pyproject.toml

[build-system]
build-backend = "hatchling.build"
requires = ["hatchling"]

[project]
name = "scalex"
authors = [{name = "Lei Xiong"}]
version = "1.0.6"
readme = "README.md"
requires-python = ">=3.7"
description = "Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space"
license = { text = "MIT" }
classifiers = [
    "Programming Language :: Python :: 3",
    "License :: OSI Approved :: BSD License",
    "Operating System :: OS Independent",
    "Development Status :: 3 - Alpha",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Intended Audience :: Science/Research"
]
dependencies = [
    "numpy>=1.26.4",
    "pandas>=2.2.2",
    "scipy>=1.13.0",
    "scikit-learn>=1.4.2",
    "torch>=2.2.2",
    "scanpy>=1.10.1",
    "tqdm>=4.66.2",
    "matplotlib>=3.8.4",
    "seaborn>=0.13.2",
    "leidenalg>=0.8.3",
    "gseapy",
]

[project.scripts]
SCALEX = "scalex.function:main"

[project.optional-dependencies]
dev = [
    "pre-commit",
    "twine>=4.0.2",
]
doc = [
    "docutils>=0.8,!=0.18.*,!=0.19.*",
    "sphinx>=4",
    "sphinx-book-theme>=1.0.0",
    "myst-nb",
    "sphinxcontrib-bibtex>=1.0.0",
    "sphinx-autodoc-typehints",
    "sphinxext-opengraph",
    "nbsphinx",
    # For notebooks
    "ipykernel",
    "ipython",
    "sphinx-copybutton",
    "pandas",
]
test = [
    "pytest>=6.0",
    "coverage",
]

[tool.coverage.run]
source = ["scalex"]
omit = [
    "**/test_*.py",
]

[tool.pytest.ini_options]
testpaths = ["tests"]
xfail_strict = true
addopts = [
    "--import-mode=importlib",  # allow using test files with same name
]

[tool.ruff]
line-length = 120
src = ["scalex"]
extend-include = ["*.ipynb"]

[tool.ruff.format]
docstring-code-format = true