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pyproject.toml
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[build-system]
requires = [
"setuptools >= 64.0.0",
"setuptools_scm >= 6.4.0",
]
build-backend = "setuptools.build_meta"
[project]
name = "ngs_test_utils"
description = "Utilities for generation of synthetic NGS files"
authors = [
{name = "Genialis, Inc."},
{email = "[email protected]"},
]
dynamic = ["version"]
readme = "README.rst"
license = {text = "Apache 2.0"}
requires-python = ">=3.11, <3.13"
keywords = [
"ngs",
"test",
"bioinformatics",
]
classifiers = [
"Development Status :: 2 - Pre-Alpha",
"Environment :: Console",
"Intended Audience :: Developers",
"Topic :: Software Development :: Libraries :: Python Modules",
"Operating System :: OS Independent",
"Programming Language :: Python",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
]
dependencies = [
"numpy",
"pybedtools",
"pysam",
]
[project.optional-dependencies]
docs = [
"sphinx",
]
package = [
"build>=0.8.0",
"check-manifest>=0.48",
"twine>=4.0.1",
]
test = [
"ruff",
"pytest>=7.2.0",
"pytest-cov>=4.0.0",
"pytest-mock>=3.10.0",
"toml>=0.10.2",
]
[project.urls]
repository = "https://github.com/genialis/ngs-test-utils"
[tool.setuptools_scm]
[tool.ruff]
line-length = 99
target-version = "py312"
# Necessary for isort
src = ["src"]
[tool.ruff.lint]
select = [
# pydocstyle
"D",
# pycodestyle
"E", "W",
# pyflakes
"F",
# isort
"I",
# Pyupgrade - use a more modern / newer syntax if it exists
"UP",
# Mccabe - detect too complex code
"C901",
# flake8-2022 - Checks for misuse of sys.version or sys.version_info
"YTT",
# flake8 bugbear - find common bugs and design problems
"B",
# find unused `noqa` directive
"RUF100",
]
ignore = [
# `one-blank-line-before-class` (D203) and
# `no-blank-line-before-class` (D211) are incompatible.
"D203",
# `multi-line-summary-first-line` (D212) and
# `multi-line-summary-second-line` (D213) are incompatible.
"D213",
# Setting an explicit stacklevel in warnings.warn(...) is just a reccomendation
"B028",
# We need assert statemets in tests
"S101",
]
[tool.ruff.lint.per-file-ignores]
# tests folder does not enforce pydocstyle
"tests/*" = ["D"]