jointly-hic/pyproject.toml at main · abdenlab/jointly-hic · GitHub

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

[project]
name = "jointly-hic"
description = "Genomics research toolkit for jointly embedding Hi-C 3D chromatin contact matrices into the same vector space"
authors = [
    {name = "Thomas Reimonn", email = "thomas.reimonn@umassmed.edu"},
    {name = "Guoyun Chen", email = "guoyun.chen5@umassmed.edu"},
    {name = "Nezar Abdennur", email = "nezar.abdennur@umassmed.edu"},
    {name = "Hoang Tran", email ="hoang.tran5@umassmed.edu"}
]
readme = "README.md"
license = {text = "GPL-3.0"}
requires-python = ">=3.10"
dynamic = ["version"]
dependencies = [
    "bioframe>=0.8.0",
    "cooler>=0.10.3",
    "cooltools>=0.7.1",
    "cython>3.0.5",
    "datashader>=0.17.0",
    "leidenalg>=0.10.1",
    "matplotlib>=3.6.0",
    "numpy>=2.1",
    "pandas>=2.1",
    "pyarrow>=14",
    "pydantic>=2.4.2",
    "scikit-learn>=1.3.2",
    "umap-learn[plot]>=0.5.4",
    "pybbi>=0.3.6"
]

[project.optional-dependencies]
dev = [
    "pre-commit>=4.0.0",
    "isort>=5.12.0",
    "pytest>=8.1.0",
    "pytest-mock>=3.12.0",
    "pytest-cov>=4.1.0",
    "ruff>=0.10.0",
    "hatch>=1.10.0"
]
notebook = [
    "black>=25.0",
    "jupyter-black>=0.4.0",
    "jupyter>=1.0.0",
    "jupyterlab>=4.0.10",
    "plotly>=5.18.0"
]

[project.scripts]
jointly = "jointly_hic.__main__:main"

[tool.hatch.version]
path = "jointly_hic/__init__.py"

[tool.hatch.envs.default.scripts]
fix = "ruff check --fix --exit-non-zero-on-fix jointly_hic"
lint = "ruff check --exit-non-zero-on-fix jointly_hic"
test = "pytest --cov=jointly_hic --cov-report=html --cov-report=term-missing --cov-fail-under=90 --color=yes --verbose tests"

[tool.ruff]
exclude = [
    "__init__.py",
]
lint.extend-select = [
    "E",  # style errors
    "D",  # pydocstyle
    "F",  # pyflakes
    "S",  # mypy
    "T",  # tests
    "UP", # pyupgrade
    "I",  # isort
    "RUF", # ruff-specific rules
    "UP", # pyupgrade
    "W",  # style  warnings
]
line-length = 120
indent-width = 4
lint.ignore = ["S101", "D203", "D213"]


[tool.isort]
profile = "black"
line_length = 120
skip_gitignore = true
known_first_party = "jointly_hic"