ATHENA/pyproject.toml at main · mims-harvard/ATHENA · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "athena-r1"
version = "1.0.0"
description = "An AI agent for treatment reasoning over a biomedical tool universe"
readme = "README.md"
requires-python = ">=3.10"
license = { file = "LICENSE" }
authors = [
    { name = "Shanghua Gao", email = "shanghuagao@gmail.com" },
]
keywords = ["llm", "biomedical", "agent", "tool-use", "reinforcement-learning"]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
]
dependencies = [
    "openai>=1.0",
    "transformers>=4.40",
    "tooluniverse>=0.3",
    "jinja2",
    "numpy",
    "torch>=2.0",
]

[project.optional-dependencies]
vllm = ["vllm>=0.6"]
web = [
    "fastapi>=0.100",
    "uvicorn[standard]>=0.20",
    "ag-ui-protocol>=0.1",
]
dev = [
    "pytest>=8.0",
    "pytest-timeout>=2.0",
    "ruff>=0.7",
    "mypy>=1.10",
    "pre-commit>=4.0",
    "requests>=2.31",
]

[project.urls]
Homepage = "https://athena.openscientist.ai/"
Repository = "https://github.com/mims-harvard/ATHENA"
Issues = "https://github.com/mims-harvard/ATHENA/issues"

[project.scripts]
athena-r1 = "athena_r1.__main__:main"

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

[tool.setuptools.package-data]
athena_r1 = ["py.typed"]

[tool.ruff]
line-length = 100
target-version = "py310"
extend-exclude = ["src/athena_r1/_core.py"]  # legacy engine; tracked separately

[tool.ruff.lint]
select = [
    "E",    # pycodestyle errors
    "W",    # pycodestyle warnings
    "F",    # pyflakes
    "I",    # isort
    "B",    # flake8-bugbear
    "UP",   # pyupgrade
]
ignore = [
    "E501",  # line too long — handled by formatter
    "B008",  # default-arg-call: common for FastAPI Depends() / dataclass field()
]

[tool.pytest.ini_options]
testpaths = ["tests"]
addopts = "-ra"
filterwarnings = [
    "ignore::DeprecationWarning",
    "ignore::FutureWarning",
]

[tool.mypy]
python_version = "3.10"
# Public API is type-annotated; the legacy `_core.py` engine is not, and
# its 1.6k LoC is tracked for a future cleanup pass.
files = ["src/athena_r1/agent.py", "src/athena_r1/_version.py", "src/athena_r1/__main__.py"]
ignore_missing_imports = true
warn_unused_ignores = true
warn_redundant_casts = true
no_implicit_optional = true