--- a
+++ b/pyproject.toml
@@ -0,0 +1,117 @@
+[build-system]
+requires = ["setuptools", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "aiagents4pharma"
+description = "AI Agents for drug discovery, drug development, and other pharmaceutical R&D."
+readme = "README.md"
+requires-python = ">=3.12"
+classifiers = [
+  "Programming Language :: Python :: 3",
+  "License :: OSI Approved :: MIT License",
+  "Operating System :: OS Independent",
+]
+dependencies = [
+  "copasi_basico==0.78",
+  "coverage==7.6.4",
+  "einops==0.8.0",
+  "gdown==5.2.0",
+  "gravis==0.1.0",
+  "huggingface_hub==0.26.5",
+  "hydra-core==1.3.2",
+  "joblib==1.4.2",
+  "langchain==0.3.7",
+  "langchain-community==0.3.5",
+  "langchain-core==0.3.40",
+  "langchain-experimental==0.3.3",
+  "langchain-nvidia-ai-endpoints==0.3.9",
+  "langchain-openai==0.2.5",
+  "langchain_ollama==0.2.3",
+  "langgraph_supervisor==0.0.9",
+  "matplotlib==3.9.2",
+  "openai==1.59.4",
+  "ollama==0.4.7",
+  "pandas==2.2.3",
+  "pcst_fast==1.0.10",
+  "plotly==5.24.1",
+  "pubchempy==1.0.4",
+  "pydantic==2.9.2",
+  "pylint==3.3.1",
+  "pypdf==5.2.0",
+  "pytest==8.3.3",
+  "pytest-asyncio==0.25.2",
+  "pyzotero==1.6.9",
+  "streamlit==1.39.0",
+  "sentence_transformers==3.3.1",
+  "tabulate==0.9.0",
+  "torch==2.2.2",
+  "torch_geometric==2.6.1",
+  "transformers==4.48.0",
+  "mkdocs==1.6.1",
+  "mkdocs-jupyter==0.25.1",
+  "mkdocs-material==9.5.47",
+  "mkdocstrings-python==1.12.2",
+  "mkdocs-include-markdown-plugin==7.1.2",
+  "mkdocstrings==0.27.0",
+  "streamlit-feedback",
+  "anndata==0.11.3",
+  "h5py==3.13.0",
+  "igraph==0.11.8",
+  "ipykernel==6.29.5",
+  "ipython==8.32.0",
+  "nbformat==5.10.4",
+  "scipy==1.15.2",
+  "tqdm==4.67.1",
+  "umap-learn==0.5.7",
+  "plotly-express==0.4.1",
+  "seaborn==0.13.2",
+  "scanpy==1.11.0",
+]
+dynamic = ["version"]
+
+[tool.setuptools.dynamic]
+version = { file = "release_version.txt" }
+
+# find packages
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["aiagents4pharma*"]
+
+[tool.setuptools.package-data]
+aiagents4pharma = [
+  "talk2aiagents4pharma/configs/*",
+  "talk2aiagents4pharma/configs/agents/main_agent/*",
+  "talk2aiagents4pharma/configs/app/frontend/*",
+  "talk2biomodels/configs/*",
+  "talk2biomodels/configs/agents/t2b_agent/*",
+  "talk2biomodels/configs/tools/ask_question/*",
+  "talk2biomodels/configs/tools/get_annotation/*",
+  "talk2biomodels/configs/tools/custom_plotter/*",
+  "talk2knowledgegraphs/configs/*",
+  "talk2knowledgegraphs/configs/agents/t2kg_agent/*",
+  "talk2knowledgegraphs/configs/app/frontend/*",
+  "talk2knowledgegraphs/configs/tools/subgraph_extraction/*",
+  "talk2knowledgegraphs/configs/tools/subgraph_summarization/*",
+  "talk2knowledgegraphs/configs/tools/graphrag_reasoning/*",
+  "talk2scholars/configs/*",
+  "talk2scholars/configs/agents/talk2scholars/main_agent/*",
+  "talk2scholars/configs/agents/talk2scholars/s2_agent/*",
+  "talk2scholars/configs/agents/talk2scholars/zotero_agent/*",
+  "talk2scholars/configs/app/frontend/*",
+  "talk2scholars/configs/tools/multi_paper_recommendation/*",
+  "talk2scholars/configs/tools/search/*",
+  "talk2scholars/configs/tools/single_paper_recommendation/*",
+  "talk2scholars/configs/tools/zotero_read/*",
+  "talk2scholars/configs/tools/zotero_write/*",
+  "talk2scholars/configs/tools/retrieve_semantic_scholar_paper_id/*",
+
+]
+
+[tool.pytest.ini_options]
+asyncio_default_fixture_loop_scope = "function"
+markers = ["integration: marks tests as integration tests"]
+filterwarnings = ["ignore::DeprecationWarning"]