pyproject.toml

[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"

[tool.poetry]
name = "haptools"
version = "0.4.2"
description = "Ancestry and haplotype aware simulation of genotypes and phenotypes for complex trait analysis"
authors = ["Arya Massarat", "Michael Lamkin"]
license = "MIT"
repository = "https://github.com/cast-genomics/haptools"
homepage = "https://github.com/cast-genomics/haptools"
documentation = "https://haptools.readthedocs.io"
readme = "README.md"

[tool.poetry.dependencies]
python = ">=3.7,<4.0"
numpy = ">=1.20.0"
click = ">=8.0.3"
pysam = ">=0.19.0"
cyvcf2 = ">=0.30.14"
matplotlib = ">=3.5.1"
Pgenlib = ">=0.90.1"

[tool.poetry.group.docs.dependencies]
Sphinx = ">=4.3.2"
sphinx-autodoc-typehints = ">=1.12.0"
sphinx-rtd-theme = ">=1.0.0"
numpydoc = ">=1.1.0"
sphinx-click = ">=3.0.2"

[tool.poetry.group.tests.dependencies]
pytest = ">=7.4.3"
black = ">=23.3.0"
ipython = ">=7.34.0"
coverage = {extras = ["toml"], version = ">=7.2.7"}
filprofiler = ">=2023.3.1"

[tool.poetry.scripts]
haptools = 'haptools.__main__:main'

[tool.black]
line-length = 88
preview = true
extend-exclude = "haptools/(sim_genotype|karyogram).py"

[tool.pytest.ini_options]
log_cli_level = "DEBUG"
log_cli_format = "%(asctime)s [%(levelname)8s] %(message)s (%(filename)s:%(lineno)s)"
log_cli_date_format = "%Y-%m-%d %H:%M:%S"