pyproject.toml

[tool.poetry]
name = "funkea"
version = "1.0.0"
description = "Perform functional enrichment analysis at scale."
authors = ["benjamin.tenmann <benjamin.tenmann@benevolent.ai>"]
license = "MIT"
readme = "README.md"
packages = [
    { include = "funkea" },
    { include = "ldsc" }
]
include = [
    { path = "funkea/core/resources/*", format = ["sdist", "wheel"] },
    { path = "scala", format = "sdist" }
]

[tool.poetry.dependencies]
python = ">=3.10,<3.12"
statsmodels = "^0.13.5"
pyspark = {version = "==3.4.1", extras = ["sql"]}
pydantic = "^1.10.6"
jax = { version = "^0.4.6", optional = true }
jaxlib = { version = "^0.4.6", optional = true }
numpy = "^1.24.2"
pandas = "^1.5.3"
scipy = "^1.10.1"
networkx = "^3.0"
quinn = "^0.10.0"
pydantic-spark = "^0.2.0"
rich = "^13.3.3"
fire = "^0.5.0"


[tool.poetry.group.dev.dependencies]
pytest = "^7.2.2"
pytest-cov = "^4.0.0"
pre-commit = "^3.2.0"
mypy = "^1.1.1"
chispa = "^0.9.2"


[tool.poetry.group.docs.dependencies]
jupyterlab = "^3.6.3"
sphinx = ">=4,<6"
myst-parser = ">=0.18.0,<0.19.0"
myst-nb = "^0.17.1"

[tool.poetry.extras]
jax = ["jax", "jaxlib"]

[tool.poetry.scripts]
funkea-cli = "funkea.__main__:main"

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

[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"

 [tool.black]
 line-length = 100
 include = '\.pyi?$'
 target-version = ['py310']
 skip-string-normalization = true
 exclude = '''
 /(
     \.git
   | \.hg
   | \.mypy_cache
   | \.tox
   | \.venv
   | _build
   | buck-out
   | build
   | dist
 )/
 '''

[tool.pytest.ini_options]
filterwarnings = [
   "ignore:pkg_resources is deprecated as an API:DeprecationWarning",
    "ignore:Deprecated call to `pkg_resources.declare_namespace.+.:DeprecationWarning",
   "ignore:distutils Version classes are deprecated. Use packaging.version instead.:DeprecationWarning",
   "ignore:iteritems is deprecated and will be removed in a future version. Use .items instead.:FutureWarning"
]

 [tool.mypy]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = "ldsc.*"
# unfortunately, due to the way we handle the LA backend selection, the numpy array type hints
# causes issues. Was not able to find a better solution fot this at the moment
disable_error_code = "name-defined"