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pyproject.toml
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[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"
[project]
name = "paleomix"
dynamic = ["version"]
authors = [{ name = "Mikkel Schubert", email = "MikkelSch@gmail.com" }]
license = { file = "LICENSE" }
description = "Bioinformatics pipelines for HTS data"
readme = { file = "README.rst", content-type = "text/x-rst" }
requires-python = ">=3.8"
dependencies = [
"coloredlogs>=10.0",
"configargparse>=0.13.0",
"humanfriendly>=4.7",
"packaging>=19.0",
"pysam>=0.10.0",
"ruamel.yaml>=0.16.0",
"setproctitle>=1.1.0",
"typing_extensions>=4.0",
]
keywords = ["pipeline", "bioinformatics", "hts", "bam"]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Intended Audience :: Science/Research",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"License :: OSI Approved :: MIT License",
"Programming Language :: Python :: 3 :: Only",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
]
[project.urls]
Homepage = "https://github.com/MikkelSchubert/paleomix"
Documentation = "https://paleomix.readthedocs.io"
Repository = "https://github.com/MikkelSchubert/paleomix.git"
Issues = "https://github.com/MikkelSchubert/paleomix/issues"
[project.optional-dependencies]
dev = [
"nox",
"pytest-cov",
"pytest",
]
[project.scripts]
paleomix = "paleomix.__main__:main"
[tool.hatch.version]
path = "paleomix/__init__.py"
[tool.coverage.run]
branch = true
[tool.coverage.report]
skip_covered = true
show_missing = true
precision = 1
exclude_also = [
# Exclude code-blocks that are only used during (pyright) type-checking
"^if TYPE_CHECKING:",
]
[tool.coverage.xml]
output = "cov.xml"
[tool.isort]
profile = "black"
[tool.pyright]
# Used since `strict = [...]` prevents individual `reportX` settings:
include = ["paleomix", "tests"]
# typeCheckingMode = "strict"
# FIXME: Disabled until project is fully typed
reportUnnecessaryIsInstance = "none"
[tool.pytest.ini_options]
markers = ["slow"]
[tool.ruff]
target-version = "py37"
[tool.ruff.lint]
select = ["ALL"]
ignore = [
# Rules either deemed too burdonsome to implement or not useful
"ANN", # flake8-annotations
"B", # flake8-bugbear
"C90", # mccabe -- Complexity measures not deemed useful
"COM", # flake8-commas -- Formatting handled by ruff/black
"D", # pydocstyle
"ERA", # eradicate
"EM", # flake8-errmsg
"T20", # flake8-print
"FBT", # flake8-boolean-trap
"TD", # flake8-todos
"FIX", # flake8-fixme
"PTH", # flake8-use-pathlib
"S", # flake8-bandit
"TRY", # tryceratops
# Individual rules deemed too burdonsome or not useful
"ANN101", # missing-type-self -- Missing type annotation for `self` in method
"ANN102", # missing-type-cls -- Missing type annotation for `cls` in classmethod
"S603", # subprocess-without-shell-equals-true
"TRY003", # raise-vanilla-args
# Disabled due to too many false positives
"PLR2004", # magic-value-comparison -- Magic value used in comparison
# Disabled due to personal style preferences
"PLW2901", # redefined-loop-name -- `for` loop variable `value` overwritten
"RET505", # superfluous-else-return -- Unnecessary `elif` after `return` statement
"RET506", # superfluous-else-raise -- Unnecessary `elif` after `raise` statement
"RET507", # superfluous-else-continue --Unnecessary `elif` after `continue`
"RET508", # superfluous-else-break -- Unnecessary `elif` after `break` statement
# Disabled due to hits in non-performance critical code where manual is clearer
"PERF401", # manual-list-comprehension -- Use a list comprehension
# Disabled due to conflict with `format` command
"ISC001", # single-line-implicit-string-concatenation
# Complexity warnings disabled for now
"PLR09", # too-many-*
]
[tool.ruff.lint.per-file-ignores]
"tests/**.py" = [
"S101", # assert -- Use of assert detected
"S108", # hardcoded-temp-file -- Probable insecure usage of temporary file or dir
"S311", # suspicious-non-cryptographic-random-usage
]