aiagents4pharma 1.41.0__py3-none-any.whl → 1.42.0__py3-none-any.whl

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Files changed (12) hide show
  1. aiagents4pharma/talk2knowledgegraphs/configs/app/frontend/default.yaml +1 -1
  2. aiagents4pharma/talk2knowledgegraphs/configs/tools/multimodal_subgraph_extraction/default.yaml +37 -0
  3. aiagents4pharma/talk2knowledgegraphs/configs/utils/enrichments/ols_terms/default.yaml +3 -0
  4. aiagents4pharma/talk2knowledgegraphs/configs/utils/enrichments/reactome_pathways/default.yaml +3 -0
  5. aiagents4pharma/talk2knowledgegraphs/configs/utils/enrichments/uniprot_proteins/default.yaml +6 -0
  6. aiagents4pharma/talk2knowledgegraphs/configs/utils/pubchem_utils/default.yaml +5 -0
  7. aiagents4pharma/talk2knowledgegraphs/milvus_data_dump.py +752 -350
  8. {aiagents4pharma-1.41.0.dist-info → aiagents4pharma-1.42.0.dist-info}/METADATA +28 -14
  9. {aiagents4pharma-1.41.0.dist-info → aiagents4pharma-1.42.0.dist-info}/RECORD +12 -7
  10. {aiagents4pharma-1.41.0.dist-info → aiagents4pharma-1.42.0.dist-info}/WHEEL +0 -0
  11. {aiagents4pharma-1.41.0.dist-info → aiagents4pharma-1.42.0.dist-info}/licenses/LICENSE +0 -0
  12. {aiagents4pharma-1.41.0.dist-info → aiagents4pharma-1.42.0.dist-info}/top_level.txt +0 -0
{aiagents4pharma-1.41.0.dist-info → aiagents4pharma-1.42.0.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: aiagents4pharma
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- Version: 1.41.0
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+ Version: 1.42.0
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  Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
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  Classifier: Programming Language :: Python :: 3
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  Classifier: License :: OSI Approved :: MIT License
@@ -65,20 +65,35 @@ Requires-Dist: plotly-express==0.4.1
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  Requires-Dist: seaborn==0.13.2
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  Requires-Dist: scanpy==1.11.0
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  Requires-Dist: openpyxl==3.1.5
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- Requires-Dist: pymilvus==2.5.11
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  Dynamic: license-file
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+ <img src="docs/assets/VPE.png" alt="Virtual Patient Engine Logo" width="150"/>
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+
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+ <!-- Project Info -->
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+
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+ ![RELEASE](https://img.shields.io/github/v/release/VirtualPatientEngine/AIAgents4Pharma?label=RELEASE)
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+ ![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)
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+
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+ <!-- Deployment Workflows -->
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+
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+ [![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)
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+ [![MkDocs Deploy](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/mkdocs-deploy.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/mkdocs-deploy.yml)
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+ [![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)
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+
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+ <!-- Tests -->
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+ [![TESTS Talk2AIAgents4Pharma](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2aiagents4pharma.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2aiagents4pharma.yml)
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  [![Talk2BioModels](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml)
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- [![Talk2Cells](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml)
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  [![Talk2KnowledgeGraphs](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml)
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  [![TESTS Talk2Scholars](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2scholars.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2scholars.yml)
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- [![TESTS Talk2AIAgents4Pharma](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2aiagents4pharma.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2aiagents4pharma.yml)
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- ![GitHub Release](https://img.shields.io/github/v/release/VirtualPatientEngine/AIAgents4Pharma)
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- ![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)
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- ![Talk2AIAgents4Pharma Pulls](https://img.shields.io/docker/pulls/virtualpatientengine/talk2aiagents4pharma?label=Talk2AIAgents4Pharma%20Pulls&color=blue&logo=docker&style=flat-square)
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- ![Talk2Scholars Pulls](https://img.shields.io/docker/pulls/virtualpatientengine/talk2scholars?label=Talk2Scholars%20Pulls&color=blue&logo=docker&style=flat-square)
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- ![Talk2BioModels Pulls](https://img.shields.io/docker/pulls/virtualpatientengine/talk2biomodels?label=Talk2BioModels%20Pulls&color=blue&logo=docker&style=flat-square)
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- ![Talk2KnowledgeGraphs Pulls](https://img.shields.io/docker/pulls/virtualpatientengine/talk2knowledgegraphs?label=Talk2KnowledgeGraphs%20Pulls&color=blue&logo=docker&style=flat-square)
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+ [![Talk2Cells](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml)
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+ <!-- Docker Pulls -->
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+ ![Talk2AIAgents4Pharma Pulls](https://img.shields.io/docker/pulls/vpatientengine/talk2aiagents4pharma?label=Talk2AIAgents4Pharma%20Pulls&color=blue&logo=docker&style=flat-square)
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+ ![Talk2BioModels Pulls](https://img.shields.io/docker/pulls/vpatientengine/talk2biomodels?label=Talk2BioModels%20Pulls&color=blue&logo=docker&style=flat-square)
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+ ![Talk2KnowledgeGraphs Pulls](https://img.shields.io/docker/pulls/vpatientengine/talk2knowledgegraphs?label=Talk2KnowledgeGraphs%20Pulls&color=blue&logo=docker&style=flat-square)
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+ ![Talk2Scholars Pulls](https://img.shields.io/docker/pulls/vpatientengine/talk2scholars?label=Talk2Scholars%20Pulls&color=blue&logo=docker&style=flat-square)
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  ## Introduction
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@@ -170,14 +185,13 @@ If your machine has NVIDIA GPU(s), please install the following this:
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  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).
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- **Talk2Scholars** 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.)_
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+ **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.)_
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+ > By default, `talk2knowledgegraphs` includes a small subset of the PrimeKG knowledge graph, allowing users to start interacting with it out of the box.
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+ > To switch to a different knowledge graph or use your own, refer to the [deployment guide](https://virtualpatientengine.github.io/AIAgents4Pharma/talk2knowledgegraphs/deployment/).
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  > Additionally on **Windows**, the `pcst_fast 1.0.10` library requires **Microsoft Visual C++ 14.0 or greater**.
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  > You can download the **Microsoft C++ Build Tools** [here](https://visualstudio.microsoft.com/visual-cpp-build-tools/).
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- 📝 By default, `talk2knowledgegraphs` includes a small subset of the PrimeKG knowledge graph, allowing users to start interacting with it out of the box.
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- To switch to a different knowledge graph or use your own, refer to the [deployment guide](https://virtualpatientengine.github.io/AIAgents4Pharma/talk2knowledgegraphs/deployment/).
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  **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).
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  _Please note that this will create a new tracing project in your Langsmith
{aiagents4pharma-1.41.0.dist-info → aiagents4pharma-1.42.0.dist-info}/RECORD RENAMED
@@ -72,7 +72,7 @@ aiagents4pharma/talk2cells/tools/scp_agent/__init__.py,sha256=s7g0lyH1lMD9pcWHLP
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  aiagents4pharma/talk2cells/tools/scp_agent/display_studies.py,sha256=6q59gh_NQaiOU2rn55A3sIIFKlXi4SK3iKgySvUDrtQ,600
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  aiagents4pharma/talk2cells/tools/scp_agent/search_studies.py,sha256=MLe-twtFnOu-P8P9diYq7jvHBHbWFRRCZLcfpUzqPMg,2806
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  aiagents4pharma/talk2knowledgegraphs/__init__.py,sha256=Z0Eo7LTiKk0STsr8VI7wkCLq7PHrK1vYlH4I1hSNLiA,165
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- aiagents4pharma/talk2knowledgegraphs/milvus_data_dump.py,sha256=YOTO1HcSpNxQdc83jgwcuFkzGeCHov7CRDHQQL9PHNE,22608
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+ aiagents4pharma/talk2knowledgegraphs/milvus_data_dump.py,sha256=2LMGp2Coh7Q1TeWez-_wkMDfHzf_Tkj9cPslV0_ixOU,36202
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  aiagents4pharma/talk2knowledgegraphs/agents/__init__.py,sha256=iOAzuy_8A03tQDFtSBhC9dldUo62z5gfxcVtXAdLOJs,92
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  aiagents4pharma/talk2knowledgegraphs/agents/t2kg_agent.py,sha256=eUARAhzOz8PpHFzN2fP4L_fDEyqdllrAkBWa0otxGv4,3363
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  aiagents4pharma/talk2knowledgegraphs/configs/__init__.py,sha256=4_DVdpahaJ55yPl0aZotlFA_MYWLFF2cubWyKtBVI_Q,126
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  aiagents4pharma/talk2knowledgegraphs/configs/agents/t2kg_agent/default.yaml,sha256=ENCGROwYFpR6g4QD518h73sshdn3vPVpotBMk1QJcpU,4830
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  aiagents4pharma/talk2knowledgegraphs/configs/app/__init__.py,sha256=fKfc3FR7g5KjY9b6jzrU6cwKTVVpkoVZQS3dvUowu34,69
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  aiagents4pharma/talk2knowledgegraphs/configs/app/frontend/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
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- aiagents4pharma/talk2knowledgegraphs/configs/app/frontend/default.yaml,sha256=6qE7j4k3gO83TNA31XVDJus0gTJloO2sG5R_ovZw7VM,2269
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+ aiagents4pharma/talk2knowledgegraphs/configs/app/frontend/default.yaml,sha256=FnRUgImdaQ9wSy4EFItYAvbQAD8zm851If3K6akFCzU,2300
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  aiagents4pharma/talk2knowledgegraphs/configs/tools/__init__.py,sha256=C1yyRZW8hqWw46p_bh1vAJp2z9aVvn4HpKjKkjlWIqY,150
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  aiagents4pharma/talk2knowledgegraphs/configs/tools/graphrag_reasoning/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
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  aiagents4pharma/talk2knowledgegraphs/configs/tools/graphrag_reasoning/default.yaml,sha256=Ua99yECXiwp4ZCUDgsDskYbKzcJrv7roQuLj31Zky4c,1037
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  aiagents4pharma/talk2knowledgegraphs/configs/tools/multimodal_subgraph_extraction/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ aiagents4pharma/talk2knowledgegraphs/configs/tools/multimodal_subgraph_extraction/default.yaml,sha256=M4scS2KEgux24bWuepNyJLzTFZ-CagcF6zLCw-6JK3k,919
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  aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_summarization/default.yaml,sha256=OOSlPpJVwJK4_lu4lhA2E48yhFFbEYpyHsoi9Orgm00,561
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+ aiagents4pharma/talk2knowledgegraphs/configs/utils/enrichments/ols_terms/default.yaml,sha256=ar2w5mL3H34Dy9sNoUk6gFVyR7WxxFhywNxFV50NmU8,106
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+ aiagents4pharma/talk2knowledgegraphs/configs/utils/enrichments/reactome_pathways/default.yaml,sha256=tYSmVXt8RXSuVXKuHFJfuWnQk8SyYQ5NuhiHSu7nG44,124
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+ aiagents4pharma/talk2knowledgegraphs/configs/utils/enrichments/uniprot_proteins/default.yaml,sha256=zndlkZnExOc12H6rJUDhrnxY6_0-cE7SSJBes_egLio,183
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+ aiagents4pharma/talk2knowledgegraphs/configs/utils/pubchem_utils/default.yaml,sha256=0-ND1Bqvj1LZauTcg2ztYDjkTxsfaSCtZct9AiVrnQM,383
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  aiagents4pharma/talk2knowledgegraphs/datasets/__init__.py,sha256=L3gPuHskSegmtXskVrLIYr7FXe_ibKgJ2GGr1_Wok6k,173
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  aiagents4pharma/talk2knowledgegraphs/datasets/biobridge_primekg.py,sha256=QlzDXmXREoa9MA6-GwzqRjdzndQeGBAF11Td6NFk_9Y,23426
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@@ -278,8 +283,8 @@ aiagents4pharma/talk2scholars/tools/zotero/utils/review_helper.py,sha256=IPD1V9y
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  aiagents4pharma/talk2scholars/tools/zotero/utils/write_helper.py,sha256=ALwLecy1QVebbsmXJiDj1GhGmyhq2R2tZlAyEl1vfhw,7410
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  aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_path.py,sha256=oIrfbOySgts50ksHKyjcWjRkPRIS88g3Lc0v9mBkU8w,6375
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  aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_pdf_downloader.py,sha256=ERBha8afU6Q1EaRBe9qB8tchOzZ4_KfFgDW6EElOJoU,4816
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- aiagents4pharma-1.41.0.dist-info/licenses/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
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- aiagents4pharma-1.41.0.dist-info/METADATA,sha256=vZTucUK52stvfzDaekMcwqo7SJC4QKhsta97q7iHQlY,12064
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- aiagents4pharma-1.41.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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- aiagents4pharma-1.41.0.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
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- aiagents4pharma-1.41.0.dist-info/RECORD,,
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+ aiagents4pharma-1.42.0.dist-info/licenses/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
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+ aiagents4pharma-1.42.0.dist-info/METADATA,sha256=qbfg8yUF-3Tn5k82Ry5wCuLNzv6PWVpeL46inguNRuI,12894
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+ aiagents4pharma-1.42.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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+ aiagents4pharma-1.42.0.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
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+ aiagents4pharma-1.42.0.dist-info/RECORD,,