pyproject.toml

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

[project]
name = "sgkit"
authors = [{ name = "sgkit Developers", email = "project@sgkit.dev" }]
license = { text = "Apache" }
description = "Statistical genetics toolkit"
classifiers = [
  "Development Status :: 3 - Alpha",
  "License :: OSI Approved :: Apache Software License",
  "Operating System :: OS Independent",
  "Intended Audience :: Science/Research",
  "Programming Language :: Python",
  "Programming Language :: Python :: 3",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Topic :: Scientific/Engineering",
]
urls = { Homepage = "https://github.com/sgkit-dev/sgkit" }
requires-python = ">=3.10"
dependencies = [
  "numpy < 2.2",
  "xarray < 2025.03.1",
  "dask[array,dataframe] >= 2022.01.0, <= 2024.8.0",
  "distributed >= 2022.01.0, <= 2024.8.0",
  "scipy",
  "zarr >= 2.10.0, != 2.11.0, != 2.11.1, != 2.11.2, < 3",
  "numba",
  "typing-extensions",
  "fsspec != 2021.6.*",
  "scikit-learn",
  "pandas",
  "setuptools >= 41.2",                                   # For pkg_resources
]
dynamic = ["version"]

[project.readme]
text = """
**sgkit** is an open source project for analyzing and manipulating genetic
variation data."""
content-type = "text/x-rst"

[project.optional-dependencies]
# For plink we need dask[dataframe], we already have
# dask[array] in install_requires, and since
# https://github.com/pypa/pip/issues/4957, pip
# will essentially ignore dask[dataframe] in the extras.
# We can workaround this by either adding pip flag
# --use-feature 2020-resolver, or installing
# dask[dataframe] in the install_requires, or just listing
# the 2 missing dependencies from dataframe, the way we do
# here, when pip finally gets a resolver, this won't be
# a problem. Here we opt for listing the 2 dependencies
# since this is the least user invasive solution.
plink = ["partd", "bed-reader"]
bgen = ["rechunker", "cbgen > 1.0.5"]

[tool.setuptools]
packages = ["sgkit"]
zip-safe = false            # https://mypy.readthedocs.io/en/latest/installed_packages.html
include-package-data = true

[tool.setuptools_scm]
version_file = "sgkit/_version.py"

[tool.coverage.report]
fail_under = 100

[tool.pytest.ini_options]
addopts = "--doctest-modules --ignore=validation --cov-fail-under=100"
norecursedirs = [".eggs", "build", "docs"]
filterwarnings = ["error", "ignore::DeprecationWarning"]


[tool.isort]
profile = "black"
default_section = "THIRDPARTY"
known_first_party = ["sgkit"]
known_third_party = [
  "allel",
  "dask",
  "fire",
  "glow",
  "hail",
  "hypothesis",
  "invoke",
  "msprime",
  "numba",
  "numpy",
  "pandas",
  "pkg_resources",
  "pyspark",
  "pytest",
  "setuptools",
  "sgkit_plink",
  "sklearn",
  "sphinx",
  "typing_extensions",
  "xarray",
  "yaml",
  "zarr",
]
multi_line_output = 3
include_trailing_comma = true
force_grid_wrap = 0
use_parentheses = true
line_length = 88

[[tool.mypy.overrides]]
module = ["callee.*"]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = ["dask.*"]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = ["fsspec.*"]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = ["dask_ml.*"]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = ["numpy.*"]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = ["pandas.*"]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = ["numba.*"]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = ["pytest.*"]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = ["statsmodels.*"]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = ["hypothesis.*"]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = ["zarr.*"]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = ["numcodecs.*"]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = ["setuptools"]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = ["sklearn.*"]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = ["cbgen.*"]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = ["rechunker.*"]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = ["bed_reader.*"]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = ["sphinx.*"]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = ["yarl.*"]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = ["allel.*"]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = ["networkx.*"]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = ["toolz.*"]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = ["scipy.*"]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = ["sgkit.*"]
allow_redefinition = true

[[tool.mypy.overrides]]
module = ["sgkit.*.tests.*"]
disallow_untyped_calls = false
disallow_untyped_defs = false
disallow_untyped_decorators = false

[[tool.mypy.overrides]]
module = ["validation.*"]
ignore_errors = true