tsls/pyproject.toml at main · tskit-dev/tsls · GitHub

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[build-system]
requires = [
    "setuptools>=42",
    "setuptools_scm",
    "wheel",
    "numpy>=2"
]
build-backend = "setuptools.build_meta"

[tool.setuptools_scm]
write_to = "tsls/_version.py"
local_scheme = "no-local-version"

[project]
name = "tsls"
dynamic = ["version"]
authors = [
    {name = "Tskit Developers", email = "admin@tskit.dev"},
]
description = "The Li and Stephens HMM on a tree sequence."
readme = "README.md"
requires-python = ">=3.11"
license = "MIT"
classifiers = [
    "Programming Language :: C",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3 :: Only",
    "Development Status :: 2 - Pre-Alpha",
    "Intended Audience :: Science/Research",
    "Operating System :: POSIX",
    "Operating System :: MacOS :: MacOS X",
    "Operating System :: Microsoft :: Windows",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]
keywords = [
    "population genetics",
    "tree sequence",
    "ancestral recombination graph",
    "Li and Stephens",
    "hidden Markov model",
]
dependencies = [
    "numpy>=2",
    "tskit>=1.0.0",
]

[project.urls]
"Source Code" = "https://github.com/tskit-dev/tsls/"
"Bug Tracker" = "https://github.com/tskit-dev/tsls/issues"

[dependency-groups]
test = [
    "msprime",
    "pytest",
    "pytest-cov",
    "pytest-xdist>=3.8.0",
]

# Fully pin lint requirements for determinism.
lint = [
    "clang-format==21.1.8",
    "ruff==0.15.1",
    "prek==0.3.3",
    "zizmor==1.26.1",
]

packaging = [
  "twine",
  "validate-pyproject[all]"
]

dev = [
    {include-group = "lint"},
    {include-group = "test"},
    {include-group = "packaging"},
]

[tool.setuptools]
packages = ["tsls"]
include-package-data = true

[tool.pytest.ini_options]
testpaths = ["tests"]
pythonpath = ["tests"]

[tool.ruff]
target-version = "py311"
extend-exclude = ["git-submodules"]
line-length = 89
indent-width = 4

[tool.ruff.lint]
select = ["E", "F", "B", "W", "I", "N", "UP", "A", "PT", "PLC0415"]

ignore = [
    "A001", "A002", "RUF",
    "B905", #Don't add strict=False to zips (B905)
    "N806", "N802", "N803", # Various nags about uppercase vars
    "N818", # Exceptions not called "Error"
    "UP032", # Don't upgrade to f strings
    "B904", # raise from-issues
    "PT011", # pytest.raises(ValueError) too broad
    "PT012", # pytest.raises() block should contain a single simple statement
    "B028", # No stacklevel for warnings
    "B017", # Do not assert blind exception: `BaseException`
]

[tool.ruff.lint.isort]
known-first-party = ["_tsls", "dense", "tsls"]
known-third-party = ["numpy", "pytest", "tskit"]