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

aiagents4pharma-1.32.0.dist-info/METADATA

@@ -0,0 +1,364 @@
+Metadata-Version: 2.4
+Name: aiagents4pharma
+Version: 1.32.0
+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: 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)
+![Talk2AIAgents4Pharma Pulls](https://img.shields.io/docker/pulls/virtualpatientengine/talk2aiagents4pharma?label=Talk2AIAgents4Pharma%20Pulls&color=blue&logo=docker&style=flat-square)
+![Talk2Scholars Pulls](https://img.shields.io/docker/pulls/virtualpatientengine/talk2scholars?label=Talk2Scholars%20Pulls&color=blue&logo=docker&style=flat-square)
+![Talk2BioModels Pulls](https://img.shields.io/docker/pulls/virtualpatientengine/talk2biomodels?label=Talk2BioModels%20Pulls&color=blue&logo=docker&style=flat-square)
+![Talk2KnowledgeGraphs Pulls](https://img.shields.io/docker/pulls/virtualpatientengine/talk2knowledgegraphs?label=Talk2KnowledgeGraphs%20Pulls&color=blue&logo=docker&style=flat-square)
+
+## Introduction
+
+Welcome to **AIAgents4Pharma** – an open-source project by [Team VPE](https://bmedx.com/research-teams/artificial-intelligence/team-vpe/) 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
+
+### Installation
+
+#### Option 1: Docker (stable-release)
+
+_We now have all the agents available on Docker Hub._
+
+##### **To run Talk2AIAgents4Pharma / Talk2KnowledgeGraphs**
+
+Both agents require [Ollama](https://ollama.com/) to run embedding models like `nomic-embed-text`. We use a **single startup script** that automatically detects your hardware (NVIDIA, AMD, or CPU) and handles container startup, model loading, and service orchestration.
+
+##### **1. Clone the repository and navigate to the agent directory**
+
+```sh
+git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma
+
+cd AIAgents4Pharma/aiagents4pharma/<agent>
+```
+
+Replace `<agent>` with either:
+
+- `talk2aiagents4pharma`
+- `talk2knowledgegraphs`
+
+##### **2. Setup environment variables**
+
+Copy and configure your `.env` file:
+
+```sh
+cp .env.example .env
+```
+
+Then edit `.env` and add your API keys:
+
+```env
+OPENAI_API_KEY=...                  # Required for both agents
+NVIDIA_API_KEY=...                  # Required for both agents
+OLLAMA_HOST=http://ollama:11434     # Required for AA4P / T2KG
+LANGCHAIN_TRACING_V2=true           # Optional for both agents
+LANGCHAIN_API_KEY=...               # Optional for both agents
+```
+
+To use **Talk2AIAgents4Pharma** or **Talk2KnowledgeGraphs**, you need a free **NVIDIA API key**. Create an account and apply for free credits [here](https://build.nvidia.com/explore/discover).
+
+###### Notes for Windows Users
+
+If you are using Windows, it is recommended to install **Git Bash** for a smoother experience when running the bash commands in this guide.
+
+- For applications that use **Docker Compose**, Git Bash is **required**.
+- For applications that use **docker run** manually, Git Bash is **optional**, but recommended for consistency.
+
+You can download Git Bash here: [Git for Windows](https://git-scm.com/downloads).
+
+When using Docker on Windows, make sure you **run Docker with administrative privileges** if you face permission issues.
+
+To resolve for permission issues, you can:
+
+- Review the official Docker documentation on [Windows permission requirements](https://docs.docker.com/desktop/setup/install/windows-permission-requirements/).
+- Alternatively, follow the community discussion and solutions on [Docker Community Forums](https://forums.docker.com/t/error-when-trying-to-run-windows-containers-docker-client-must-be-run-with-elevated-privileges/136619).
+
+**LangSmith** support is optional. To enable it, create an API key [here](https://docs.smith.langchain.com/administration/how_to_guides/organization_management/create_account_api_key).
+
+##### **3. Start the application**
+
+Run the startup script. It will:
+
+- Detect your hardware configuration (NVIDIA GPU, AMD GPU, or CPU). Apple Metal is unavailable inside Docker, and Intel SIMD optimizations are automatically handled without special configuration.
+- Choose the correct Ollama image (`latest` or `rocm`)
+- Launch the Ollama container with appropriate runtime settings
+- Pull the required embedding model (`nomic-embed-text`)
+- Start the agent **after the model is available**
+
+```sh
+chmod +x startup.sh
+./startup.sh        # Add --cpu flag to force CPU mode if needed
+```
+
+##### **4. Access the Web UI**
+
+Once started, the agent is available at:
+
+```
+http://localhost:8501
+```
+
+##### **To Run Talk2Biomodels / Talk2Scholars**
+
+1. **Run the containers**
+
+###### Talk2Biomodels
+
+```docker
+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
+```
+
+###### Talk2Scholars
+
+```docker
+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> \
+  -e NVIDIA_API_KEY=<your_nvidia_api_key> \
+  -p 8501:8501 \
+  virtualpatientengine/talk2scholars
+```
+
+2. **Access the Web App**
+   Open your browser and go to:
+
+   ```
+   http://localhost:8501
+   ```
+
+To use **Talk2BioModels** or **Talk2Scholars**, you need a free **NVIDIA API key**. Create an account and apply for free credits [here](https://build.nvidia.com/explore/discover).
+
+Only for **Talk2Scholars**, you also need a **Zotero API key**, which you can generate [here](https://www.zotero.org/user/login#applications). _(For all other agents, the Zotero key is not required.)_
+
+If you are using docker on Windows, please follow these [Windows Setup Notes](#notes-for-windows-users).
+
+**LangSmith** support is optional. To enable it, create an API key [here](https://docs.smith.langchain.com/administration/how_to_guides/organization_management/create_account_api_key).
+
+#### Notes
+
+- Be sure to **replace the placeholder values** with your actual credentials before running any container:
+
+  - `<your_openai_api_key>`
+  - `<your_nvidia_api_key>`
+  - `<your_zotero_api_key>`
+  - `<your_zotero_user_id>`
+
+- All agents default to **port `8501`**. If you plan to run multiple agents simultaneously, make sure to assign **different ports** to avoid conflicts.
+
+  Example (Talk2Scholars on port `8502`):
+
+  ```docker
+  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> \
+    -e NVIDIA_API_KEY=<your_nvidia_api_key> \
+    -p 8502:8501 \
+    virtualpatientengine/talk2scholars
+  ```
+
+  Then access the app at: [http://localhost:8502](http://localhost:8502)
+
+#### Option 2: git (for developers and contributors)
+
+![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:**
+   ```sh
+   git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma
+   cd AIAgents4Pharma
+   ```
+2. **Install dependencies:**
+
+   ```python
+   pip install -r requirements.txt
+   ```
+
+3. **Initialize API Keys**
+
+   ```env
+   export OPENAI_API_KEY=....          # Required for all agents
+   export NVIDIA_API_KEY=....          # Required for all agents
+   export ZOTERO_API_KEY=....          # Required for T2S
+   export ZOTERO_USER_ID=....          # Required for T2S
+   export LANGCHAIN_TRACING_V2=true    # Optional for all agents
+   export LANGCHAIN_API_KEY=...        # Optional for all agents
+   ```
+
+To use **Talk2AIAgents4Pharma**, **Talk2BioModels**, **Talk2KnowledgeGraphs**, or **Talk2Scholars**, you need a free **NVIDIA API key**. Create an account and apply for free credits [here](https://build.nvidia.com/explore/discover).
+
+Only for **Talk2Scholars**, you also need a **Zotero API key**, which you can generate [here](https://www.zotero.org/user/login#applications). _(For all other agents, the Zotero key is not required.)_
+
+To use **Talk2Scholars**, you must have **FAISS** installed through **Conda**. Follow installation instructions for your OS [here](https://github.com/VirtualPatientEngine/AIAgents4Pharma/tree/main/aiagents4pharma/talk2scholars/install.md).
+
+To use **Talk2AIAgents4Pharma** or **Talk2KnowledgeGraphs**, you must have **Ollama** installed. Follow installation instructions for your OS [here](https://ollama.com/download).
+
+After installing, pull the `nomic-embed-text` model and start the server by running:
+
+```sh
+ollama pull nomic-embed-text && ollama serve
+```
+
+More details about the model are available [here](https://ollama.com/library/nomic-embed-text).
+
+Additionally on **Windows**, the `pcst_fast 1.0.10` library requires **Microsoft Visual C++ 14.0 or greater**.  
+You can download the **Microsoft C++ Build Tools** [here](https://visualstudio.microsoft.com/visual-cpp-build-tools/).
+
+**LangSmith** support is optional. To enable it, create an API key [here](https://docs.smith.langchain.com/administration/how_to_guides/organization_management/create_account_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._
+
+4. **Launch the app:**
+   ```sh
+   streamlit run app/frontend/streamlit_app_<agent>.py
+   ```
+   _Replace `<agent>` with the agent name you are interested to launch:_
+
+- `talk2aiagents4pharma`
+- `talk2biomodels`
+- `talk2knowledgegraphs`
+- `talk2scholars`
+- `talk2cells`
+
+For detailed instructions on each agent, please refer to their respective modules.
+
+#### Option 3: pip (beta-release)
+
+![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)
+
+```sh
+pip install aiagents4pharma
+```
+
+Check out the tutorials on each agent for detailed instructions.
+
+## Contributing
+
+We welcome your support to make **AIAgents4Pharma** even better.  
+All types of contributions are appreciated — whether you're fixing bugs, adding features, improving documentation, or helping with testing, every contribution is valuable.
+
+#### How to contribute
+
+1. Star this repository to show your support.
+2. Fork the repository.
+3. Create a new branch for your work:
+   ```sh
+   git checkout -b feat/your-feature-name
+   ```
+4. Make your changes and commit them:
+   ```sh
+   git commit -m "feat: add a brief description of your change"
+   ```
+5. Push your branch:
+   ```sh
+   git push origin feat/your-feature-name
+   ```
+6. Open a Pull Request.
+
+#### Areas where you can help
+
+- Beta testing for Talk2BioModels and Talk2Scholars.
+- Development work related to Python, bioinformatics, or knowledge graphs.
+
+#### Contacts for contributions
+
+- **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)
+
+Please refer to our [CONTRIBUTING.md](CONTRIBUTING.md) for more detailed contribution guidelines.
+
+## Feedback
+
+If you have questions, bug reports, feature requests, comments, or suggestions, we would love to hear from you.  
+Please open an `issue` or start a `discussion`

{aiagents4pharma-1.30.4.dist-info → aiagents4pharma-1.32.0.dist-info}/RECORD

@@ -136,23 +136,23 @@ aiagents4pharma/talk2knowledgegraphs/utils/extractions/__init__.py,sha256=7gwwtf
 aiagents4pharma/talk2knowledgegraphs/utils/extractions/pcst.py,sha256=m5p0yoJb7I19ua5yeQfXPf7c4r6S1XPwttsrM7Qoy94,9336
 aiagents4pharma/talk2scholars/__init__.py,sha256=NOZxTklAH1j1ggu97Ib8Xn9LCKudEWt-8dx8w7yxVD8,180
 aiagents4pharma/talk2scholars/agents/__init__.py,sha256=c_0Pk85bt-RfK5RMyALM3MXo3qXVMoYS7BOqM9wuFME,317
-aiagents4pharma/talk2scholars/agents/main_agent.py,sha256=KdKbnc-5zxktLUkzEZHC3bvn8_iKa8Kk4So90i48cdE,3275
-aiagents4pharma/talk2scholars/agents/paper_download_agent.py,sha256=wrK9CPy5evH56fyOZ2BlkBfY5aEj6tefc4jSDPVzYvs,3041
-aiagents4pharma/talk2scholars/agents/pdf_agent.py,sha256=xt_bgCTVJ6jOCkhc_rHh8pngq4uS8kuNOevuP3eC-sA,3702
-aiagents4pharma/talk2scholars/agents/s2_agent.py,sha256=ua1bjKE2HBKZuLnDn8me5fuV1lSvdZbwAlo3Yp27TT4,4659
-aiagents4pharma/talk2scholars/agents/zotero_agent.py,sha256=f11kNqtyZnpBiIf3Fe9gU0WqQ0-ohhngTKl-o0u997Q,4442
+aiagents4pharma/talk2scholars/agents/main_agent.py,sha256=oCSWPj3TUgTIERmYbBTYipNrU1g956LXJEUx-7-KAQ0,3354
+aiagents4pharma/talk2scholars/agents/paper_download_agent.py,sha256=pYHW3R7VQjRA3PhgWGQYI3ErfdILYQ0FM1WGXii3r1k,2996
+aiagents4pharma/talk2scholars/agents/pdf_agent.py,sha256=GEXzJMQxIeZ7zLP-AlnTMU-n_KXZ7g22Qd9L3USIc_4,3626
+aiagents4pharma/talk2scholars/agents/s2_agent.py,sha256=oui0CMSyXmBGBJ7LnYq8Ce0V8Qc3BS6GgH5Qx5wI6oM,4565
+aiagents4pharma/talk2scholars/agents/zotero_agent.py,sha256=NAmEURIhH-sjXGO-dqAigUA10m-Re9Qe1hY8db4CIP0,4370
 aiagents4pharma/talk2scholars/configs/__init__.py,sha256=Y9-4PxsNCMoxyyQgDSbPByJnO9wnyem5SYL3eOZt1HY,189
 aiagents4pharma/talk2scholars/configs/config.yaml,sha256=-8X0_gTmjEuXAeIrnppw3Npy8HICelHZOvTKEScI-rs,596
 aiagents4pharma/talk2scholars/configs/agents/__init__.py,sha256=plv5Iw34gvbGZbRyJapvoOiiFXekRQIwjV_yy5AR_SI,104
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/__init__.py,sha256=D94LW4cXLmJe4dNl5qoR9QN0JnBqGLbQDgDLqhCNUE0,213
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/default.yaml,sha256=GZRqZoUy8eAWXyd9GJDh-A4mYSJOhnkid6TaIJTGBeU,1192
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/default.yaml,sha256=EmUAxeQSnH4U5Op5_XOzCbcexDCp-Rpz3z0yVPRtQUg,1315
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/paper_download_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/pdf_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/default.yaml,sha256=UIYkr060IpoLHMXVPxGAjrkCJSjX7H0DzcFSasyW6sE,1185
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/default.yaml,sha256=_sSt2jCgSILwrXkywDAxkXONCZn896owLBaf46iFI0I,1323
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/default.yaml,sha256=09nMAlI4CTLlss03trR0ZaEeLdABQfkwUUE6ZCK4WzY,718
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/default.yaml,sha256=SOdjRiGUxjW9JeCRDd_U1RjCclItkoPODrj5RpIrxSY,2030
 aiagents4pharma/talk2scholars/configs/app/__init__.py,sha256=tXpOW3R4eAfNoqvoaHfabSG-DcMHmUGSTg_4zH_vlgw,94
 aiagents4pharma/talk2scholars/configs/app/frontend/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 aiagents4pharma/talk2scholars/configs/app/frontend/default.yaml,sha256=A6nYjrgzEyRv5JYsGN7oqNX4-tufMBZ6mg-A7bMX6V4,906
@@ -172,39 +172,37 @@ aiagents4pharma/talk2scholars/configs/tools/zotero_read/default.yaml,sha256=ifOt
 aiagents4pharma/talk2scholars/configs/tools/zotero_write/__inti__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 aiagents4pharma/talk2scholars/configs/tools/zotero_write/default.yaml,sha256=gB7y7pznviQUzu49Eu4ONNkjQjT8wPKNSw6S_vfd9kI,1222
 aiagents4pharma/talk2scholars/state/__init__.py,sha256=ReScKLpEvedq4P6ww52NRQS0Xr6SSQV7hqoQ83Mt75U,138
-aiagents4pharma/talk2scholars/state/state_talk2scholars.py,sha256=8ZFfv55tXO3LU-2DzKC5JjH4_ryodgu-H1ieKBmVFvw,2844
+aiagents4pharma/talk2scholars/state/state_talk2scholars.py,sha256=MGB-rWjbOpLN-pK3nY9YKAuskcjeR62rjXbZl1Ppjas,2836
 aiagents4pharma/talk2scholars/tests/__init__.py,sha256=U3PsTiUZaUBD1IZanFGkDIOdFieDVJtGKQ5-woYUo8c,45
 aiagents4pharma/talk2scholars/tests/test_llm_main_integration.py,sha256=FBRqS06IKJYFOudQEHQr-9oJ4tftkH-gTCowTAqwWSg,3686
-aiagents4pharma/talk2scholars/tests/test_main_agent.py,sha256=hgKgMXAGGqGJ6EXbjfsdZ5t1IWo2W67tc_F7vK747Qg,6844
-aiagents4pharma/talk2scholars/tests/test_paper_download_agent.py,sha256=CP4fKFU_JYP_AXvTptnwpjaVar1d5lVKV5vxYgH_1j4,5309
-aiagents4pharma/talk2scholars/tests/test_paper_download_tools.py,sha256=_bGuoo4b6zD_vwLa7jGziWDT5qRtavsf02Jiaa7JIRU,5817
-aiagents4pharma/talk2scholars/tests/test_pdf_agent.py,sha256=TN4Sq5-SCxv-9VfFyq7sOlBlxbekmnWuB7-qh4MrhkA,4656
-aiagents4pharma/talk2scholars/tests/test_question_and_answer_tool.py,sha256=te6w1tPvuNSNCTihIwaCT083BzUCowjOQPwuCodXR4k,8723
+aiagents4pharma/talk2scholars/tests/test_main_agent.py,sha256=IZYSocYVwqPil2lF6L07mKm8PUq7vjopmqNiCm6IJEA,6876
+aiagents4pharma/talk2scholars/tests/test_paper_download_agent.py,sha256=gKSQp-sw62FplNnGYW0wv2ZIUEefh3o0tFWbRzy9yLs,5068
+aiagents4pharma/talk2scholars/tests/test_paper_download_tools.py,sha256=3mycLeEgH5XkwxuoXfTpQb8c8xFtIX2HjVnACPrSf60,7141
+aiagents4pharma/talk2scholars/tests/test_pdf_agent.py,sha256=scGCTgka2JuoUhzZwzDn0OgIYihOLhXbwb5uGFR02aI,4302
+aiagents4pharma/talk2scholars/tests/test_question_and_answer_tool.py,sha256=_zzg4_XVVEuvYDsJ5la0kFLf9dT45P67-UnUZWDUkhY,34874
 aiagents4pharma/talk2scholars/tests/test_routing_logic.py,sha256=g79tG68ZrUOL3-duCCJwvFK6OieR5KedRf3yTUDqIFk,2784
-aiagents4pharma/talk2scholars/tests/test_s2_agent.py,sha256=BhW1wGc-wUPS4fwNBQRtBXJaJ_i7L6t_G9Bq57fK7rI,7784
-aiagents4pharma/talk2scholars/tests/test_s2_display.py,sha256=w1TqgEdl9WpW_A2Ud1slfI5fkRFkKtKadAlkEfSLOZk,2247
+aiagents4pharma/talk2scholars/tests/test_s2_agent.py,sha256=xvlPU4Lz_DdQLTpdtoHW9l_AMvFrzC-FXE5royGbtLM,7806
+aiagents4pharma/talk2scholars/tests/test_s2_display.py,sha256=TfJE74KsocAHLbitMLjVrfUwAwyIYpzEvkdrQMBzM2g,2263
 aiagents4pharma/talk2scholars/tests/test_s2_multi.py,sha256=VCTfexhtX7FgWOBS0YtSm1zghbByZnni1NBLGVTJVGI,11166
-aiagents4pharma/talk2scholars/tests/test_s2_query.py,sha256=hEcBt142nn_bKV9lor__Yk4LusgE1tN5dA-qpT606Bc,2443
+aiagents4pharma/talk2scholars/tests/test_s2_query.py,sha256=_pDVolOmhrjZnh37Ig97-LcDHUe0lm3GvTWjNDKgMkc,2461
 aiagents4pharma/talk2scholars/tests/test_s2_retrieve.py,sha256=YtA2nbPRtoSR7mPqEjqLF5ERGVzTfeULztsNoCI48X8,2003
 aiagents4pharma/talk2scholars/tests/test_s2_search.py,sha256=mCGpoCYVn0SJ9BPcEjTz2MLy_K2XJIxvPngwsMoKijA,9945
 aiagents4pharma/talk2scholars/tests/test_s2_single.py,sha256=KjSh7V2cl1IuO_M9O6dj0vnMHr13H-xKxia_ZgT4qag,10313
 aiagents4pharma/talk2scholars/tests/test_state.py,sha256=_iHXvoZnU_eruf8l1sQKBSCIVnxNkH_9VzkVtZZA6bY,384
-aiagents4pharma/talk2scholars/tests/test_zotero_agent.py,sha256=fQDQj28uFNC1TyMPzNaNfDJacuw1_DqwGiX6IgliR3Y,6130
+aiagents4pharma/talk2scholars/tests/test_zotero_agent.py,sha256=jFEtfQVEwEQ6v3kq7A1_p2MKCu5wbtX47V4bE-fKD6M,6158
 aiagents4pharma/talk2scholars/tests/test_zotero_human_in_the_loop.py,sha256=YelLQu9Y_r1SNQsC1xoLHJoJ3soIZtBt1MFbbNhY-Dg,10744
-aiagents4pharma/talk2scholars/tests/test_zotero_path.py,sha256=i1bS-5uSv25z4UFrc_W5rKZ0bwOg6ZK5cwLHMkjWgt8,18592
-aiagents4pharma/talk2scholars/tests/test_zotero_read.py,sha256=ecu9C-RWaLNgmAFqGN8s7dzCrtODqXOSZDievzjtAfQ,15511
+aiagents4pharma/talk2scholars/tests/test_zotero_path.py,sha256=Ko0HyXCrpm-vs8Bkf-syxp3MfL1IvZwXXgPExyQy_F8,18618
+aiagents4pharma/talk2scholars/tests/test_zotero_read.py,sha256=yQTksJhqW036Scs7pnc_bBC23N210mcjaZ6sJZl8QnM,29492
 aiagents4pharma/talk2scholars/tests/test_zotero_write.py,sha256=qWlO0XoZJ6vxUxgisjYv9Np87CoTEDxiQBEOhdj9foo,6111
 aiagents4pharma/talk2scholars/tools/__init__.py,sha256=c8pYHDqR9P0Frz2jWjbvyizfSTBMlMFzGsiQzx2KC9c,189
-aiagents4pharma/talk2scholars/tools/paper_download/__init__.py,sha256=0XmPLEqCply536Y1uWksmHYjlgNWcmcMpZx63XvGEFI,413
-aiagents4pharma/talk2scholars/tools/paper_download/abstract_downloader.py,sha256=nwVhRUqkdta3WLgd9roAWpx-bhJm3aAgJLx4RSYSJXQ,1327
-aiagents4pharma/talk2scholars/tools/paper_download/arxiv_downloader.py,sha256=hM9fdbwtOxuW1mpAfmfbILTI7kSVALgrGpjC2vMsvf8,3970
-aiagents4pharma/talk2scholars/tools/paper_download/download_arxiv_input.py,sha256=zndAnNFRBztuBK-tpW9UyYsGL8tB3gFjYhiTq6nzZu4,2203
+aiagents4pharma/talk2scholars/tools/paper_download/__init__.py,sha256=tNTLSPNdir4XSKRF0HjXI_tBGBXXXwDhWRI5VnwbZpM,214
+aiagents4pharma/talk2scholars/tools/paper_download/download_arxiv_input.py,sha256=WTWvXbh0C96OoMoPf8Bgu0AgorsdkWslac_WqlHc4bo,3900
 aiagents4pharma/talk2scholars/tools/pdf/__init__.py,sha256=DPpOfON3AySko5EBBAe_3udOoSaAdQWNyGeNvJyV5R8,138
-aiagents4pharma/talk2scholars/tools/pdf/question_and_answer.py,sha256=tNv0frCr0dxA0lfbwf5yudKRyWtbuRGMwqW5mk9u4eE,8797
-aiagents4pharma/talk2scholars/tools/s2/__init__.py,sha256=u_qh1bpDhVdyTr_S2wVfPwQ_lMz77NQ-ZDWtOP_PWzo,420
-aiagents4pharma/talk2scholars/tools/s2/display_results.py,sha256=UR0PtEHGDpOhPH0Di5HT8-Fip2RkEMTJgzROsChb1gc,2959
+aiagents4pharma/talk2scholars/tools/pdf/question_and_answer.py,sha256=RfICBn4VorvpTrb_GunFFAi6fnzUlees_k0poQm0VKc,21853
+aiagents4pharma/talk2scholars/tools/s2/__init__.py,sha256=w_eiw0pG8HNp79F9O_icXs_Yl_4odsmagYNKDTjIsvk,428
+aiagents4pharma/talk2scholars/tools/s2/display_dataframe.py,sha256=YtnCrI0c3Fhi68R6ndPUnVM3E5u7CuBB_myIzLN6nXg,3040
 aiagents4pharma/talk2scholars/tools/s2/multi_paper_rec.py,sha256=N6GwG3oCQFEcntpjTQObAELzM5OpZq0u9J9-gUWU2kc,2716
-aiagents4pharma/talk2scholars/tools/s2/query_results.py,sha256=5yXuHqz5UKO9BbovEUnqgjcMvqVG4vp9VJO8Zaz5N1w,2029
+aiagents4pharma/talk2scholars/tools/s2/query_dataframe.py,sha256=inaWWctaylJAJsXinQA63qPs5n-gn7axJz8ijj66Jmw,2746
 aiagents4pharma/talk2scholars/tools/s2/retrieve_semantic_scholar_paper_id.py,sha256=llzMMnEQKeYVamJbF4_DTMx-BgVe79vwDcUIFGLrmUY,2615
 aiagents4pharma/talk2scholars/tools/s2/search.py,sha256=NGzo1rF5VJJuZJbSLDwy2f220wSh7DWEw6xT1qQA2V0,2452
 aiagents4pharma/talk2scholars/tools/s2/single_paper_rec.py,sha256=7VivBGHcmaJZN7v7gYwddC-rfrDHaZo74pSNBYlJ2xU,2673
@@ -213,16 +211,16 @@ aiagents4pharma/talk2scholars/tools/s2/utils/multi_helper.py,sha256=rrR0DRNeGHpY
 aiagents4pharma/talk2scholars/tools/s2/utils/search_helper.py,sha256=_eP7q4ZTSWisEF4Stffe-IpR2MD9WrQ0u3jbbeJBRLU,6363
 aiagents4pharma/talk2scholars/tools/s2/utils/single_helper.py,sha256=ahTDT0lp5VRZS5hLL3-hsHx4wB3LUVY2OBTCTEJyR3Y,6983
 aiagents4pharma/talk2scholars/tools/zotero/__init__.py,sha256=wXiQILLq-utV35PkDUpm_F074mG9yRMyGQAFlr9UAOw,197
-aiagents4pharma/talk2scholars/tools/zotero/zotero_read.py,sha256=B21TOdB1nR--2Ug6Zx7nYjAKfCbndMF4L-cWcHPBWII,2267
+aiagents4pharma/talk2scholars/tools/zotero/zotero_read.py,sha256=RqFXP2DXmkHLhVLirrTnmSk-E8Jipi4ue_Zw65npbnM,2263
 aiagents4pharma/talk2scholars/tools/zotero/zotero_review.py,sha256=iqwpolg7GWAjXizubLrPaAsgOpsOhKz-tFRyLOiBvC0,6325
 aiagents4pharma/talk2scholars/tools/zotero/zotero_write.py,sha256=KnDcnUBB0lwMcxNpC3hsVnICWkj23MDAePdHlK-Kekk,3024
 aiagents4pharma/talk2scholars/tools/zotero/utils/__init__.py,sha256=uIyKZSFB07-zd3vjS9ABL0r6fdBX9JHw60j8oUfxHQs,209
-aiagents4pharma/talk2scholars/tools/zotero/utils/read_helper.py,sha256=6f2yu5admNZp7xw5VW2TFGF4wh_oyVn9aLaQF47FLMc,6038
+aiagents4pharma/talk2scholars/tools/zotero/utils/read_helper.py,sha256=lyrfpx8NHYiAN1qQSJWqPka7cML5BASwRXaI66fb-u8,13662
 aiagents4pharma/talk2scholars/tools/zotero/utils/review_helper.py,sha256=IPD1V9yrBYaDnRe7sR6PrpwR82OBJbA2P_Tc6RbxAbM,2748
 aiagents4pharma/talk2scholars/tools/zotero/utils/write_helper.py,sha256=ALwLecy1QVebbsmXJiDj1GhGmyhq2R2tZlAyEl1vfhw,7410
 aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_path.py,sha256=oIrfbOySgts50ksHKyjcWjRkPRIS88g3Lc0v9mBkU8w,6375
-aiagents4pharma-1.30.4.dist-info/licenses/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
-aiagents4pharma-1.30.4.dist-info/METADATA,sha256=0Sr-ukEvXz5sLl0PdoHYJ9bqFHjdScBvP75GSvxeUHc,13267
-aiagents4pharma-1.30.4.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-aiagents4pharma-1.30.4.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
-aiagents4pharma-1.30.4.dist-info/RECORD,,
+aiagents4pharma-1.32.0.dist-info/licenses/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
+aiagents4pharma-1.32.0.dist-info/METADATA,sha256=o3uHTzLfOPglRJUlK6_vKAuJ0qwKhGt7BeiQHeF4U_o,16043
+aiagents4pharma-1.32.0.dist-info/WHEEL,sha256=0CuiUZ_p9E4cD6NyLD6UG80LBXYyiSYZOKDm5lp32xk,91
+aiagents4pharma-1.32.0.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
+aiagents4pharma-1.32.0.dist-info/RECORD,,

{aiagents4pharma-1.30.4.dist-info → aiagents4pharma-1.32.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (78.1.0)
+Generator: setuptools (80.3.1)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

aiagents4pharma/talk2scholars/tools/paper_download/abstract_downloader.py

@@ -1,45 +0,0 @@
-"""
-Abstract Base Class for Paper Downloaders.
-
-This module defines the `AbstractPaperDownloader` class, which serves as a
-base class for downloading scholarly papers from different sources
-(e.g., arXiv, PubMed, IEEE Xplore). Any specific downloader should
-inherit from this class and implement its methods.
-"""
-
-from abc import ABC, abstractmethod
-from typing import Any, Dict
-
-
-class AbstractPaperDownloader(ABC):
-    """
-    Abstract base class for scholarly paper downloaders.
-
-    This is designed to be extended for different paper sources
-    like arXiv, PubMed, IEEE Xplore, etc. Each implementation
-    must define methods for fetching metadata and downloading PDFs.
-    """
-
-    @abstractmethod
-    def fetch_metadata(self, paper_id: str) -> Dict[str, Any]:
-        """
-        Fetch metadata for a given paper ID.
-
-        Args:
-            paper_id (str): The unique identifier for the paper.
-
-        Returns:
-            Dict[str, Any]: The metadata dictionary (format depends on the data source).
-        """
-
-    @abstractmethod
-    def download_pdf(self, paper_id: str) -> bytes:
-        """
-        Download the PDF for a given paper ID.
-
-        Args:
-            paper_id (str): The unique identifier for the paper.
-
-        Returns:
-            bytes: The binary content of the downloaded PDF.
-        """

aiagents4pharma/talk2scholars/tools/paper_download/arxiv_downloader.py

@@ -1,115 +0,0 @@
-"""
-Arxiv Paper Downloader
-
-This module provides an implementation of `AbstractPaperDownloader` for arXiv.
-It connects to the arXiv API, retrieves metadata for a research paper, and
-downloads the corresponding PDF.
-
-By using an abstract base class, this implementation is extendable to other
-APIs like PubMed, IEEE Xplore, etc.
-"""
-
-import xml.etree.ElementTree as ET
-from typing import Any, Dict
-import logging
-import hydra
-import requests
-from .abstract_downloader import AbstractPaperDownloader
-
-# Configure logging
-logging.basicConfig(level=logging.INFO)
-logger = logging.getLogger(__name__)
-
-
-class ArxivPaperDownloader(AbstractPaperDownloader):
-    """
-    Downloader class for arXiv.
-
-    This class interfaces with the arXiv API to fetch metadata
-    and retrieve PDFs of academic papers based on their arXiv IDs.
-    """
-
-    def __init__(self):
-        """
-        Initializes the arXiv paper downloader.
-
-        Uses Hydra for configuration management to retrieve API details.
-        """
-        with hydra.initialize(version_base=None, config_path="../../configs"):
-            cfg = hydra.compose(
-                config_name="config", overrides=["tools/download_arxiv_paper=default"]
-            )
-            self.api_url = cfg.tools.download_arxiv_paper.api_url
-            self.request_timeout = cfg.tools.download_arxiv_paper.request_timeout
-            self.chunk_size = cfg.tools.download_arxiv_paper.chunk_size
-            self.pdf_base_url = cfg.tools.download_arxiv_paper.pdf_base_url
-
-    def fetch_metadata(self, paper_id: str) -> Dict[str, Any]:
-        """
-        Fetch metadata from arXiv for a given paper ID.
-
-        Args:
-            paper_id (str): The arXiv ID of the paper.
-
-        Returns:
-            Dict[str, Any]: A dictionary containing metadata, including the XML response.
-        """
-        logger.info("Fetching metadata from arXiv for paper ID: %s", paper_id)
-        api_url = f"{self.api_url}?search_query=id:{paper_id}&start=0&max_results=1"
-        response = requests.get(api_url, timeout=self.request_timeout)
-        response.raise_for_status()
-        return {"xml": response.text}
-
-    def download_pdf(self, paper_id: str) -> Dict[str, Any]:
-        """
-        Download the PDF of a paper from arXiv.
-
-        This function first retrieves the paper's metadata to locate the PDF link
-        before downloading the file.
-
-        Args:
-            paper_id (str): The arXiv ID of the paper.
-
-        Returns:
-            Dict[str, Any]: A dictionary containing:
-                - `pdf_object`: The binary content of the downloaded PDF.
-                - `pdf_url`: The URL from which the PDF was fetched.
-                - `arxiv_id`: The arXiv ID of the downloaded paper.
-        """
-        metadata = self.fetch_metadata(paper_id)
-
-        # Parse the XML response to locate the PDF link.
-        root = ET.fromstring(metadata["xml"])
-        ns = {"atom": "http://www.w3.org/2005/Atom"}
-        pdf_url = next(
-            (
-                link.attrib.get("href")
-                for entry in root.findall("atom:entry", ns)
-                for link in entry.findall("atom:link", ns)
-                if link.attrib.get("title") == "pdf"
-            ),
-            None,
-        )
-
-        if not pdf_url:
-            raise RuntimeError(f"Failed to download PDF for arXiv ID {paper_id}.")
-
-        logger.info("Downloading PDF from: %s", pdf_url)
-        pdf_response = requests.get(pdf_url, stream=True, timeout=self.request_timeout)
-        pdf_response.raise_for_status()
-        # print (pdf_response)
-
-        # Combine the PDF data from chunks.
-        pdf_object = b"".join(
-            chunk
-            for chunk in pdf_response.iter_content(chunk_size=self.chunk_size)
-            if chunk
-        )
-        # print (pdf_object)
-        print("PDF_URL", pdf_url)
-
-        return {
-            "pdf_object": pdf_object,
-            "pdf_url": pdf_url,
-            "arxiv_id": paper_id,
-        }