pyproject.toml

[build-system]
requires = ["setuptools", "numpy", "cython"]
build-backend = "setuptools.build_meta"

[project]
name = "msyd"
# project homepage: https://github.com/schneebergerlab/msyd
authors = [
    {name = "Leon Rauschning"},
    {name = "Manish Goel"},
]
description = "Synteny identification across multiple genome assemblies"
readme = "README.md"
requires-python = ">=3.8"
keywords = ["Structural Variation", "SV", "Pangenomics", "Bioinformatics"]
license = {text = "MIT"}
dependencies = [
	"cython",
	"intervaltree",
	"mappy",
	"numpy", 
	"pandas",
	"pysam >= 0.21",
	"scipy",
	"syri >= 1.6.5",
]
dynamic = ["version"]


[project.scripts]
msyd = "msyd:main"

[tool.setuptools.dynamic]
version = {attr = "msyd.__version__"}

[tool.cython-lint]
max-line-length = 200
#ignore = ['E266', 'E265'] # don't lint comment style
no-pycodestyle = 'True'

[tool.pylint.'MESSAGES CONTROL']
disable=['no-name-in-module', 'import-error']

[tool.pylint]
errors-only = 'True'
ignore = 'annotate_sv.py,io.py'