PyPI - aiagents4pharma - Versions diffs - 1.40.1__py3-none-any.whl → 1.42.0__py3-none-any.whl - Mend

aiagents4pharma 1.40.1py3-none-any.whl → 1.42.0py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (53) hide show

{aiagents4pharma-1.40.1.dist-info → aiagents4pharma-1.42.0.dist-info}/METADATA RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aiagents4pharma
-Version: 1.40.1
+Version: 1.42.0
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
@@ -20,6 +20,7 @@ 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-milvus==0.2.0
 Requires-Dist: langchain-nvidia-ai-endpoints==0.3.9
 Requires-Dist: langchain-openai==0.2.5
 Requires-Dist: langchain_ollama==0.2.3
@@ -37,6 +38,7 @@ 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: pymilvus==2.5.11
 Requires-Dist: streamlit==1.39.0
 Requires-Dist: sentence_transformers==3.3.1
 Requires-Dist: tabulate==0.9.0
@@ -63,20 +65,35 @@ Requires-Dist: plotly-express==0.4.1
 Requires-Dist: seaborn==0.13.2
 Requires-Dist: scanpy==1.11.0
 Requires-Dist: openpyxl==3.1.5
-Requires-Dist: pymilvus==2.5.11
 Dynamic: license-file
+<img src="docs/assets/VPE.png" alt="Virtual Patient Engine Logo" width="150"/>
+<!--  Project Info -->
+![RELEASE](https://img.shields.io/github/v/release/VirtualPatientEngine/AIAgents4Pharma?label=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)
+<!--  Deployment Workflows -->
+[![Pages Deployment](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/pages/pages-build-deployment/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/pages/pages-build-deployment)
+[![MkDocs Deploy](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/mkdocs-deploy.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/mkdocs-deploy.yml)
+[![Docker Build & Push](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_build.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_build.yml)
+<!--  Tests -->
+[![TESTS Talk2AIAgents4Pharma](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2aiagents4pharma.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2aiagents4pharma.yml)
 [![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)
+[![Talk2Cells](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml)
+<!--  Docker Pulls -->
+![Talk2AIAgents4Pharma Pulls](https://img.shields.io/docker/pulls/vpatientengine/talk2aiagents4pharma?label=Talk2AIAgents4Pharma%20Pulls&color=blue&logo=docker&style=flat-square)
+![Talk2BioModels Pulls](https://img.shields.io/docker/pulls/vpatientengine/talk2biomodels?label=Talk2BioModels%20Pulls&color=blue&logo=docker&style=flat-square)
+![Talk2KnowledgeGraphs Pulls](https://img.shields.io/docker/pulls/vpatientengine/talk2knowledgegraphs?label=Talk2KnowledgeGraphs%20Pulls&color=blue&logo=docker&style=flat-square)
+![Talk2Scholars Pulls](https://img.shields.io/docker/pulls/vpatientengine/talk2scholars?label=Talk2Scholars%20Pulls&color=blue&logo=docker&style=flat-square)
 ## Introduction
@@ -111,103 +128,12 @@ Our toolkit currently consists of the following agents:
 _We now have all the agents available on Docker Hub._
-##### **To run Talk2AIAgents4Pharma / Talk2KnowledgeGraphs**
-If your machine has NVIDIA GPU(s), please install the following this:
-- [nvidia-cuda-toolkit](https://developer.nvidia.com/cuda-toolkit)
-- [nvidia-container-toolkit](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/1.17.8/install-guide.html) (required for GPU support with Docker; enables containers to access NVIDIA GPUs for accelerated computing). After installing `nvidia-container-toolkit`, please restart Docker to ensure GPU support is enabled.
-##### **1. Download docker-compose.yml, .env.example and startup.sh from GitHub**
-###### Talk2Agents4Pharma
-```sh
-mkdir talk2aiagents4pharma && cd talk2aiagents4pharma && wget https://raw.githubusercontent.com/VirtualPatientEngine/AIAgents4Pharma/main/aiagents4pharma/talk2aiagents4pharma/docker-compose.yml https://raw.githubusercontent.com/VirtualPatientEngine/AIAgents4Pharma/main/aiagents4pharma/talk2aiagents4pharma/.env.example https://raw.githubusercontent.com/VirtualPatientEngine/AIAgents4Pharma/main/aiagents4pharma/talk2aiagents4pharma/startup.sh
-```
-###### Talk2KnowledgeGraphs
-```sh
-mkdir talk2knowledgegraphs && cd talk2knowledgegraphs && wget https://raw.githubusercontent.com/VirtualPatientEngine/AIAgents4Pharma/main/aiagents4pharma/talk2knowledgegraphs/docker-compose.yml https://raw.githubusercontent.com/VirtualPatientEngine/AIAgents4Pharma/main/aiagents4pharma/talk2knowledgegraphs/.env.example https://raw.githubusercontent.com/VirtualPatientEngine/AIAgents4Pharma/main/aiagents4pharma/talk2knowledgegraphs/startup.sh
-```
-##### **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
-LANGCHAIN_TRACING_V2=true           # Optional for both agents
-LANGCHAIN_API_KEY=...               # Optional for both agents
-```
-[Additional Notes for Windows Users](https://github.com/VirtualPatientEngine/AIAgents4Pharma/blob/main/aiagents4pharma/talk2aiagents4pharma/install.md#notes-for-windows-users)
-##### **3. Start the application**
-```sh
-chmod +x startup.sh
-./startup.sh        # Add --cpu flag to force CPU mode if needed
-```
-[More about startup script](https://github.com/VirtualPatientEngine/AIAgents4Pharma/blob/main/aiagents4pharma/talk2aiagents4pharma/install.md#about-startupsh)
-##### **To Run Talk2Biomodels / Talk2Scholars**
-###### 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
-```
-##### **4. Access the Web UI**
-Once started, the agent is available at:
-```
-http://localhost:8501
-```
-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).
-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](https://github.com/VirtualPatientEngine/AIAgents4Pharma/blob/main/aiagents4pharma/talk2aiagents4pharma/install.md#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).
-[More on running multiple agents simultaneously](https://github.com/VirtualPatientEngine/AIAgents4Pharma/blob/main/aiagents4pharma/talk2aiagents4pharma/install.md#to-run-multiple-agents-simultaneously)
-📝 By default, `talk2knowledgegraphs` includes a small subset of the PrimeKG knowledge graph, allowing users to start interacting with it out of the box.
-To switch to a different knowledge graph or use your own, refer to the [deployment guide](https://virtualpatientengine.github.io/AIAgents4Pharma/talk2knowledgegraphs/deployment/).
+Choose your agent below for detailed Docker instructions:
+- [Talk2AIAgents4Pharma](aiagents4pharma/talk2aiagents4pharma/install.md)
+- [Talk2KnowledgeGraphs](aiagents4pharma/talk2knowledgegraphs/install.md)
+- [Talk2BioModels](aiagents4pharma/talk2biomodels/install.md)
+- [Talk2Scholars](aiagents4pharma/talk2scholars/install.md)
 #### Option 2: git (for developers and contributors)
@@ -238,23 +164,6 @@ 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).
-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
@@ -269,10 +178,27 @@ _Replace `<agent>` with the agent name you are interested to launch:_
 - `talk2scholars`
 - `talk2cells`
-📝 By default, `talk2knowledgegraphs` includes a small subset of the PrimeKG knowledge graph, allowing users to start interacting with it out of the box.
-To switch to a different knowledge graph or use your own, refer to the [deployment guide](https://virtualpatientengine.github.io/AIAgents4Pharma/talk2knowledgegraphs/deployment/).
+If your machine has NVIDIA GPU(s), please install the following this:
+- [nvidia-cuda-toolkit](https://developer.nvidia.com/cuda-toolkit)
+- [nvidia-container-toolkit](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/1.17.8/install-guide.html) (required for GPU support with Docker; enables containers to access NVIDIA GPUs for accelerated computing). After installing `nvidia-container-toolkit`, please restart Docker to ensure GPU support is enabled.
+To use the **Agents**, you need a free **NVIDIA API key**. Create an account and apply for free credits [here](https://build.nvidia.com/explore/discover).
+**Talk2Scholars** and **Talk2KnowledgeGraphs** requires Milvus to be set up as the vector database — install Milvus depending on your setup by following the official instructions for [CPU](https://milvus.io/docs/install_standalone-docker-compose.md) or [GPU](https://milvus.io/docs/install_standalone-docker-compose-gpu.md). You will also need a **Zotero API key**, which you can generate [here](https://www.zotero.org/user/login#applications). _(The Zotero key is only required for Talk2Scholars; all other agents do not need it.)_
+> By default, `talk2knowledgegraphs` includes a small subset of the PrimeKG knowledge graph, allowing users to start interacting with it out of the box.
+> To switch to a different knowledge graph or use your own, refer to the [deployment guide](https://virtualpatientengine.github.io/AIAgents4Pharma/talk2knowledgegraphs/deployment/).
+> 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).
-For detailed instructions on each agent, please refer to their respective modules.
+_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._
 #### Option 3: pip (beta-release)

{aiagents4pharma-1.40.1.dist-info → aiagents4pharma-1.42.0.dist-info}/RECORD RENAMED Viewed

@@ -72,7 +72,7 @@ aiagents4pharma/talk2cells/tools/scp_agent/__init__.py,sha256=s7g0lyH1lMD9pcWHLP
 aiagents4pharma/talk2cells/tools/scp_agent/display_studies.py,sha256=6q59gh_NQaiOU2rn55A3sIIFKlXi4SK3iKgySvUDrtQ,600
 aiagents4pharma/talk2cells/tools/scp_agent/search_studies.py,sha256=MLe-twtFnOu-P8P9diYq7jvHBHbWFRRCZLcfpUzqPMg,2806
 aiagents4pharma/talk2knowledgegraphs/__init__.py,sha256=Z0Eo7LTiKk0STsr8VI7wkCLq7PHrK1vYlH4I1hSNLiA,165
-aiagents4pharma/talk2knowledgegraphs/milvus_data_dump.py,sha256=YOTO1HcSpNxQdc83jgwcuFkzGeCHov7CRDHQQL9PHNE,22608
+aiagents4pharma/talk2knowledgegraphs/milvus_data_dump.py,sha256=2LMGp2Coh7Q1TeWez-_wkMDfHzf_Tkj9cPslV0_ixOU,36202
 aiagents4pharma/talk2knowledgegraphs/agents/__init__.py,sha256=iOAzuy_8A03tQDFtSBhC9dldUo62z5gfxcVtXAdLOJs,92
 aiagents4pharma/talk2knowledgegraphs/agents/t2kg_agent.py,sha256=eUARAhzOz8PpHFzN2fP4L_fDEyqdllrAkBWa0otxGv4,3363
 aiagents4pharma/talk2knowledgegraphs/configs/__init__.py,sha256=4_DVdpahaJ55yPl0aZotlFA_MYWLFF2cubWyKtBVI_Q,126
@@ -81,15 +81,20 @@ aiagents4pharma/talk2knowledgegraphs/configs/agents/t2kg_agent/__init__.py,sha25
 aiagents4pharma/talk2knowledgegraphs/configs/agents/t2kg_agent/default.yaml,sha256=ENCGROwYFpR6g4QD518h73sshdn3vPVpotBMk1QJcpU,4830
 aiagents4pharma/talk2knowledgegraphs/configs/app/__init__.py,sha256=fKfc3FR7g5KjY9b6jzrU6cwKTVVpkoVZQS3dvUowu34,69
 aiagents4pharma/talk2knowledgegraphs/configs/app/frontend/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
-aiagents4pharma/talk2knowledgegraphs/configs/app/frontend/default.yaml,sha256=6qE7j4k3gO83TNA31XVDJus0gTJloO2sG5R_ovZw7VM,2269
+aiagents4pharma/talk2knowledgegraphs/configs/app/frontend/default.yaml,sha256=FnRUgImdaQ9wSy4EFItYAvbQAD8zm851If3K6akFCzU,2300
 aiagents4pharma/talk2knowledgegraphs/configs/tools/__init__.py,sha256=C1yyRZW8hqWw46p_bh1vAJp2z9aVvn4HpKjKkjlWIqY,150
 aiagents4pharma/talk2knowledgegraphs/configs/tools/graphrag_reasoning/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
 aiagents4pharma/talk2knowledgegraphs/configs/tools/graphrag_reasoning/default.yaml,sha256=Ua99yECXiwp4ZCUDgsDskYbKzcJrv7roQuLj31Zky4c,1037
 aiagents4pharma/talk2knowledgegraphs/configs/tools/multimodal_subgraph_extraction/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+aiagents4pharma/talk2knowledgegraphs/configs/tools/multimodal_subgraph_extraction/default.yaml,sha256=M4scS2KEgux24bWuepNyJLzTFZ-CagcF6zLCw-6JK3k,919
 aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_extraction/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
 aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_extraction/default.yaml,sha256=U8HvMsYbaOwDwQPATj7EFvLtTy7XZEplE5WMoNjgYYc,1469
 aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_summarization/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
 aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_summarization/default.yaml,sha256=OOSlPpJVwJK4_lu4lhA2E48yhFFbEYpyHsoi9Orgm00,561
+aiagents4pharma/talk2knowledgegraphs/configs/utils/enrichments/ols_terms/default.yaml,sha256=ar2w5mL3H34Dy9sNoUk6gFVyR7WxxFhywNxFV50NmU8,106
+aiagents4pharma/talk2knowledgegraphs/configs/utils/enrichments/reactome_pathways/default.yaml,sha256=tYSmVXt8RXSuVXKuHFJfuWnQk8SyYQ5NuhiHSu7nG44,124
+aiagents4pharma/talk2knowledgegraphs/configs/utils/enrichments/uniprot_proteins/default.yaml,sha256=zndlkZnExOc12H6rJUDhrnxY6_0-cE7SSJBes_egLio,183
+aiagents4pharma/talk2knowledgegraphs/configs/utils/pubchem_utils/default.yaml,sha256=0-ND1Bqvj1LZauTcg2ztYDjkTxsfaSCtZct9AiVrnQM,383
 aiagents4pharma/talk2knowledgegraphs/datasets/__init__.py,sha256=L3gPuHskSegmtXskVrLIYr7FXe_ibKgJ2GGr1_Wok6k,173
 aiagents4pharma/talk2knowledgegraphs/datasets/biobridge_primekg.py,sha256=QlzDXmXREoa9MA6-GwzqRjdzndQeGBAF11Td6NFk_9Y,23426
 aiagents4pharma/talk2knowledgegraphs/datasets/dataset.py,sha256=-LaPLse8BkALqwFetNK7wch2dt9Dz6QKGKZKBKM6bIk,409
@@ -167,7 +172,7 @@ aiagents4pharma/talk2scholars/configs/agents/talk2scholars/paper_download_agent/
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/pdf_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/pdf_agent/default.yaml,sha256=p3hFJi-1xbHCNagTG13WHvsrPt11XQg1nHS7VJx2XOY,166
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/default.yaml,sha256=N3a_brrB1ilUCeqHQrqu97Olz2snko3tTNPMNR8yTHI,208
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/default.yaml,sha256=CHMsW3cpGtfYWpSIY5XgNEYPvbI31OjOYfl_VbbKIyY,707
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/default.yaml,sha256=FUbJIiH_FHeL0n1M-HSsLX_R2gMBRxBnPcejhd0HrYc,399
 aiagents4pharma/talk2scholars/configs/app/__init__.py,sha256=tXpOW3R4eAfNoqvoaHfabSG-DcMHmUGSTg_4zH_vlgw,94
@@ -183,7 +188,7 @@ aiagents4pharma/talk2scholars/configs/tools/download_medrxiv_paper/default.yaml,
 aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/default.yaml,sha256=comNgL9hRpH--IWuEsrN6hV5WdrJmh-ZsRh7hbryVhg,631
 aiagents4pharma/talk2scholars/configs/tools/question_and_answer/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/tools/question_and_answer/default.yaml,sha256=lZ_DM0UIj8j2Xryt90YOEj4Bl9_FZ-Z4dhLxaAbgNFY,977
+aiagents4pharma/talk2scholars/configs/tools/question_and_answer/default.yaml,sha256=Pa3JVyA9tabXZ4Bk3n5dAml7P-nXUcT7HgkA8Kr_sXk,2238
 aiagents4pharma/talk2scholars/configs/tools/retrieve_semantic_scholar_paper_id/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 aiagents4pharma/talk2scholars/configs/tools/retrieve_semantic_scholar_paper_id/default.yaml,sha256=HG-N8yRjlX9zFwbIBvaDI9ndKjfL-gqPTCCPMLgdUpw,271
 aiagents4pharma/talk2scholars/configs/tools/search/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
@@ -198,13 +203,25 @@ aiagents4pharma/talk2scholars/state/__init__.py,sha256=ReScKLpEvedq4P6ww52NRQS0X
 aiagents4pharma/talk2scholars/state/state_talk2scholars.py,sha256=Z2zV-SXB2SMnn8PnjWjmK-OD5KjUwMTChBpXBAcl2hg,3885
 aiagents4pharma/talk2scholars/tests/__init__.py,sha256=U3PsTiUZaUBD1IZanFGkDIOdFieDVJtGKQ5-woYUo8c,45
 aiagents4pharma/talk2scholars/tests/test_main_agent.py,sha256=4Z3xLq8MGlayGhQE5qKOirYotwJrlf7fk8rqAaORorg,7617
-aiagents4pharma/talk2scholars/tests/test_nvidia_nim_reranker_utils.py,sha256=-q4Y2CMTAOvrSyyZ1MmpeEuKvJcZSPe6jmUD0rZhUew,947
+aiagents4pharma/talk2scholars/tests/test_nvidia_nim_reranker.py,sha256=ftfn4VenufZ-zt2nSOyOoCjfSbwFOW9CS1DLzPtBEaM,4410
 aiagents4pharma/talk2scholars/tests/test_paper_download_agent.py,sha256=gKSQp-sw62FplNnGYW0wv2ZIUEefh3o0tFWbRzy9yLs,5068
 aiagents4pharma/talk2scholars/tests/test_paper_download_biorxiv.py,sha256=gosuW4VBXyorQXbf0TpgAIT2hQjEeuvTTnT1jnoBYqM,6405
 aiagents4pharma/talk2scholars/tests/test_paper_download_medrxiv.py,sha256=iNq9vEIVapmnUZTRJXCv_UoaWThGapW7Vt_2BmZG9NE,6414
 aiagents4pharma/talk2scholars/tests/test_paper_download_tools.py,sha256=lGXbHl3lEXDjMHAX9uCgrREBOUuOHWv9TsYEshiG_tc,10421
 aiagents4pharma/talk2scholars/tests/test_pdf_agent.py,sha256=9Kr0FcyFWmUDTasYh6ZdS-OWQqy37mH9K3p5Y0dqQHw,4283
-aiagents4pharma/talk2scholars/tests/test_question_and_answer_tool.py,sha256=7S9bqQSdvm7xihtBSAQD3RQimFtVHejPIkaaEddeNRs,22057
+aiagents4pharma/talk2scholars/tests/test_pdf_answer_formatter.py,sha256=a1a_z1M9sOQ_SFo-gHM3xA_f5MoJJmEoW8Tc3AX9vL0,2239
+aiagents4pharma/talk2scholars/tests/test_pdf_batch_processor.py,sha256=e8KQJ80nbOmCH4mgDnIXXjlrRk0zf0g-5Odt2jsCU0s,3251
+aiagents4pharma/talk2scholars/tests/test_pdf_collection_manager.py,sha256=M7mT_t2X4DUw-oSicnUnRU73exVDldQIcHlwQmIyV2s,5147
+aiagents4pharma/talk2scholars/tests/test_pdf_document_processor.py,sha256=G_LPOqfIDAah-24GScIaXu6-McpddLd-1i779bbJg-c,2576
+aiagents4pharma/talk2scholars/tests/test_pdf_generate_answer.py,sha256=h2MITyWsaRWrW3vxTGKht0JyhEfRW0Tomhyq257eNrY,2657
+aiagents4pharma/talk2scholars/tests/test_pdf_gpu_detection.py,sha256=nh8VyzqMEIQ3IjbTYSX29tjqLLCXmmHY74AQG6ZOUis,4952
+aiagents4pharma/talk2scholars/tests/test_pdf_paper_loader.py,sha256=QOwFnKN-fl6h7b_yaOfos96G0qR4AxQvyJfH6TK4u_Q,3678
+aiagents4pharma/talk2scholars/tests/test_pdf_rag_pipeline.py,sha256=DfiyzVlx-ZXQK99C2ieVgVafL7ujcC9k2dRPZ82tTNk,2949
+aiagents4pharma/talk2scholars/tests/test_pdf_retrieve_chunks.py,sha256=2cjbCrf86z6kajV-8QDEW_J0ZWtzA3jRILaIscfsGyI,7729
+aiagents4pharma/talk2scholars/tests/test_pdf_singleton_manager.py,sha256=gOk8L9wNRPUnAiB89n1a4pQQPI7UtonRi7-IcCip94k,5628
+aiagents4pharma/talk2scholars/tests/test_pdf_vector_normalization.py,sha256=pu9I3tromjToIN5r4S8sWanaLBVhhk71UPP5zTTGwZY,3928
+aiagents4pharma/talk2scholars/tests/test_pdf_vector_store.py,sha256=-7CUiPLT4mOBVkNV2qlF7t4yU_mRArM0uAcUAKgEY4k,15644
+aiagents4pharma/talk2scholars/tests/test_question_and_answer_tool.py,sha256=UKSD7wLJ1cZunw8a1BHM7E-NUML6blxpqoDroCYuvQs,4245
 aiagents4pharma/talk2scholars/tests/test_read_helper_utils.py,sha256=yTT1aLpTydDSdGcRZur5cMktwYZbFK5NEUgOBvltcWg,3819
 aiagents4pharma/talk2scholars/tests/test_s2_agent.py,sha256=TsdNlZ6vHz18bbX6Vto28nbBLRDI94wSFt5-1acDK64,7768
 aiagents4pharma/talk2scholars/tests/test_s2_display_dataframe.py,sha256=2VPPZitQRWDZV0ceaK2-hQqkIvoigSPWNHoFOgKJjQE,3107
@@ -215,7 +232,7 @@ aiagents4pharma/talk2scholars/tests/test_s2_search.py,sha256=mCGpoCYVn0SJ9BPcEjT
 aiagents4pharma/talk2scholars/tests/test_s2_single.py,sha256=KjSh7V2cl1IuO_M9O6dj0vnMHr13H-xKxia_ZgT4qag,10313
 aiagents4pharma/talk2scholars/tests/test_s2_utils_ext_ids.py,sha256=6xbHzClkYI_ZcR3-Xl7nGs8-hB0IyLlxn8rzeXrJxFQ,15129
 aiagents4pharma/talk2scholars/tests/test_state.py,sha256=A2lqA4h37QptLnwKWwm1Y79yELE4wtEBXzCiQ13YdLw,1270
-aiagents4pharma/talk2scholars/tests/test_tool_helper_utils.py,sha256=gJBzV1-hkzGi3VY9SG4JSoKTyz7KavPy1HjEF6bnfIQ,6141
+aiagents4pharma/talk2scholars/tests/test_tool_helper_utils.py,sha256=64Z2JggDk-S8I00CNR69os8NGVLu63zd5pEJmMhC2wc,3365
 aiagents4pharma/talk2scholars/tests/test_zotero_agent.py,sha256=iWbWlat5RWE8mmCSqKGNG7Xzbdieua6cKGq-jwqP4ws,6119
 aiagents4pharma/talk2scholars/tests/test_zotero_human_in_the_loop.py,sha256=YelLQu9Y_r1SNQsC1xoLHJoJ3soIZtBt1MFbbNhY-Dg,10744
 aiagents4pharma/talk2scholars/tests/test_zotero_path.py,sha256=Ko0HyXCrpm-vs8Bkf-syxp3MfL1IvZwXXgPExyQy_F8,18618
@@ -225,23 +242,33 @@ aiagents4pharma/talk2scholars/tests/test_zotero_write.py,sha256=qWlO0XoZJ6vxUxgi
 aiagents4pharma/talk2scholars/tools/__init__.py,sha256=c8pYHDqR9P0Frz2jWjbvyizfSTBMlMFzGsiQzx2KC9c,189
 aiagents4pharma/talk2scholars/tools/paper_download/__init__.py,sha256=Lu5FmBxDH8mIIYE41G8_BKYXUf-vHIYVwujidbeydl4,295
 aiagents4pharma/talk2scholars/tools/paper_download/download_arxiv_input.py,sha256=e3S8JusJVVSEC_tFh8H5CS9ZqD20jX8hkFO9EYESBXo,5653
-aiagents4pharma/talk2scholars/tools/paper_download/download_biorxiv_input.py,sha256=R92OaR4Omilj-v-rT0Me_BhxN8-AF0sbDwhUxNCUTm4,3718
-aiagents4pharma/talk2scholars/tools/paper_download/download_medrxiv_input.py,sha256=UaHsdZXseUMQfiIovD0kS8r9DZ6KJpRGtTZyOCTRYVs,3786
+aiagents4pharma/talk2scholars/tools/paper_download/download_biorxiv_input.py,sha256=Iipvv0P-KLbW8ELMDBLr-FxgoGBjRjPToVw7pBVJS-Y,3676
+aiagents4pharma/talk2scholars/tools/paper_download/download_medrxiv_input.py,sha256=2ONhx7rygCACf_SYc1cxDAmQP4ZzkB39OoLZYsbFMyI,3752
 aiagents4pharma/talk2scholars/tools/pdf/__init__.py,sha256=DPpOfON3AySko5EBBAe_3udOoSaAdQWNyGeNvJyV5R8,138
-aiagents4pharma/talk2scholars/tools/pdf/question_and_answer.py,sha256=PI9ltnKZpORXAPPowPt6qVbXclXXoY4mamj8ZKA0tsM,5586
-aiagents4pharma/talk2scholars/tools/pdf/utils/__init__.py,sha256=Ghsh5nnESckMqvnokMRW_3mo2sDstOPKAAuiAHF1b8o,273
-aiagents4pharma/talk2scholars/tools/pdf/utils/generate_answer.py,sha256=YvnBWD7yn12H5nchPBFBD9txviwJtX56f3fDRwkGBBE,3299
-aiagents4pharma/talk2scholars/tools/pdf/utils/nvidia_nim_reranker.py,sha256=M4OSqact8QMk-Ov05Bcz7Y7tr2rBAgdM3DRsQKB0r0o,2851
-aiagents4pharma/talk2scholars/tools/pdf/utils/retrieve_chunks.py,sha256=agV7SHy5ool0x_N7WmNI-C1Wpc-6EToYoiqkMJX6xWs,2599
-aiagents4pharma/talk2scholars/tools/pdf/utils/tool_helper.py,sha256=maOIh6sLSOqU3PTsty5AZKIoBGxziFDi-LliSULQyK0,4702
-aiagents4pharma/talk2scholars/tools/pdf/utils/vector_store.py,sha256=8yumaryNLZdRP_WcRt6GHk9Oi8asYPkOS9vKSn7zJak,5810
+aiagents4pharma/talk2scholars/tools/pdf/question_and_answer.py,sha256=_HLO04bzTSlnEEWwkJ3rC9Gjz8MPeHVglqovoTDOSp4,5844
+aiagents4pharma/talk2scholars/tools/pdf/utils/__init__.py,sha256=AlvoJY0hI4MCS4zHO3EtFkFJpKqjO7ZxWkoE3QvHi88,820
+aiagents4pharma/talk2scholars/tools/pdf/utils/answer_formatter.py,sha256=E8XCA-R744nSgkSl7OIBdcAHjXLMFGaeZAFzOY4TPYI,1645
+aiagents4pharma/talk2scholars/tools/pdf/utils/batch_processor.py,sha256=4lCQ4TOOIca3zZg4mF4uCQuRE5A2dI0Z7Kk1Z5y3Y2I,5893
+aiagents4pharma/talk2scholars/tools/pdf/utils/collection_manager.py,sha256=CSYim0zZ_S0MNWecTz5U8KEX1L9Rtu1Ki8Kp_aX73iQ,5698
+aiagents4pharma/talk2scholars/tools/pdf/utils/document_processor.py,sha256=-9o9OE6O0WpHw55Ps2RhR-uDjJlMDbYTnU2ZueS9KAw,2586
+aiagents4pharma/talk2scholars/tools/pdf/utils/generate_answer.py,sha256=zTXo09zfGhPeU1IdfF8sk6lFOkx0GKOQrhbEnKGQujw,3299
+aiagents4pharma/talk2scholars/tools/pdf/utils/get_vectorstore.py,sha256=u90DHqckgpC4BftzKRyd998GM5VG294ybA6Xby5clXs,2069
+aiagents4pharma/talk2scholars/tools/pdf/utils/gpu_detection.py,sha256=VkTBkAWrV2RekO0swnxrRmbG5YtP3-Rl3fu2CaZ1b_Y,5402
+aiagents4pharma/talk2scholars/tools/pdf/utils/nvidia_nim_reranker.py,sha256=k800UKpG7krqsfkwX_cHBm0Einu7MbmIwhi8Smj_nsM,3407
+aiagents4pharma/talk2scholars/tools/pdf/utils/paper_loader.py,sha256=gMZasRX6XT-EbZ9EQlhB0un6bcFNbQb_xkQ76rhxQfQ,4060
+aiagents4pharma/talk2scholars/tools/pdf/utils/rag_pipeline.py,sha256=avsw40v5MwoWrXKbiT0krLmwCY_5mYtCc-_LDYf-0ZY,3492
+aiagents4pharma/talk2scholars/tools/pdf/utils/retrieve_chunks.py,sha256=u16hklQnGG7Mp0uBzpFDwV3PwAn6FtCrkabjhenw2Lg,6917
+aiagents4pharma/talk2scholars/tools/pdf/utils/singleton_manager.py,sha256=KIz0ypThzaHyUHCbcg_mchW9Qr1uFK4OsmhD2NLUYZo,5052
+aiagents4pharma/talk2scholars/tools/pdf/utils/tool_helper.py,sha256=NCc778mfWD4OAeA6On2me1c6n9YfFWujsd5h2L2L568,3034
+aiagents4pharma/talk2scholars/tools/pdf/utils/vector_normalization.py,sha256=f4erq3JJW7Fdk7vM1qQf3i1si6FZzPoFHVfV98U3b7Y,4675
+aiagents4pharma/talk2scholars/tools/pdf/utils/vector_store.py,sha256=X9OGwV3RHZIjglIbYJ7sK5feUAOfITgXdFRCcVjelXg,12817
 aiagents4pharma/talk2scholars/tools/s2/__init__.py,sha256=w_eiw0pG8HNp79F9O_icXs_Yl_4odsmagYNKDTjIsvk,428
 aiagents4pharma/talk2scholars/tools/s2/display_dataframe.py,sha256=qnY7AQDnAs0SrmV7AZ9pWm10HEmPlO7EBfzYvpb3jvs,3965
-aiagents4pharma/talk2scholars/tools/s2/multi_paper_rec.py,sha256=NY8nTsW9xP6qakiQ0wbq9AXP2mcT5-GMZoa9cnr4EjY,3770
-aiagents4pharma/talk2scholars/tools/s2/query_dataframe.py,sha256=omff-2g85qcLZj5Qo35m2LJlE1AOzESEfT4jt3ZVYz0,7066
-aiagents4pharma/talk2scholars/tools/s2/retrieve_semantic_scholar_paper_id.py,sha256=aJTIbUKXLvjD9P7S-SM0O5iTRdUdomOcE67lHwsmGjg,3954
+aiagents4pharma/talk2scholars/tools/s2/multi_paper_rec.py,sha256=TEt4jOX1u8v3w_u10sGx-Ghwhe4yjuaYmUjD62nJQJM,3886
+aiagents4pharma/talk2scholars/tools/s2/query_dataframe.py,sha256=EJ-EV-pk2kLS12Q5HatBdGue3t-MB8mx5PrSxtLN7Co,7042
+aiagents4pharma/talk2scholars/tools/s2/retrieve_semantic_scholar_paper_id.py,sha256=0yILvpqraXldd61nLHSCfITvKyLIxts6HBC5GaGVfBQ,3995
 aiagents4pharma/talk2scholars/tools/s2/search.py,sha256=SUAN32x1d9dNikFKitcXZZ0BhFfsGMdLDk0z0DpJXuA,3334
-aiagents4pharma/talk2scholars/tools/s2/single_paper_rec.py,sha256=3lvrIPlgP8gp_3YQCcUQKyHmNMHevN8OqLTq4mPeBEY,3502
+aiagents4pharma/talk2scholars/tools/s2/single_paper_rec.py,sha256=JTggOB4sqhTF1kP81Gl_54RjpbHIfqtJEoUTxlZ82N8,3630
 aiagents4pharma/talk2scholars/tools/s2/utils/__init__.py,sha256=wBTPVgiXbmIJUMouOQRwojgk5PJXeEinDJzHzEToZbU,229
 aiagents4pharma/talk2scholars/tools/s2/utils/multi_helper.py,sha256=Z5G4e7R7cUO60_HYbcd3BJC_-jtybc5DGcOC8yjpprY,8642
 aiagents4pharma/talk2scholars/tools/s2/utils/search_helper.py,sha256=wVkQW2KTmS2av4W5PqqRhCb53n-egZLpAD95xV2mO68,7839
@@ -256,8 +283,8 @@ aiagents4pharma/talk2scholars/tools/zotero/utils/review_helper.py,sha256=IPD1V9y
 aiagents4pharma/talk2scholars/tools/zotero/utils/write_helper.py,sha256=ALwLecy1QVebbsmXJiDj1GhGmyhq2R2tZlAyEl1vfhw,7410
 aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_path.py,sha256=oIrfbOySgts50ksHKyjcWjRkPRIS88g3Lc0v9mBkU8w,6375
 aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_pdf_downloader.py,sha256=ERBha8afU6Q1EaRBe9qB8tchOzZ4_KfFgDW6EElOJoU,4816
-aiagents4pharma-1.40.1.dist-info/licenses/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
-aiagents4pharma-1.40.1.dist-info/METADATA,sha256=Uh1B7RydWo-Kws3BmYpTVRDU4qTIfzPSr8FEo_pXl7o,15945
-aiagents4pharma-1.40.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-aiagents4pharma-1.40.1.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
-aiagents4pharma-1.40.1.dist-info/RECORD,,
+aiagents4pharma-1.42.0.dist-info/licenses/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
+aiagents4pharma-1.42.0.dist-info/METADATA,sha256=qbfg8yUF-3Tn5k82Ry5wCuLNzv6PWVpeL46inguNRuI,12894
+aiagents4pharma-1.42.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+aiagents4pharma-1.42.0.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
+aiagents4pharma-1.42.0.dist-info/RECORD,,

aiagents4pharma/talk2scholars/tests/test_nvidia_nim_reranker_utils.py DELETED Viewed

@@ -1,28 +0,0 @@
-"""
-Unit tests for NVIDIA NIM reranker error handling in nvidia_nim_reranker.py
-"""
-import unittest
-from types import SimpleNamespace
-from aiagents4pharma.talk2scholars.tools.pdf.utils.nvidia_nim_reranker import (
-    rank_papers_by_query,
-)
-class TestNVIDIARerankerError(unittest.TestCase):
-    """Tests for NVIDIA NIM reranker error handling."""
-    def test_missing_api_key_raises_value_error(self):
-        """Ensure missing API key triggers ValueError."""
-        vector_store = SimpleNamespace(documents={})
-        # Config without API key
-        cfg = SimpleNamespace(
-            reranker=SimpleNamespace(model="m", api_key=None), top_k_papers=3
-        )
-        with self.assertRaises(ValueError) as cm:
-            rank_papers_by_query(vector_store, "query", cfg, top_k=cfg.top_k_papers)
-        self.assertEqual(
-            str(cm.exception),
-            "Configuration 'reranker.api_key' must be set for reranking",
-        )

{aiagents4pharma-1.40.1.dist-info → aiagents4pharma-1.42.0.dist-info}/WHEEL RENAMED Viewed

File without changes

{aiagents4pharma-1.40.1.dist-info → aiagents4pharma-1.42.0.dist-info}/licenses/LICENSE RENAMED Viewed

File without changes

{aiagents4pharma-1.40.1.dist-info → aiagents4pharma-1.42.0.dist-info}/top_level.txt RENAMED Viewed

File without changes

aiagents4pharma 1.40.1__py3-none-any.whl → 1.42.0__py3-none-any.whl

aiagents4pharma 1.40.1py3-none-any.whl → 1.42.0py3-none-any.whl