Cc1RitlLGzJ5d_dCSUdguZH417nlJux1qVCVS2M9t30,129
-aiagents4pharma/talk2aiagents4pharma/agents/main_agent.py,sha256=oVHYFXHmwq8y6e41JvmRYDXvCjItqY7setpcC2U2y6Q,1870
+aiagents4pharma/talk2aiagents4pharma/agents/main_agent.py,sha256=s0mrOk4DuAg7IkzB1YGyl_8wjxF2T_ReZENZirvjr94,2810
 aiagents4pharma/talk2aiagents4pharma/configs/__init__.py,sha256=5ah__-8XyRblwT0U1ByRigNjt_GyCheu7zce4aM-eZE,68
 aiagents4pharma/talk2aiagents4pharma/configs/config.yaml,sha256=VnbMbVSYfCh68cHZ0JLu00UjOUmapejN3EsN3lnBXtU,51
 aiagents4pharma/talk2aiagents4pharma/configs/agents/__init__.py,sha256=zrJcq-4m0YUKfSlRGC8KzBmEooaASKuL_Y75yDp-ZoA,72
@@ -9,10 +9,10 @@ aiagents4pharma/talk2aiagents4pharma/configs/agents/main_agent/default.yaml,sha2
 aiagents4pharma/talk2aiagents4pharma/states/__init__.py,sha256=3wSvCpM29oqvVjhbhabm7FNm9Zt0rHO5tEn63YW6doc,108
 aiagents4pharma/talk2aiagents4pharma/states/state_talk2aiagents4pharma.py,sha256=NxujEBDKubvpV9UG7ERTDRB6psr0XnObCNHyztLAhgo,485
 aiagents4pharma/talk2aiagents4pharma/tests/__init__.py,sha256=Jbw5tJxSrjGoaK5IX3pJWDCNzhrVQ10lkYq2oQ_KQD8,45
-aiagents4pharma/talk2aiagents4pharma/tests/test_main_agent.py,sha256=H8jcSZlzyt0wkijF_hgX8p63moXejbdP_W2xrWGTu3g,4122
+aiagents4pharma/talk2aiagents4pharma/tests/test_main_agent.py,sha256=ndHQT4ycWy-uKRAND7JmX_SuNg4g9hJw4UCW0CbKSp0,4165
 aiagents4pharma/talk2biomodels/__init__.py,sha256=1cq1HX2xoi_a0nDPuXYoSTrnL26OHQBW3zXNwwwjFO0,181
 aiagents4pharma/talk2biomodels/agents/__init__.py,sha256=sn5-fREjMdEvb-OUan3iOqrgYGjplNx3J8hYOaW0Po8,128
-aiagents4pharma/talk2biomodels/agents/t2b_agent.py,sha256=1NxSQbh5wbDpnap4mHwzSIjjHP1xakE2d1Pg5bHtDrE,3522
+aiagents4pharma/talk2biomodels/agents/t2b_agent.py,sha256=g0DIW5P-dtJoVyG4weFdDgTrJPL_Dx1MMbTWextJDZ4,3455
 aiagents4pharma/talk2biomodels/api/__init__.py,sha256=_GmDQqDLYpsUPUeE1nBNlT5AI9oTXIcqgOfNfvmonqA,123
 aiagents4pharma/talk2biomodels/api/kegg.py,sha256=QzYDAfJ16E7tbHGxP8ZNWRizMkMRS_HJuucueXEC1Gg,2943
 aiagents4pharma/talk2biomodels/api/ols.py,sha256=qq0Qy-gJDxanQW-HfCChDsTQsY1M41ua8hMlTnfuzrA,2202
@@ -36,17 +36,17 @@ aiagents4pharma/talk2biomodels/states/__init__.py,sha256=YLg1-N0D9qyRRLRqwqfLCLA
 aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py,sha256=S1UtXvocWR8Y9OVUp6pIDFnmaCcjbwmUbW8u79TuGcg,1508
 aiagents4pharma/talk2biomodels/tests/__init__.py,sha256=Jbw5tJxSrjGoaK5IX3pJWDCNzhrVQ10lkYq2oQ_KQD8,45
 aiagents4pharma/talk2biomodels/tests/test_api.py,sha256=7Kz2r5F5tjmn3F0LoM33oP-21W633936YHiyf5toGg0,1716
-aiagents4pharma/talk2biomodels/tests/test_ask_question.py,sha256=rdForKfj2zj2IXl6ntK9_I0AbgsCv8MXOZ2khBnaPms,1620
+aiagents4pharma/talk2biomodels/tests/test_ask_question.py,sha256=jrv0MUERirSjFz7gWwpZMMR0IqRgIMu0YMw4_LyECco,1555
 aiagents4pharma/talk2biomodels/tests/test_basico_model.py,sha256=-2g7HGHXsJeaE06FUI380Br3uh1Wb-JV51mgqcb3GJw,2423
-aiagents4pharma/talk2biomodels/tests/test_get_annotation.py,sha256=GbobfjtCAOV0HddM4pb2o3c49Q05fKIM0Ubnf8BRxHM,8273
-aiagents4pharma/talk2biomodels/tests/test_getmodelinfo.py,sha256=CIKeIm5FGTCyW-FR2nIo3Tr5AyAdxBelNngkdUd5-kk,3206
-aiagents4pharma/talk2biomodels/tests/test_integration.py,sha256=9nYRqpJ_OtmUypuHm4URzoHhcpKEldCEwKxLzh8jcZU,5193
+aiagents4pharma/talk2biomodels/tests/test_get_annotation.py,sha256=UGuLWhueSunZyg7vDTcKGMLNMfyg6UlAAUMG4j9o-fk,8282
+aiagents4pharma/talk2biomodels/tests/test_getmodelinfo.py,sha256=FtxdLZVC1iiFXfgbeaDhbvf-Pobmrn3OiVbHpjHxLTA,3338
+aiagents4pharma/talk2biomodels/tests/test_integration.py,sha256=ioeE1laUZDleRPc8AQKNeC8Q4Id5dWOA4dobiNEsCno,5159
 aiagents4pharma/talk2biomodels/tests/test_load_biomodel.py,sha256=Th5EVlfowwoM0tAu1R2oPISqW7SFduC-TYa3jIqIvC0,892
-aiagents4pharma/talk2biomodels/tests/test_param_scan.py,sha256=vRbnn4uVWFbfZbU4gVCjHi5WDCUrErut8ElzAPE5y84,2648
-aiagents4pharma/talk2biomodels/tests/test_query_article.py,sha256=lArISS111mQUZmjLY82PkRVPSTcN2h8KNF4gpTTvwL0,3185
-aiagents4pharma/talk2biomodels/tests/test_search_models.py,sha256=543uNSIPVLrD1mwH0Ru5l1tlTZ452MIr4aIgCssMw3g,1270
-aiagents4pharma/talk2biomodels/tests/test_simulate_model.py,sha256=GjLE1DZpcKUAFSmoHD86vkfK0b5LJPM8a4WYyraazig,1487
-aiagents4pharma/talk2biomodels/tests/test_steady_state.py,sha256=2bzxj74vekazgLG7hiMALRiqP_4sVmue9cN4zCZ42T8,3556
+aiagents4pharma/talk2biomodels/tests/test_param_scan.py,sha256=qnhDRlKLIPZbWHJdsxIYCUuM7CmfCGXIQ6_1NxKCHIE,2710
+aiagents4pharma/talk2biomodels/tests/test_query_article.py,sha256=6rB99N6wuh4P551Bdcj1M1VuaSoTbon358Yb-4nW3IQ,3250
+aiagents4pharma/talk2biomodels/tests/test_search_models.py,sha256=b7wU1cDPA_gvJ2eGouGD7r1RlWMQagn72E4ZzeoAkmE,1303
+aiagents4pharma/talk2biomodels/tests/test_simulate_model.py,sha256=BS6aNrjDCz5eSBj7xKOrljOydIJSvTxJ08hYG2y87J0,1549
+aiagents4pharma/talk2biomodels/tests/test_steady_state.py,sha256=_6oJAJn-8aP8glTANEBub0_Hnp--Yg9DlN0_8srVIxI,3611
 aiagents4pharma/talk2biomodels/tests/test_sys_bio_model.py,sha256=HSmBBViMi0jYf4gWX21IbppAfDzG0nr_S3KtKS9fZVQ,2165
 aiagents4pharma/talk2biomodels/tools/__init__.py,sha256=6H2HWv5Q4NZYEmw-Ti5KZnJlEqhaC2HXSDZa6kiSl-U,350
 aiagents4pharma/talk2biomodels/tools/ask_question.py,sha256=NZwKT7DHc4TW9e8LOkHaRG_nqUs_lEandvi89DTXilQ,4640
@@ -73,7 +73,7 @@ aiagents4pharma/talk2cells/tools/scp_agent/display_studies.py,sha256=6q59gh_NQai
 aiagents4pharma/talk2cells/tools/scp_agent/search_studies.py,sha256=MLe-twtFnOu-P8P9diYq7jvHBHbWFRRCZLcfpUzqPMg,2806
 aiagents4pharma/talk2knowledgegraphs/__init__.py,sha256=Z0Eo7LTiKk0STsr8VI7wkCLq7PHrK1vYlH4I1hSNLiA,165
 aiagents4pharma/talk2knowledgegraphs/agents/__init__.py,sha256=iOAzuy_8A03tQDFtSBhC9dldUo62z5gfxcVtXAdLOJs,92
-aiagents4pharma/talk2knowledgegraphs/agents/t2kg_agent.py,sha256=GdogSyTJa0LlSWPqDWdO41EXcS-PThatblPWpuHih-M,3125
+aiagents4pharma/talk2knowledgegraphs/agents/t2kg_agent.py,sha256=IcXSZ2qQA1m-gS-o0Pj_g1oar8uPdhsbaovloUFka3Q,3058
 aiagents4pharma/talk2knowledgegraphs/configs/__init__.py,sha256=4_DVdpahaJ55yPl0aZotlFA_MYWLFF2cubWyKtBVI_Q,126
 aiagents4pharma/talk2knowledgegraphs/configs/config.yaml,sha256=bag4w3JCSqaojG37MTksy3ZehAPe3qoVzjIN2uh3nrc,229
 aiagents4pharma/talk2knowledgegraphs/configs/agents/t2kg_agent/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
@@ -136,9 +136,9 @@ aiagents4pharma/talk2knowledgegraphs/utils/extractions/__init__.py,sha256=7gwwtf
 aiagents4pharma/talk2knowledgegraphs/utils/extractions/pcst.py,sha256=m5p0yoJb7I19ua5yeQfXPf7c4r6S1XPwttsrM7Qoy94,9336
 aiagents4pharma/talk2scholars/__init__.py,sha256=gphERyVKZHvOnMQsml7TIHlaIshHJ75R1J3FKExkfuY,120
 aiagents4pharma/talk2scholars/agents/__init__.py,sha256=WxEauzCzLEGyhdIRkxSBpNW5c_Uzf7iJUdM57IQkXH8,144
-aiagents4pharma/talk2scholars/agents/main_agent.py,sha256=ZJf1VAk2eA4Hxk8L7K2btiHTrv1CWRxebf4PAJbntuE,9487
-aiagents4pharma/talk2scholars/agents/s2_agent.py,sha256=XilKQvlxEVNYK5cEc44x-62OZZ1qG77v1r0FkwLexcw,4581
-aiagents4pharma/talk2scholars/agents/zotero_agent.py,sha256=E-w4avjDLviwrNOII0gVtHYLeO4wv2umykICJLZxfMU,4049
+aiagents4pharma/talk2scholars/agents/main_agent.py,sha256=nZIhOyEUSHECM4-wEHbDrfHRLkqoxW0H4fy6-MpA6N8,9397
+aiagents4pharma/talk2scholars/agents/s2_agent.py,sha256=ZiXtQVX2UbIyMOSXajuloWepEm7DKs6ZpPS0HgHzw0g,4492
+aiagents4pharma/talk2scholars/agents/zotero_agent.py,sha256=flIvg1ORaMiQpGEbsRM4zJHRNXi6UUv7emHDjH5HVY4,3961
 aiagents4pharma/talk2scholars/configs/__init__.py,sha256=tf2gz8n7M4ko6xLdX_C925ELVIxoP6SgkPcbeh59ad4,151
 aiagents4pharma/talk2scholars/configs/config.yaml,sha256=IBrHX_mACNb7R4rrI_zbWgscAMUdIAkOg9LDgLN1o28,386
 aiagents4pharma/talk2scholars/configs/agents/__init__.py,sha256=yyh7PB2oY_JulnpSQCWS4wwCH_uzIdt47O2Ay48x_oU,75
@@ -166,15 +166,15 @@ aiagents4pharma/talk2scholars/configs/tools/zotero_read/default.yaml,sha256=iILs
 aiagents4pharma/talk2scholars/state/__init__.py,sha256=S6SxlszIMZSIMJehjevPF9sKyR-PAwWb5TEdo6xWXE8,103
 aiagents4pharma/talk2scholars/state/state_talk2scholars.py,sha256=DoCtKP2qd69mXPwfOb-aYw9Hq2fYmx6b76S-HlsVSNo,2382
 aiagents4pharma/talk2scholars/tests/__init__.py,sha256=U3PsTiUZaUBD1IZanFGkDIOdFieDVJtGKQ5-woYUo8c,45
-aiagents4pharma/talk2scholars/tests/test_call_s2.py,sha256=kWvjWWjQC3LJuEVmOv5RnHpDqEeGzALZ5-esv65mQvU,3256
-aiagents4pharma/talk2scholars/tests/test_call_zotero.py,sha256=00854fAYJQtd96pb9zlBJ41WgCEWPEra0fwE7gxNnCk,3195
+aiagents4pharma/talk2scholars/tests/test_call_s2.py,sha256=ZL5HmnYNVyaBJgPGQi9JnbD1d1rtWnWusVxVRVW3aHc,3375
+aiagents4pharma/talk2scholars/tests/test_call_zotero.py,sha256=N4g6Pt2vuaxIhHQbIqlMaDUF4O7vIvRqa7pPIkpL8FI,3314
 aiagents4pharma/talk2scholars/tests/test_llm_main_integration.py,sha256=SAMG-Kb2S9sei8Us5vUWCUJikTKXPZVKQ6aJJPEhJsc,1880
-aiagents4pharma/talk2scholars/tests/test_main_agent.py,sha256=VS5M5sqL0rfSma_pxsGDOH-39K8pJJEbCfTocaWBTOc,4276
+aiagents4pharma/talk2scholars/tests/test_main_agent.py,sha256=8FKujCVhkurCe5IE6OGPTmz1p4eH1CDi467vM6VtM5A,4318
 aiagents4pharma/talk2scholars/tests/test_routing_logic.py,sha256=AZrvaEBDk51KL6edrZY3GpQ_N6VbrlADqXFeg_jxDoQ,2284
-aiagents4pharma/talk2scholars/tests/test_s2_agent.py,sha256=-yEoG2v5SMkCLCrSA2DFcNE-xMOSn97N4UTomzCeW40,7559
+aiagents4pharma/talk2scholars/tests/test_s2_agent.py,sha256=BhW1wGc-wUPS4fwNBQRtBXJaJ_i7L6t_G9Bq57fK7rI,7784
 aiagents4pharma/talk2scholars/tests/test_s2_tools.py,sha256=QEwraJk9_Kp6ZSGYyYDXWH62wIjSwi1Pptwwbx1fuG0,13176
 aiagents4pharma/talk2scholars/tests/test_state.py,sha256=_iHXvoZnU_eruf8l1sQKBSCIVnxNkH_9VzkVtZZA6bY,384
-aiagents4pharma/talk2scholars/tests/test_zotero_agent.py,sha256=sqoMo2nZPChRiTIb4kWKDLp8iPzCOEKSYcnj9XzE6wg,5932
+aiagents4pharma/talk2scholars/tests/test_zotero_agent.py,sha256=3TKz6yjNfYulaQv-MBv1zXCmR9xh9g3ju4Ge5HDdt1o,6136
 aiagents4pharma/talk2scholars/tests/test_zotero_tool.py,sha256=LI7KBTxPga7E-841pugjpNqtWgoIz0mDIJEZzdIL9eI,5759
 aiagents4pharma/talk2scholars/tools/__init__.py,sha256=-9iXVIGzFLak6a14Ib8yDg1bfiHgJz2nAhwWEk1jhOk,89
 aiagents4pharma/talk2scholars/tools/s2/__init__.py,sha256=wytqCmGm8Fbl8y5qLdIkxhhG8VHLYMifCGjbH_LK2Fc,258
@@ -186,8 +186,8 @@ aiagents4pharma/talk2scholars/tools/s2/search.py,sha256=i5KMFJWK31CjYtVT1McJpLzg
 aiagents4pharma/talk2scholars/tools/s2/single_paper_rec.py,sha256=7PoZfcstxDThWX6NYOgxN_9M_nwgMPAALch8OmjraVY,5568
 aiagents4pharma/talk2scholars/tools/zotero/__init__.py,sha256=1UW4r5ECvAwYpo1Fjf7lQPO--M8I85baYCHocFOAq4M,53
 aiagents4pharma/talk2scholars/tools/zotero/zotero_read.py,sha256=NJ65fAJ4u2Zq15uvEajVOhI4QnNvyqA6FHPaEDqvMw0,4321
-aiagents4pharma-1.25.0.dist-info/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
-aiagents4pharma-1.25.0.dist-info/METADATA,sha256=GcI8CTr7TUVIlC35PVwhhBi-5LEn6bTd2r3FVhtHCC4,9469
-aiagents4pharma-1.25.0.dist-info/WHEEL,sha256=jB7zZ3N9hIM9adW7qlTAyycLYW9npaWKLRzaoVcLKcM,91
-aiagents4pharma-1.25.0.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
-aiagents4pharma-1.25.0.dist-info/RECORD,,
+aiagents4pharma-1.25.1.dist-info/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
+aiagents4pharma-1.25.1.dist-info/METADATA,sha256=b6pqbn3KJ-oCdO-rupWLZegRk594gIE-tfA9BnFnBCg,10297
+aiagents4pharma-1.25.1.dist-info/WHEEL,sha256=jB7zZ3N9hIM9adW7qlTAyycLYW9npaWKLRzaoVcLKcM,91
+aiagents4pharma-1.25.1.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
+aiagents4pharma-1.25.1.dist-info/RECORD,,