pyproject.toml

[build-system]
requires = ["setuptools>=42"]
build-backend = "setuptools.build_meta"

[project]
name = "chemgraphagent"
version = "0.5.0"
description = "A computational chemistry agent for molecular simulation tasks."
authors = [
    { name = "Thang Pham", email = "tpham@anl.gov" },
    { name = "Murat Keçeli", email = "keceli@anl.gov" },
    { name = "Aditya Tanikanti", email = "atanikanti@anl.gov" }
]
requires-python = ">=3.10"
dependencies = [
    "langgraph==0.4.7",
    "langgraph-checkpoint==2.1.0",
    "langgraph-prebuilt==0.5.2",
    "langgraph-sdk==0.1.72",
    "langchain",
    "langchain-openai",
    "langchain-ollama",
    "langchain-anthropic",
    "langchain-google-genai",
    "langchain-groq",
    "langchain-experimental",
    "langchain-mcp-adapters",
    "pydantic",
    "pandas==2.2.3",
    "pubchempy==1.0.5",
    "pyppeteer==2.0.0",
    "numpy==2.2.6",
    "numexpr==2.11.0",
    "pytest==8.4.1",
    "deepdiff==8.5.0",
    "matplotlib",

    "ase",
    "rdkit",
    "pymatgen",
    "mace-torch",
    "globus_sdk",
    "streamlit==1.48.1",
    "stmol==0.0.9",
    "ipython-genutils==0.2.0",
    "langsmith==0.3.45",
    "rich==14.1.0",
    "toml==0.10.2",
    "mcp",
    "fastmcp",
    "pytest-asyncio",
    "grandalf==0.8"
    ]

[project.optional-dependencies]
calculators = [
    "tblite==0.4.0; python_version < '3.13' or platform_system != 'Darwin'",
]
uma = [
    "fairchem-core==2.3.0",
    "e3nn>=0.5",
]
ui = [
    "streamlit",
    "stmol",
    "ipython-genutils",
]
parsl = [
    "parsl",
]
xanes = [
    "mp-api; python_version >= '3.11'",
    "parsl"
]
rag = [
    "faiss-cpu>=1.7.4",
    "langchain-text-splitters",
    "langchain-huggingface",
    "sentence-transformers>=2.2.2",
    "pymupdf>=1.24.0",
]

[project.urls]
"Homepage" = "https://github.com/argonne-lcf/ChemGraph"
"Repository" = "https://github.com/argonne-lcf/ChemGraph"

[project.scripts]
chemgraph = "chemgraph.cli:main"
chemgraph-eval = "chemgraph.eval.cli:main"

[tool.setuptools.packages.find]
where = ["src/"]

[tool.setuptools.package-data]
"chemgraph.eval" = ["data/*.json"]
"ui" = ["assets/*.png"]

[tool.ruff]
line-length = 88  # Match Black's default (adjust as needed)
target-version = "py310"  # Adjust based on your Python version
exclude = ["notebooks/"]  # Add files/folders to ignore

[tool.ruff.format]
quote-style = "preserve"  # Keep existing quote style
indent-style = "space"  # Use spaces for indentation
skip-magic-trailing-comma = false  # Ensure Black-style formatting

[tool.pytest.ini_options]
testpaths = ["tests"]
markers = [
    "llm: marks tests as requiring LLM API access (run with --run-llm)",
    "asyncio: marks async tests",
]
filterwarnings = [
    "ignore:Environment variable TORCH_FORCE_NO_WEIGHTS_ONLY_LOAD detected.*:UserWarning",
    "ignore:In future, it will be an error for 'np.bool' scalars to be interpreted as an index:DeprecationWarning",
    "ignore:authlib.jose module is deprecated.*:authlib.deprecate.AuthlibDeprecationWarning",
    "ignore:`torch.jit.script` is deprecated.*:DeprecationWarning:torch.jit._script",
    "ignore:`torch.jit.load` is deprecated.*:DeprecationWarning:torch.jit._serialization",
]