aiagents4pharma 1.25.0__tar.gz → 1.25.1__tar.gz

{aiagents4pharma-1.25.0 → aiagents4pharma-1.25.1}/PKG-INFO

@@ -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 → aiagents4pharma-1.25.1}/README.md

@@ -69,7 +69,7 @@ _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:
 
    ```
@@ -99,6 +99,33 @@ _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 → aiagents4pharma-1.25.1}/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-1.25.0 → aiagents4pharma-1.25.1}/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-1.25.0 → aiagents4pharma-1.25.1}/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-1.25.0 → aiagents4pharma-1.25.1}/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-1.25.0 → aiagents4pharma-1.25.1}/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-1.25.0 → aiagents4pharma-1.25.1}/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-1.25.0 → aiagents4pharma-1.25.1}/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-1.25.0 → aiagents4pharma-1.25.1}/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-1.25.0 → aiagents4pharma-1.25.1}/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-1.25.0 → aiagents4pharma-1.25.1}/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-1.25.0 → aiagents4pharma-1.25.1}/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-1.25.0 → aiagents4pharma-1.25.1}/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-1.25.0 → aiagents4pharma-1.25.1}/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-1.25.0 → aiagents4pharma-1.25.1}/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-1.25.0 → aiagents4pharma-1.25.1}/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-1.25.0 → aiagents4pharma-1.25.1}/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-1.25.0 → aiagents4pharma-1.25.1}/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-1.25.0 → aiagents4pharma-1.25.1}/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-1.25.0 → aiagents4pharma-1.25.1}/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-1.25.0 → aiagents4pharma-1.25.1}/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)