aiagents4pharma 1.30.4__py3-none-any.whl → 1.32.0__py3-none-any.whl

aiagents4pharma/talk2scholars/tools/s2/query_results.py

@@ -1,61 +0,0 @@
-#!/usr/bin/env python3
-
-"""
-This tool is used to display the table of studies.
-"""
-
-import logging
-from typing import Annotated
-import pandas as pd
-from langchain_experimental.agents import create_pandas_dataframe_agent
-from langchain_core.tools import tool
-from langgraph.prebuilt import InjectedState
-
-# Configure logging
-logging.basicConfig(level=logging.INFO)
-logger = logging.getLogger(__name__)
-
-
-class NoPapersFoundError(Exception):
-    """Exception raised when no papers are found in the state."""
-
-
-@tool("query_results", parse_docstring=True)
-def query_results(question: str, state: Annotated[dict, InjectedState]) -> str:
-    """
-    Query the last displayed papers from the state. If no papers are found,
-    raises an exception.
-
-    Use this also to get the last displayed papers from the state,
-    and then use the papers to get recommendations for a single paper or
-    multiple papers.
-
-    Args:
-        question (str): The question to ask the agent.
-        state (dict): The state of the agent containing the papers.
-
-    Returns:
-        str: A message with the last displayed papers.
-    """
-    logger.info("Querying last displayed papers with question: %s", question)
-    llm_model = state.get("llm_model")
-    if not state.get("last_displayed_papers"):
-        logger.info("No papers displayed so far, raising NoPapersFoundError")
-        raise NoPapersFoundError(
-            "No papers found. A search needs to be performed first."
-        )
-    context_key = state.get("last_displayed_papers", "pdf_data")
-    dic_papers = state.get(context_key)
-    df_papers = pd.DataFrame.from_dict(dic_papers, orient="index")
-    df_agent = create_pandas_dataframe_agent(
-        llm_model,
-        allow_dangerous_code=True,
-        agent_type="tool-calling",
-        df=df_papers,
-        max_iterations=5,
-        include_df_in_prompt=True,
-        number_of_head_rows=df_papers.shape[0],
-        verbose=True,
-    )
-    llm_result = df_agent.invoke(question, stream_mode=None)
-    return llm_result["output"]

aiagents4pharma-1.30.4.dist-info/METADATA

@@ -1,334 +0,0 @@
-Metadata-Version: 2.4
-Name: aiagents4pharma
-Version: 1.30.4
-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: gravis==0.1.0
-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==0.3.40
-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==0.2.3
-Requires-Dist: langgraph_supervisor==0.0.9
-Requires-Dist: matplotlib==3.9.2
-Requires-Dist: openai==1.59.4
-Requires-Dist: ollama==0.4.7
-Requires-Dist: pandas==2.2.3
-Requires-Dist: pcst_fast==1.0.10
-Requires-Dist: plotly==5.24.1
-Requires-Dist: pubchempy==1.0.4
-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: pyzotero==1.6.9
-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: 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
-Requires-Dist: anndata==0.11.3
-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: nbformat==5.10.4
-Requires-Dist: scipy==1.15.2
-Requires-Dist: tqdm==4.67.1
-Requires-Dist: umap-learn==0.5.7
-Requires-Dist: plotly-express==0.4.1
-Requires-Dist: seaborn==0.13.2
-Requires-Dist: scanpy==1.11.0
-Dynamic: license-file
-
-[![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)
-[![TESTS Talk2AIAgents4Pharma](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2aiagents4pharma.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2aiagents4pharma.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)
-![Docker Pulls](https://img.shields.io/docker/pulls/virtualpatientengine/talk2biomodels?link=https%3A%2F%2Fhub.docker.com%2Frepository%2Fdocker%2Fvirtualpatientengine%2Ftalk2biomodels%2Fgeneral)
-
-## 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.
-- **Talk2AIAgents4Pharma** _(v1 in progress)_: Converse with all the agents above (currently supports T2B and T2KG)
-
-![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
-
-_Please use version 1.26.2 or later for better support with NVIDIA NIM models._
-
-#### Option 1: PyPI
-
-![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)
-
-```bash
-pip install aiagents4pharma
-```
-
-Check out the tutorials on each agent for detailed instructions.
-
-#### Option 2: Docker Hub
-
-_We now have `Talk2AIAgents4Pharma`, `Talk2Biomodels`, and `Talk2Scholars` available on Docker Hub._
-
-##### **Run Talk2AIAgents4Pharma and Talk2KnowledgeGraphs**
-
-Talk2AIAgents4Pharma and Talk2KnowledgeGraphs require Ollama for embedding models, so Docker Compose is used to run both containers in the same network.
-
-###### **Setup Environment Variables**
-
-1. Choose the app you want to use:
-
-```sh
-# Navigate to the correct directory before setting up environment variables.
-# Use one of the following commands based on the agent you want to use:
-cd AIAgents4Pharma/aiagents4pharma/talk2aiagents4pharma
-cd AIAgents4Pharma/aiagents4pharma/talk2knowledgegraphs
-```
-
-2. Copy the `.env.example` file and rename it to `.env`:
-   ```sh
-   cp .env.example .env
-   ```
-3. Open the `.env` file and add your API keys:
-
-   ```plaintext
-   OPENAI_API_KEY=your_openai_api_key
-   NVIDIA_API_KEY=your_nvidia_api_key
-   OLLAMA_HOST=http://ollama:11434
-   LANGCHAIN_TRACING_V2=true
-   LANGCHAIN_API_KEY=your_langchain_api_key_here
-   # Notes:
-   # The API endpoint for Ollama is already set in env.example.
-   # Both API keys (OPENAI_API_KEY and NVIDIA_API_KEY) are required for Talk2AIAgents4Pharma.
-   # If using Talk2KnowledgeGraphs separately, only the OPENAI_API_KEY is needed.
-   # Langsmith API for tracing is optional for both, set it in env.example if required.
-   ```
-
-4. Save the file.
-
-To start the containers, run the following command:
-
-```sh
-docker compose --profile cpu up # for CPU mode
-docker compose --profile nvidia up # for GPU mode
-docker compose --profile amd up # for AMD mode
-```
-
-This will:
-
-- Pull the latest images if they are not already available.
-- Start both Talk2AIAgents4Pharma or Talk2KnowledgeGraphs and Ollama containers in the same network.
-- Ensure Ollama is running first before launching Talk2AIAgents4Pharma or Talk2KnowledgeGraphs.
-
-To Access the web app, open your browser and go to:
-
-```
-http://localhost:8501
-```
-
-To stop the containers, run:
-
-```sh
-docker compose down
-```
-
-##### **Run Talk2Biomodels and Talk2Scholars**
-
-1. **Run the containers**
-
-   ```bash
-   docker run -d \
-     --name talk2biomodels \
-     -e OPENAI_API_KEY=<your_openai_api_key> \
-     -e NVIDIA_API_KEY=<your_nvidia_api_key> \
-     -p 8501:8501 \
-     virtualpatientengine/talk2biomodels
-   ```
-
-   ```bash
-   docker run -d \
-     --name talk2scholars \
-     -e OPENAI_API_KEY=<your_openai_api_key> \
-     -e ZOTERO_API_KEY=<your_zotero_api_key> \
-     -e ZOTERO_USER_ID=<your_zotero_user_id> \
-     -p 8501:8501 \
-     virtualpatientengine/talk2scholars
-   ```
-
-2. **Access the Web App**
-   Open your browser and go to:
-
-   ```
-   http://localhost:8501
-   ```
-
-   _You can create a free account at NVIDIA and apply for their
-   free credits [here](https://build.nvidia.com/explore/discover)._
-
-#### **Notes**
-
-- Ensure you **replace `<your_openai_api_key>`, `<your_nvidia_api_key>`, `<your_zotero_api_key>`, and `<your_zotero_user_id>`** with your actual credentials.
-- Both applications use **port `8501`**, so run them on different ports if needed:
-  ```bash
-  docker run -d -e OPENAI_API_KEY=<your_openai_api_key> -p 8501:8501 virtualpatientengine/talk2scholars
-  ```
-  Then, access it via `http://localhost:8501`.
-
-#### Option 3: git
-
-![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)
-
-1. **Clone the repository:**
-   ```bash
-   git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma
-   cd AIAgents4Pharma
-   ```
-2. **Install dependencies:**
-
-   ```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
-   ```
-
-   ⚠️ `pcst_fast 1.0.10` library requires `Microsoft Visual C++ 14.0` or greater to be installed.
-   You can download `Microsoft C++ Build Tools` from [here](https://visualstudio.microsoft.com/visual-cpp-build-tools/).
-
-3. **Initialize OPENAI_API_KEY and NVIDIA_API_KEY**
-
-   ```bash
-   export OPENAI_API_KEY=....
-   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. **Initialize ZOTERO_API_KEY and ZOTERO_USER_ID**
-
-   ```bash
-   export ZOTERO_API_KEY=....
-   export ZOTERO_USER_ID=....
-   ```
-
-   _Please note that ZOTERO keys are requried only if you want to launch Talk2Scholars. For all the other agents, please ignore this step._
-
-5. **[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 `AA4P` (Main Agent),
-   `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._
-
-6. **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 `Issues` or `Discussions` 😀