pyproject.toml

[project]
name = "ALLCools"
description = "Toolkit for single-cell DNA methylome and multiomic data analysis."
authors = [{ name = "Hanqing Liu" }]
maintainers = [
    { name = "Hanqing Liu", email = "hanliu@salk.edu" },
    { name = "Jingtian Zhou", email = "jzhou@salk.edu" },
    { name = "Wei Tian", email = "wtian@salk.edu" },
]
urls.Documentation = "https://lhqing.github.io/ALLCools/intro.html"
urls.Source = "https://github.com/lhqing/ALLCools"
urls.Home-page = "https://github.com/lhqing/ALLCools"
version = "1.1.0"
requires-python = ">=3.7"
license = { file = "LICENSE" }
readme = "README.md"
dependencies = [
    "anndata",
    "numpy",
    'matplotlib',
    "natsort",
    "pandas",
    "pybedtools",
    "pyBigWig",
    "pysam",
    'seaborn',
    "xarray",
    "pyyaml",
]

[project.optional-dependencies]
dev = [
    # dev version generation
    "bump2version",
    "pre-commit",
]
analysis = [
    "biopython",
    "dask",
    "numba",
    "imblearn",
    "leidenalg",
    "networkx",
    "opentsne",
    "pynndescent",
    "scanpy",
    "scikit-learn",
    "statsmodels",
    "rpy2",
    "tpot",
    "cooler",
]
doc = ["jupyter-book", "ghp-import"]
test = ["pytest", "pytest-cov"]

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

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

[tool.isort]
include_trailing_comma = true
multi_line_output = 3
profile = "black"
skip_glob = ["docs/*"]

[tool.black]
line-length = 120
target-version = ['py38']
include = '\.pyi?$'
exclude = '''
(
  /(
      \.eggs
    | \.git
    | \.hg
    | \.mypy_cache
    | \.tox
    | \.venv
    | _build
    | buck-out
    | build
    | dist
  )/
)
'''

[build-system]
build-backend = "flit_core.buildapi"
requires = [
    "flit_core >=3.4,<4",
    "importlib_metadata>=0.7; python_version < '3.8'",
]

[project.scripts]
allcools = "ALLCools.__main__:main"