pyproject.toml

[build-system]
requires = ["setuptools>=41", "wheel", "setuptools_scm[toml]>=6.2", "numpy", "Cython"]
build-backend = "setuptools.build_meta"

[tool.setuptools-git-versioning]
enabled = true

[project]
name = "chromatinhd"
authors = [
    {name = "Wouter Saelens", email = "wouter.saelens@gmail.com"},
]
description = "High-definition modeling of (single-cell) chromatin + transcriptomics data"
requires-python = ">=3.8"
keywords = ["bioinformatics", "chromatin accessibility", "transcriptomics"]
classifiers = [
    "Programming Language :: Python :: 3",
]
dependencies = [
    "torch",  # --extra-index-url https://download.pytorch.org/whl/cu113
    "scanpy",
    "matplotlib",
    "numpy",
    "seaborn",
    "diskcache",
    "appdirs",
    "xarray",
    "requests",
    "zarr",
    "pathlibfs",
]
dynamic = ["version", "readme"]
license = {text = "MIT"}

[project.urls]
"Homepage" = "https://github.com/DeplanckeLab/ChromatinHD"
"Bug Tracker" = "https://github.com/DeplanckeLab/ChromatinHD/issues"

[tool.setuptools.dynamic]
readme = {file = "README.md", content-type = "text/markdown"}

[project.optional-dependencies]
sam = [
    "pysam",
]
dev = [
    "pre-commit",
    "pytest",
    "coverage",
    "polyptich",
    "black",
    "pylint",
    "jupytext",
    "mkdocs",
    "mkdocs-material",
    "mkdocstrings[python]",
    "mkdocs-jupyter",
    "mike",
    "cairosvg",  # for mkdocs social
    "pillow",  # for mkdocs social
    "mkdocs-awesome-pages-plugin",
    "setuptools_scm",
    "Cython",
]
test = [
    "pytest",
    "ruff",
]
full = ["chromatinhd[sam]"]

[tool.setuptools_scm]

[tool.pytest.ini_options]
filterwarnings = [
    "ignore",
]

[tool.pylint.'MESSAGES CONTROL']
max-line-length = 120
disable = [
    "too-many-arguments",
    "not-callable",
    "redefined-builtin",
    "redefined-outer-name",
]

[tool.ruff]
line-length = 90
include = ['src/**/*.py']
exclude = ['scripts/*']


[tool.jupytext]
formats = "ipynb,py:percent"