aiagents4pharma 1.17.0__tar.gz → 1.18.0__tar.gz

aiagents4pharma-1.18.0/PKG-INFO

@@ -0,0 +1,157 @@
+Metadata-Version: 2.2
+Name: aiagents4pharma
+Version: 1.18.0
+Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+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-nvidia-ai-endpoints==0.3.9
+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 and NVIDIA_API_KEY**
+   ```bash
+   export OPENAI_API_KEY=....
+   ```
+   ```bash
+   export NVIDIA_API_KEY=....
+   ```
+_You can create a free account at NVIDIA and apply for their
+free credits [here](https://build.nvidia.com/explore/discover)._
+
+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-1.18.0/README.md

@@ -0,0 +1,107 @@
+[![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 and NVIDIA_API_KEY**
+   ```bash
+   export OPENAI_API_KEY=....
+   ```
+   ```bash
+   export NVIDIA_API_KEY=....
+   ```
+_You can create a free account at NVIDIA and apply for their
+free credits [here](https://build.nvidia.com/explore/discover)._
+
+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-1.17.0 → aiagents4pharma-1.18.0}/aiagents4pharma/__init__.py

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

{aiagents4pharma-1.17.0 → aiagents4pharma-1.18.0}/aiagents4pharma/talk2biomodels/__init__.py

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

{aiagents4pharma-1.17.0 → aiagents4pharma-1.18.0}/aiagents4pharma/talk2biomodels/agents/t2b_agent.py

@@ -8,6 +8,7 @@ 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
 from langgraph.prebuilt import create_react_agent, ToolNode, InjectedState
@@ -26,7 +27,8 @@ from ..states.state_talk2biomodels import Talk2Biomodels
 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: BaseChatModel = ChatOpenAI(model='gpt-4o-mini', temperature=0)):
     '''
     This function returns the langraph app.
     '''
@@ -51,18 +53,16 @@ def get_app(uniq_id, llm_model='gpt-4o-mini'):
                     QueryArticle()
                 ])
 
-    # Define the model
-    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(
-                llm,
+                llm_model,
                 tools=tools,
                 state_schema=Talk2Biomodels,
                 state_modifier=cfg.state_modifier,

{aiagents4pharma-1.17.0/aiagents4pharma/configs/talk2biomodels → aiagents4pharma-1.18.0/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-1.17.0/aiagents4pharma/configs/talk2biomodels → aiagents4pharma-1.18.0/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,
@@ -10,22 +10,14 @@ steady_state_prompt: >
 
   Here are some instructions to help you answer questions:
 
-  1. Before you answer any question, follow the plan and solve
-  technique. Start by understanding the question, then plan your
-  approach to solve the question, and finally solve the question
-  by following the plan. Always give a brief explanation of your
-  answer to the user.
+  1. If the user wants to know the time taken by the model to reach
+  steady state, you should look at the `steady_state_transition_time`
+  column of the data for the model species.
+  
+  2. The highest value in the column `steady_state_transition_time`
+  is the time taken by the model to reach steady state.
 
-  2. If the user wants to know the time taken by the model to reach
-  steady state, you should look at the steady_state_transition_time
-  column of the data for the model species. The highest value in
-  this column is the time taken by the model to reach steady state.
-
-  3. To get accurate results, trim the data to the relevant columns
-  before performing any calculations. This will help you avoid
-  errors in your calculations, and ignore irrelevant data.
-
-  4. Please use the units provided below to answer the questions.
+  3. Please use the units provided below to answer the questions.
 simulation_prompt: >
   Following is the information about the data frame:
   1. First column is the time column, and the rest of the columns

{aiagents4pharma-1.17.0/aiagents4pharma/configs/talk2biomodels → aiagents4pharma-1.18.0/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-1.17.0 → aiagents4pharma-1.18.0}/aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py

@@ -7,6 +7,8 @@ This is the state file for the Talk2BioModels agent.
 from typing import Annotated
 import operator
 from langgraph.prebuilt.chat_agent_executor import AgentState
+from langchain_core.language_models import BaseChatModel
+from langchain_core.embeddings import Embeddings
 
 def add_data(data1: dict, data2: dict) -> dict:
     """
@@ -26,7 +28,8 @@ class Talk2Biomodels(AgentState):
     """
     The state for the Talk2BioModels agent.
     """
-    llm_model: str
+    llm_model: BaseChatModel
+    text_embedding_model: Embeddings
     pdf_file_name: str
     # A StateGraph may receive a concurrent updates
     # which is not supported by the StateGraph. Hence,

{aiagents4pharma-1.17.0 → aiagents4pharma-1.18.0}/aiagents4pharma/talk2biomodels/tests/test_ask_question.py

@@ -3,6 +3,7 @@ Test cases for Talk2Biomodels.
 '''
 
 from langchain_core.messages import HumanMessage, ToolMessage
+from langchain_openai import ChatOpenAI
 from ..agents.t2b_agent import get_app
 
 def test_ask_question_tool():
@@ -10,7 +11,7 @@ def test_ask_question_tool():
     Test the ask_question tool without the simulation results.
     '''
     unique_id = 12345
-    app = get_app(unique_id, llm_model='gpt-4o-mini')
+    app = get_app(unique_id)
     config = {"configurable": {"thread_id": unique_id}}
 
     ##########################################
@@ -20,7 +21,8 @@ def test_ask_question_tool():
     # case, the tool should return an error
     ##########################################
     # Update state
-    app.update_state(config, {"llm_model": "gpt-4o-mini"})
+    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-1.17.0 → aiagents4pharma-1.18.0}/aiagents4pharma/talk2biomodels/tests/test_get_annotation.py

@@ -5,6 +5,7 @@ Test cases for Talk2Biomodels get_annotation tool.
 import random
 import pytest
 from langchain_core.messages import HumanMessage, ToolMessage
+from langchain_openai import ChatOpenAI
 from ..agents.t2b_agent import get_app
 from ..tools.get_annotation import prepare_content_msg
 
@@ -16,7 +17,9 @@ def make_graph_fixture():
     unique_id = random.randint(1000, 9999)
     graph = get_app(unique_id)
     config = {"configurable": {"thread_id": unique_id}}
-    graph.update_state(config, {"llm_model": "gpt-4o-mini"})
+    graph.update_state(config, {"llm_model": ChatOpenAI(model='gpt-4o-mini',
+                                    temperature=0)
+                                })
     return graph, config
 
 def test_no_model_provided(make_graph):
@@ -85,7 +88,6 @@ def test_invalid_species_provided(make_graph):
                 # (likely due to an invalid species).
                 test_condition = True
                 break
-    # assert test_condition
     assert test_condition
 
 def test_invalid_and_valid_species_provided(make_graph):

{aiagents4pharma-1.17.0 → aiagents4pharma-1.18.0}/aiagents4pharma/talk2biomodels/tests/test_integration.py

@@ -4,8 +4,11 @@ Test cases for Talk2Biomodels.
 
 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_integration():
     '''
     Test the integration of the tools.
@@ -13,7 +16,7 @@ def test_integration():
     unique_id = 1234567
     app = get_app(unique_id)
     config = {"configurable": {"thread_id": unique_id}}
-    app.update_state(config, {"llm_model": "gpt-4o-mini"})
+    app.update_state(config, {"llm_model": LLM_MODEL})
     # ##########################################
     # ## Test simulate_model tool
     # ##########################################
@@ -34,7 +37,7 @@ def test_integration():
     # results are available
     ##########################################
     # Update state
-    app.update_state(config, {"llm_model": "gpt-4o-mini"})
+    app.update_state(config, {"llm_model": LLM_MODEL})
     prompt = """What is the concentration of CRP in serum after 100 hours?
     Round off the value to 2 decimal places."""
     # Test the tool get_modelinfo
@@ -49,12 +52,15 @@ def test_integration():
 
     ##########################################
     # Test custom_plotter tool when the
-    # simulation results are available
+    # simulation results are available but
+    # the species is not available
     ##########################################
-    prompt = "Plot only CRP related species."
-
+    prompt = """Call the custom_plotter tool to make a plot
+        showing only species `TP53` and `Pyruvate`. Let me
+        know if these species were not found. Do not
+        invoke any other tool."""
     # Update state
-    app.update_state(config, {"llm_model": "gpt-4o-mini"}
+    app.update_state(config, {"llm_model": LLM_MODEL}
                     )
     # Test the tool get_modelinfo
     response = app.invoke(
@@ -66,11 +72,8 @@ def test_integration():
     # Get the messages from the current state
     # and reverse the order
     reversed_messages = current_state.values["messages"][::-1]
-    # Loop through the reversed messages
-    # until a ToolMessage is found.
-    expected_header = ['Time', 'CRP{serum}', 'CRPExtracellular']
-    expected_header += ['CRP Suppression (%)', 'CRP (% of baseline)']
-    expected_header += ['CRP{liver}']
+    # Loop through the reversed messages until a
+    # ToolMessage is found.
     predicted_artifact = []
     for msg in reversed_messages:
         if isinstance(msg, ToolMessage):
@@ -80,24 +83,17 @@ def test_integration():
             if msg.name == "custom_plotter":
                 predicted_artifact = msg.artifact
                 break
-    # Convert the artifact into a pandas dataframe
-    # for easy comparison
-    df = pd.DataFrame(predicted_artifact)
-    # Extract the headers from the dataframe
-    predicted_header = df.columns.tolist()
-    # Check if the header is in the expected_header
-    # assert expected_header in predicted_artifact
-    assert set(expected_header).issubset(set(predicted_header))
+    # Check if the the predicted artifact is `None`
+    assert predicted_artifact is None
+
     ##########################################
     # Test custom_plotter tool when the
-    # simulation results are available but
-    # the species is not available
+    # simulation results are available
     ##########################################
-    prompt = """Make a custom plot showing the
-        concentration of the species `TP53` over
-        time. Do not show any other species."""
+    prompt = "Plot only CRP related species."
+
     # Update state
-    app.update_state(config, {"llm_model": "gpt-4o-mini"}
+    app.update_state(config, {"llm_model": LLM_MODEL}
                     )
     # Test the tool get_modelinfo
     response = app.invoke(
@@ -105,13 +101,15 @@ def test_integration():
                         config=config
                     )
     assistant_msg = response["messages"][-1].content
-    # print (response["messages"])
     current_state = app.get_state(config)
     # Get the messages from the current state
     # and reverse the order
     reversed_messages = current_state.values["messages"][::-1]
-    # Loop through the reversed messages until a
-    # ToolMessage is found.
+    # Loop through the reversed messages
+    # until a ToolMessage is found.
+    expected_header = ['Time', 'CRP{serum}', 'CRPExtracellular']
+    expected_header += ['CRP Suppression (%)', 'CRP (% of baseline)']
+    expected_header += ['CRP{liver}']
     predicted_artifact = []
     for msg in reversed_messages:
         if isinstance(msg, ToolMessage):
@@ -121,5 +119,11 @@ def test_integration():
             if msg.name == "custom_plotter":
                 predicted_artifact = msg.artifact
                 break
-    # Check if the the predicted artifact is `None`
-    assert predicted_artifact is None
+    # Convert the artifact into a pandas dataframe
+    # for easy comparison
+    df = pd.DataFrame(predicted_artifact)
+    # Extract the headers from the dataframe
+    predicted_header = df.columns.tolist()
+    # Check if the header is in the expected_header
+    # assert expected_header in predicted_artifact
+    assert set(expected_header).issubset(set(predicted_header))

{aiagents4pharma-1.17.0 → aiagents4pharma-1.18.0}/aiagents4pharma/talk2biomodels/tests/test_query_article.py

@@ -5,6 +5,7 @@ Test cases for Talk2Biomodels query_article tool.
 from pydantic import BaseModel, Field
 from langchain_core.messages import HumanMessage, ToolMessage
 from langchain_openai import ChatOpenAI
+from langchain_nvidia_ai_endpoints import NVIDIAEmbeddings
 from ..agents.t2b_agent import get_app
 
 class Article(BaseModel):
@@ -21,8 +22,10 @@ def test_query_article_with_an_article():
     app = get_app(unique_id)
     config = {"configurable": {"thread_id": unique_id}}
     # Update state by providing the pdf file name
+    # and the text embedding model
     app.update_state(config,
-      {"pdf_file_name": "aiagents4pharma/talk2biomodels/tests/article_on_model_537.pdf"})
+      {"pdf_file_name": "aiagents4pharma/talk2biomodels/tests/article_on_model_537.pdf",
+       "text_embedding_model": NVIDIAEmbeddings(model='nvidia/llama-3.2-nv-embedqa-1b-v2')})
     prompt = "What is the title of the article?"
     # Test the tool query_article
     response = app.invoke(
@@ -55,6 +58,9 @@ def test_query_article_without_an_article():
     app = get_app(unique_id)
     config = {"configurable": {"thread_id": unique_id}}
     prompt = "What is the title of the uploaded article?"
+    # Update state by providing the text embedding model
+    app.update_state(config,
+      {"text_embedding_model": NVIDIAEmbeddings(model='nvidia/llama-3.2-nv-embedqa-1b-v2')})
     # Test the tool query_article
     app.invoke(
             {"messages": [HumanMessage(content=prompt)]},

{aiagents4pharma-1.17.0 → aiagents4pharma-1.18.0}/aiagents4pharma/talk2biomodels/tests/test_search_models.py

@@ -3,6 +3,7 @@ Test cases for Talk2Biomodels search models tool.
 '''
 
 from langchain_core.messages import HumanMessage
+from langchain_nvidia_ai_endpoints import ChatNVIDIA
 from ..agents.t2b_agent import get_app
 
 def test_search_models_tool():
@@ -13,7 +14,8 @@ def test_search_models_tool():
     app = get_app(unique_id)
     config = {"configurable": {"thread_id": unique_id}}
     # Update state
-    app.update_state(config, {"llm_model": "gpt-4o-mini"})
+    app.update_state(config,
+            {"llm_model": ChatNVIDIA(model="meta/llama-3.3-70b-instruct")})
     prompt = "Search for models on Crohn's disease."
     # Test the tool get_modelinfo
     response = app.invoke(

{aiagents4pharma-1.17.0 → aiagents4pharma-1.18.0}/aiagents4pharma/talk2biomodels/tests/test_steady_state.py

@@ -3,8 +3,11 @@ Test cases for Talk2Biomodels steady state 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_steady_state_tool():
     '''
     Test the steady_state tool.
@@ -12,7 +15,7 @@ def test_steady_state_tool():
     unique_id = 123
     app = get_app(unique_id)
     config = {"configurable": {"thread_id": unique_id}}
-    app.update_state(config, {"llm_model": "gpt-4o-mini"})
+    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
@@ -37,8 +40,8 @@ def test_steady_state_tool():
     #########################################################
     # In this case, we will test if the tool is indeed invoked
     # successfully
-    prompt = """Run a steady state analysis of model 64.
-    Set the initial concentration of `Pyruvate` to 0.2. The
+    prompt = """Bring model 64 to a steady state. Set the
+    initial concentration of `Pyruvate` to 0.2. The
     concentration of `NAD` resets to 100 every 2 time units."""
     # Invoke the agent
     app.invoke(