pyproject.toml

[build-system]
requires = ["poetry-core", "setuptools>=61.0", "setuptools-cpp"]
build-backend = "poetry.core.masonry.api"

[tool.poetry]
name = "rafael"
version = "0.1.0"
description = "A federated analysis framework for bioinformatics analysis"
readme = "README.md"

authors = [
    "Jian-Hung Wen <jianhung.wen@ailabs.tw>",
    "Yi-Lun Lee <yilun.lee@ailabs.tw>",
    "Yueh-Hua Tu <yuehhua.tu@ailabs.tw>"
]

classifiers = [
   "Programming Language :: Python :: 3",
   "Operating System :: OS Independent",
]

include = ["rafael/fedalgo/externals"]

[tool.poetry.build]
script = "build.py"
generate-setup-file = true

[tool.poetry.dependencies]
python = ">=3.9,<3.12"
numpy = {version = "~1", python = ">=3.9,<3.12"}
jax = "~0.4"
jaxlib = "^0.4"
ruamel-yaml = "~0.18"
tqdm = "*"
pydantic = "~2"
aiohttp = "~3"
lifelines = "*"
seaborn = "*"
fastapi = "*"
plotnine = "0.13.4"
polars = "0.20.20"
pyarrow = "*"
uvicorn = {extras = ["standard"], version = "*"}
scipy = {version = "~1", python = ">=3.9,<3.12"}
pooch = "~1"
bed_reader = "*"
pandas = "^2"
ordered_set = "~4"

[tool.poetry.group.test.dependencies]
pytest = "^7.4"

[tool.poetry.group.doc.dependencies]
sphinx = "^7.3.7"
myst-parser = "^3.0"

[tool.poetry.group.packaging.dependencies]
build = "~1"

[tool.poetry.group.publishing.dependencies]
twine = "~4"

[tool.poetry.group.benchmark.dependencies]
pyperf = "^2"

[tool.poetry.group.dev.dependencies]
sphinx = "^7.3.7"
sphinx-autodoc-typehints = "^2.1.1"
pydata-sphinx-theme = "^0.15.3"
myst-parser = "^3.0"

[[tool.poetry.source]]
name = "PyPI"
priority = "primary"