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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 = "pycisTopic"
authors = [
{ name = "Carmen Bravo", email = "[email protected]" },
{ name = "Gert Hulselmans", email = "[email protected]" },
{ name = "Seppe De Winter", email = "[email protected]" }
]
description = "pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data."
readme = "README.rst"
version = "2.0a"
requires-python = "~=3.11"
keywords = ["scATAC", "cell state", "topic modeling", "LDA", "enhancer"]
license = { file = "LICENSE.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",
]
dependencies = [
"numpy >= 1.20.3",
"pandas == 1.5",
"polars >= 0.18.3",
"pyarrow >= 8.0.0",
"pyranges < 0.0.128",
"ray",
"scatac_fragment_tools",
"scikit-learn",
"lda",
"matplotlib < 3.7",
"tmtoolkit",
"gensim",
"macs2",
"pybiomart",
"pyscenic",
"scrublet",
"harmonypy",
"igraph",
"leidenalg",
"seaborn",
"adjustText",
"statsmodels",
"scanpy",
"scanorama",
"bbknn",
"loomxpy",
"bs4",
"lxml"
]
[project.optional-dependencies]
docs = [
"sphinx_rtd_theme",
"nbsphinx",
"nbsphinx_link",
"numpydoc",
"sphinx_autosummary_accessors",
"autodocsumm",
"sphinx_copybutton",
"sphinx_design",
"sphinx_favicon",
"pandoc"
]
development = [
"mypy",
"ruff"
]
[project.urls]
Homepage = "https://github.com/aertslab/pycisTopic"
Documentation = "https://pycistopic.readthedocs.io/"
Repository = "https://github.com/aertslab/pycisTopic"
Changelog = "https://github.com/aertslab/pycisTopic/releases"
[project.scripts]
pycistopic = "pycisTopic.cli.pycistopic: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"