pyproject.toml

[build-system]
requires = ["hatchling>=1.21.0"]
build-backend = "hatchling.build"

[project]
name = "demuxalot"

description = "Scalable and reliable demulitplexing for single-cell RNA sequencing."
readme = "README.md"
requires-python = ">=3.8"

keywords = [
    "genotype learning",
    "single cell RNA sequencing",
    "demultiplexing",
    "bayesian modelling",
]

license = { text = "MIT" }

classifiers = [
    "Programming Language :: Python :: 3",
    "License :: OSI Approved :: MIT License",
]

dependencies = [
    "pysam", # reads BAM files (alignment)
    "scipy",
    "numpy",
    "joblib", # multiprocessing in separate processes
    "pandas",
    "pyarrow", # required to read and write parquet files
]
dynamic = ["version"]
authors = [{ name = "Alex Rogozhnikov, System1 Biosciences" }]

[project.urls]
Homepage = "https://github.com/arogozhnikov/demuxalot"

[tool.setuptools]
packages = ["demuxalot"]

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

[tool.hatch.build.targets.sdist]
exclude = [
    "/.github",
    "/.idea",
    "/.pytest_cache",
    "/build",
    "/dist",
    "/tests",
    "/examples",
]

[tool.hatch.build.targets.wheel]
# should use packages from main section


[tool.hatch.envs.pypi.scripts]
# hatch run pypi:deploy_test
deploy_test = "hatch build --clean && hatch publish -r test"
deploy = "hatch build --clean && hatch publish"


[tool.hatch.envs.testing.scripts]
# hatch run testing:test
test = "pytest tests"


[tool.ruff]
line-length = 120