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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["setuptools", "setuptools-scm"]
build-backend = "setuptools.build_meta"
[project]
name = "scenicplus"
authors = [
{ name = "Seppe De Winter", email = "[email protected]" },
{ name = "Carmen Bravo", email = "[email protected]" },
]
description = "SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data."
readme = "README.md"
version = "1.0a1"
requires-python = ">=3.8"
keywords = ["scATAC", "GRN inference", "eGRN inference"]
license = { file = "LICENCE.txt" }
classifiers = [
"Development Status :: 4 - Beta",
"Environment :: Console",
"Intended Audience :: Science/Research",
"License :: Other/Proprietary License",
"Operating System :: OS Independent",
"Programming Language :: Python",
"Programming Language :: Python :: 3",
"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",
"Topic :: Scientific/Engineering :: Bio-Informatics",
]
dynamic = ["dependencies"]
[tool.setuptools.dynamic]
dependencies = {file = ["requirements.txt"]}
[project.optional-dependencies]
docs = [
"sphinx_rtd_theme",
"nbsphinx",
"nbsphinx_link",
"numpydoc",
"sphinx_book_theme"
]
development = [
"ruff",
"mypy"
]
[project.urls]
Homepage = "https://github.com/aertslab/scenicplus"
Documentation = "https://scenicplus.readthedocs.io"
Repository = "https://github.com/aertslab/scenicplus"
Changelog = "https://github.com/aertslab/scenicplus/releases"
[project.scripts]
scenicplus = "scenicplus.cli.scenicplus:main"
[tool.ruff]
target-version = "py38"
line-length = 88
fix = true
lint.select = [
"E", # pycodestyle
"W", # pycodestyle
"F", # Pyflakes
"B", # flake8-bugbear
"C4", # flake8-comprehensions
"D", # flake8-docstrings
"I", # isort
"SIM", # flake8-simplify
"TCH", # flake8-type-checking
"TID", # flake8-tidy-imports
"Q", # flake8-quotes
"UP", # pyupgrade
"PT", # flake8-pytest-style
"RUF", # Ruff-specific rules
]
lint.ignore = [
# Line length regulated by black
"E501",
# pydocstyle: http://www.pydocstyle.org/en/stable/error_codes.html
# numpy convention with a few additional lints
"D107",
"D203",
"D212",
"D401",
"D402",
"D415",
"D416",
# flake8-pytest-style:
"PT011", # pytest.raises({exception}) is too broad, set the match parameter or use a more specific exception
# flake8-simplify
"SIM102", # Use a single `if` statement instead of nested `if` statements
# ruff
"RUF005", # unpack-instead-of-concatenating-to-collection-literal
# pycodestyle
# TODO: Remove errors below to further improve docstring linting
# Ordered from most common to least common errors.
"D105",
"D100",
"D103",
"D102",
"D104",
"D101",
]
[tool.ruff.lint.pycodestyle]
max-doc-length = 88
[tool.ruff.lint.flake8-tidy-imports]
ban-relative-imports = "all"