acore/pyproject.toml at main · Multiomics-Analytics-Group/acore · GitHub

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[project]
authors = [
  { name = "Alberto Santos Delgado", email = "albsad@dtu.dk" },
  { name = "Henry Webel", email = "heweb@dtu.dk" },
]
name = "acore"
dynamic = ["version"]
description = "A Python package with statistical functions to analyse multimodal molecular data"
license = { text = "GNU General Public License v3" }
readme = "README.rst"
requires-python = ">=3.9"
classifiers = [
  "Development Status :: 2 - Pre-Alpha",
  "Intended Audience :: Developers",
  "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
  "Natural Language :: English",
  "Programming Language :: Python :: 3.9",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
]

dependencies = [
  "numpy",
  "pandas",
  "dsp-pandas",        # has only pandas related dependencies
  "vuecore",
  "scipy",
  "scikit-learn>=1.5",
  "networkx",
  "biopython",
  "combat",
  "gseapy!=1.1.5",
  "kmapper",
  "lifelines",
  "pingouin<0.6.0",    # ToDo: update column name changes, https://pingouin-stats.org/changelog.html#v0-6-0-february-2026
  "python-louvain",
  "PyWGCNA!=2.2.0",    # to fix.
  "snfpy",
  "umap-learn",
  "statsmodels",
  "inmoose",           # combat batch correction
  "requests",
  "rarfile",
  "pandera",
]

[project.optional-dependencies]
docs = [
  "sphinx",
  "sphinx-book-theme",
  "myst-nb",
  "ipywidgets",
  "sphinx-new-tab-link!=0.2.2",
  "jupytext",
  "sphinx-copybutton",
  "sphinx-llms-txt",
]
dev = [
  "black[jupyter]",
  "flake8",
  "ruff",
  "isort",
  "pytest",
  "pytest-cov",
  "twine",
  "wheel",
  "jupytext",
  "ipykernel",
]

[project.urls]
Homepage = "https://github.com/Multiomics-Analytics-Group/acore"
Issues = "https://github.com/Multiomics-Analytics-Group/acore/issues"
Documentation = "https://analytics-core.readthedocs.io/"

[tool.ruff]
# https://docs.astral.sh/ruff/rules/#flake8-bandit-s

[tool.ruff.lint]
# https://docs.astral.sh/ruff/tutorial/#rule-selection
# 1. Enable flake8-bugbear (`B`) rules
# 2. Enable pycodestyle (`E`) errors and (`W`) warnings
# 3. Pyflakes (`F`) errors
# extend-select = ["E", "W", "F", "B"]
# Ignore line length errors:
# ignore = ["E501"]

[build-system]
requires = ["setuptools>=64", "setuptools_scm>=8"]
build-backend = "setuptools.build_meta"

[tool.setuptools_scm]
# https://setuptools-scm.readthedocs.io/
# used to pick up the version from the git tags or the latest commit.

[tool.isort]
profile = "black"

# [entrypoints]
# console_scripts = {
#     "acore = acore.cli:main"
# }

# [package]
# include = [
#     "README.rst",
#     "HISTORY.rst",
# ]