bio2zarr/pyproject.toml at main · sgkit-dev/bio2zarr · GitHub

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[build-system]
requires = ["setuptools >= 69", "setuptools_scm[toml] >= 8"]
build-backend = "setuptools.build_meta"

[project]
name = "bio2zarr"
description = "Convert bioinformatics data to Zarr"
readme = "README.md"
license = "Apache-2.0"
authors = [
  {name = "sgkit Developers", email = "project@sgkit.dev"},
]
dependencies = [
  "numpy>=2",
  "zarr>=3.1",
  "tabulate",
  "tqdm",
  "humanfriendly",
  # cyvcf2 also pulls in coloredlogs and click
  "coloredlogs",
  "click",
  # Using pandas for reading plink files, but will be useful more generally
  "pandas"
]
requires-python = ">=3.11"
classifiers = [
  "Development Status :: 4 - Beta",
  "Operating System :: POSIX",
  "Operating System :: POSIX :: Linux",
  "Operating System :: MacOS",
  "Operating System :: MacOS :: MacOS X",
  "Operating System :: Microsoft :: Windows",
  "Intended Audience :: Science/Research",
  "Programming Language :: Python",
  "Programming Language :: Python :: 3",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Programming Language :: Python :: 3.13",
  "Topic :: Scientific/Engineering"
]
dynamic = ["version"]

[project.urls]
repository = "https://github.com/sgkit-dev/bio2zarr"
documentation = "https://sgkit-dev.github.io/bio2zarr/"

[project.scripts]
vcf2zarr = "bio2zarr.cli:vcf2zarr_main"
vcfpartition = "bio2zarr.cli:vcfpartition"
tskit2zarr = "bio2zarr.cli:tskit2zarr_main"
plink2zarr = "bio2zarr.cli:plink2zarr_main"
zipzarr = "bio2zarr.cli:zipzarr"

[project.optional-dependencies]
tskit = ["tskit>=1"]
vcf = ["cyvcf2"]
all = [
  "tskit>=1",
  "cyvcf2"
]

[dependency-groups]
test = [
  "click>=8.2.0",
  "hypothesis-vcf",
  "msprime",
  "pysam ; sys_platform != 'win32'",
  "pytest",
  "pytest-coverage",
  "pytest-xdist",
  "tqdm",
  "tskit>=1",
  "bed_reader",
  "cyvcf2 ; sys_platform != 'win32'",
  "xarray<2025.03.1",
  "dask[array]",
]

docs = [
  "asciinema-automation",
  "bash_kernel",
  "jupyter-book<2",
  "sphinx-click",
  "tskit>=1",
  "cyvcf2 ; sys_platform != 'win32'",
]

lint = [
  "ruff==0.15.1",
  "prek==0.3.3",
  "zizmor==1.24.1",
]

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

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

[tool.setuptools]
packages = ["bio2zarr"]

[tool.setuptools_scm]
version_file = "bio2zarr/_version.py"
local_scheme = "no-local-version"

[tool.pytest.ini_options]
testpaths = "tests"
addopts = "--cov=bio2zarr --cov-report term-missing"

[tool.ruff]
# Assume Python 3.11
target-version = "py311"

# Same as Black.
line-length = 88
indent-width = 4

[tool.ruff.lint]
select = ["E", "F", "B", "W", "I", "N", "UP", "A", "PT", "PLC0415"]
#Allow uppercase names for e.g. call_AD
#Don't add strict=False to zips (B905)
ignore = ["N806", "N802", "A001", "A002", "B905", "RUF"]

fixable = ["ALL"]
unfixable = []

[tool.ruff.lint.isort]
known-third-party = [
  "hypothesis",
  "msprime",
  "numpy",
  "pandas",
  "pytest",
  "setuptools",
  "xarray",
  "zarr"
]