PySnpTools/pyproject.toml at master · fastlmm/PySnpTools · GitHub

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[build-system]
requires = ["uv_build==0.12.2"]
build-backend = "uv_build"

[project]
name = "pysnptools"
version = "0.5.15"
description = "PySnpTools"
readme = "README.md"
requires-python = ">=3.10"
keywords = [
    "gwas",
    "bioinformatics",
    "sets",
    "intervals",
    "ranges",
    "regions",
    "plink",
    "genomics",
    "file-format",
    "reader",
    "genotype",
    "bed-format",
    "writer",
    "python",
    "snps",
]
authors = [{ name = "FaST-LMM Team", email = "fastlmm-dev@python.org" }]
license = "Apache-2.0"
license-files = ["LICENSE.md"]
classifiers = [
    "Programming Language :: Python",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
]
dependencies = [
    "scipy>=1.7.0",
    "numpy>=1.22.0; python_version < '3.14'",
    "numpy>=2.3.5; python_version >= '3.14'",
    "psutil>=6.1.0",
    "pandas>=1.3.0,<4",
    "h5py>=3.12.1",
    "cloudpickle>=3.1.0",
    "bed-reader[samples]>=1.0.6",
    "more-itertools>=10.5.0",
]

[project.urls]
Homepage = "https://fastlmm.github.io/"
Documentation = "https://fastlmm.github.io/PySnpTools"
Issues = "https://github.com/fastlmm/PySnpTools/issues"
Source = "https://github.com/fastlmm/PySnpTools"


[project.optional-dependencies]
bgen = ["cbgen>=1.0.6", "bgen-reader>=4.0.9"]
dev = [
    "pytest",
    "pytest-cov",
    "pytest-doctestplus",
    "pytest-datadir",
    "limix-sphinx-theme>=0.0.4",
    "pytest-sphinx>=0.2.2",
    "sphinx>=6.2.1",
    "sphinx_rtd_theme>=3.0.1",
    "ruff>=0.7.2",
]


[tool.ruff]
line-length = 250
exclude = [
    "*.ipynb",
    "doc/source/conf.py",
    "bed_reader/tests/benchmark/benchmark.py",
]

[tool.ruff.lint]
select = ["E", "F", "W"]


[tool.pytest.ini_options]
addopts = "--doctest-modules --doctest-glob=*.rst --doctest-glob=*.md"
doctest_optionflags = ["ELLIPSIS", "NORMALIZE_WHITESPACE"]
filterwarnings = [
    "ignore:Converting float64 to float32 can cause loss of information:UserWarning",
    "ignore:'count_A1' was not set.*will default to 'False':FutureWarning",
    "ignore:standardizing an ndarray instead of a SnpData is deprecated:DeprecationWarning",
    "ignore:.*\\.kernel.*deprecated.*read_kernel.*val:DeprecationWarning",
    "ignore:'parent_string' is deprecated. Use 'name':DeprecationWarning",
]

[dependency-groups]
dev = ["pytest-xdist>=3.6.1", "twine>=5.1.1"]
notebook = [
    "ipykernel>=7.3.0",
    "ipywidgets>=8.1.8",
    "matplotlib>=3.10.9",
    "nbconvert>=7.17.1",
]


[tool.uv.build-backend]
module-name = "pysnptools"
module-root = ""
source-include = ["AUTHORS.txt"]
source-exclude = [
    "/pysnptools/examples/**",
    "/pysnptools/pysnptools.pyproj",
    "/pysnptools/pysnptools.sln",
    ".work_directory.*",
    "*.profraw",
    "ignore",
    "localcache1",
    "peertopeer1",
    "runs",
    "temp",
    "tempdir",
    "tempdircmk",
]
wheel-exclude = ["/pysnptools/examples/**"]