a b/pyproject.toml 

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[build-system]





  
  

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requires = ["setuptools", "wheel"]





  
  

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build-backend = "setuptools.build_meta"





  
  

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[project]





  
  

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name = "aiagents4pharma"





  
  

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description = "AI Agents for drug discovery, drug development, and other pharmaceutical R&D."





  
  

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readme = "README.md"





  
  

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requires-python = ">=3.12"





  
  

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classifiers = [





  
  

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  "Programming Language :: Python :: 3",





  
  

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  "License :: OSI Approved :: MIT License",





  
  

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  "Operating System :: OS Independent",





  
  

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]





  
  

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dependencies = [





  
  

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  "copasi_basico==0.78",





  
  

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  "coverage==7.6.4",





  
  

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  "einops==0.8.0",





  
  

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  "gdown==5.2.0",





  
  

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  "gravis==0.1.0",





  
  

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  "huggingface_hub==0.26.5",





  
  

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  "hydra-core==1.3.2",





  
  

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  "joblib==1.4.2",





  
  

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  "langchain==0.3.7",





  
  

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  "langchain-community==0.3.5",





  
  

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  "langchain-core==0.3.40",





  
  

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  "langchain-experimental==0.3.3",





  
  

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  "langchain-nvidia-ai-endpoints==0.3.9",





  
  

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  "langchain-openai==0.2.5",





  
  

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  "langchain_ollama==0.2.3",





  
  

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  "langgraph_supervisor==0.0.9",





  
  

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  "matplotlib==3.9.2",





  
  

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  "openai==1.59.4",





  
  

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  "ollama==0.4.7",





  
  

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  "pandas==2.2.3",





  
  

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  "pcst_fast==1.0.10",





  
  

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  "plotly==5.24.1",





  
  

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  "pubchempy==1.0.4",





  
  

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  "pydantic==2.9.2",





  
  

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  "pylint==3.3.1",





  
  

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  "pypdf==5.2.0",





  
  

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  "pytest==8.3.3",





  
  

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  "pytest-asyncio==0.25.2",





  
  

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  "pyzotero==1.6.9",





  
  

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  "streamlit==1.39.0",





  
  

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  "sentence_transformers==3.3.1",





  
  

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  "tabulate==0.9.0",





  
  

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  "torch==2.2.2",





  
  

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  "torch_geometric==2.6.1",





  
  

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  "transformers==4.48.0",





  
  

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  "mkdocs==1.6.1",





  
  

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  "mkdocs-jupyter==0.25.1",





  
  

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  "mkdocs-material==9.5.47",





  
  

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  "mkdocstrings-python==1.12.2",





  
  

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  "mkdocs-include-markdown-plugin==7.1.2",





  
  

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  "mkdocstrings==0.27.0",





  
  

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  "streamlit-feedback",





  
  

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  "anndata==0.11.3",





  
  

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  "h5py==3.13.0",





  
  

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  "igraph==0.11.8",





  
  

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  "ipykernel==6.29.5",





  
  

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  "ipython==8.32.0",





  
  

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  "nbformat==5.10.4",





  
  

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  "scipy==1.15.2",





  
  

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  "tqdm==4.67.1",





  
  

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  "umap-learn==0.5.7",





  
  

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  "plotly-express==0.4.1",





  
  

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  "seaborn==0.13.2",





  
  

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  "scanpy==1.11.0",





  
  

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]





  
  

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dynamic = ["version"]





  
  

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[tool.setuptools.dynamic]





  
  

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version = { file = "release_version.txt" }





  
  

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# find packages





  
  

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[tool.setuptools]





  
  

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include-package-data = true





  
  

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[tool.setuptools.packages.find]





  
  

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where = ["."]





  
  

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include = ["aiagents4pharma*"]





  
  

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[tool.setuptools.package-data]





  
  

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aiagents4pharma = [





  
  

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  "talk2aiagents4pharma/configs/*",





  
  

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  "talk2aiagents4pharma/configs/agents/main_agent/*",





  
  

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  "talk2aiagents4pharma/configs/app/frontend/*",





  
  

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  "talk2biomodels/configs/*",





  
  

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  "talk2biomodels/configs/agents/t2b_agent/*",





  
  

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  "talk2biomodels/configs/tools/ask_question/*",





  
  

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  "talk2biomodels/configs/tools/get_annotation/*",





  
  

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  "talk2biomodels/configs/tools/custom_plotter/*",





  
  

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  "talk2knowledgegraphs/configs/*",





  
  

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  "talk2knowledgegraphs/configs/agents/t2kg_agent/*",





  
  

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  "talk2knowledgegraphs/configs/app/frontend/*",





  
  

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  "talk2knowledgegraphs/configs/tools/subgraph_extraction/*",





  
  

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  "talk2knowledgegraphs/configs/tools/subgraph_summarization/*",





  
  

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  "talk2knowledgegraphs/configs/tools/graphrag_reasoning/*",





  
  

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  "talk2scholars/configs/*",





  
  

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  "talk2scholars/configs/agents/talk2scholars/main_agent/*",





  
  

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  "talk2scholars/configs/agents/talk2scholars/s2_agent/*",





  
  

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  "talk2scholars/configs/agents/talk2scholars/zotero_agent/*",





  
  

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  "talk2scholars/configs/app/frontend/*",





  
  

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  "talk2scholars/configs/tools/multi_paper_recommendation/*",





  
  

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  "talk2scholars/configs/tools/search/*",





  
  

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  "talk2scholars/configs/tools/single_paper_recommendation/*",





  
  

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  "talk2scholars/configs/tools/zotero_read/*",





  
  

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  "talk2scholars/configs/tools/zotero_write/*",





  
  

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  "talk2scholars/configs/tools/retrieve_semantic_scholar_paper_id/*",





  
  

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]





  
  

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[tool.pytest.ini_options]





  
  

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asyncio_default_fixture_loop_scope = "function"





  
  

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markers = ["integration: marks tests as integration tests"]





  
  

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filterwarnings = ["ignore::DeprecationWarning"]