cnaster/pyproject.toml at main · michaelJwilson/cnaster · GitHub

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[project]
name = "cnaster"
version = "0.1.0"
description = ""
authors = [{ name = "M. J. Wilson", email = "mjwilson@princeton.edu" }]
requires-python = ">=3.12.2"
readme = "README.md"
dependencies = [
    "numpy>=1.26.0,<2",
    "matplotlib",
    "scipy",
    "scikit-learn",
    "pandas>=2.0.0",
    "scanpy>=1.9.0",
    "anndata>=0.8.0",
    "numba>=0.61.0",
    "rich==14.0.0",
    "polars>=1.30.0",
    "pyyaml>=6.0",
    "pybedtools",
    "hmmlearn",
    "pysam"
]

[project.optional-dependencies]
dev = [
    "pytest>=8.3.5,<9",
    "ruff>=0.9.9,<0.10",
    "black>=25.1.0",
    "mypy>=1.0.0",
    "pre-commit>=3.0.0",
    "isort",
    "mock",
    "sphinx",
    "sphinxcontrib-bibtex<2.0.0",
    "sphinx-rtd-theme",
    "recommonmark",
    "sphinx-markdown-tables",
]
build = [
    "setuptools>=65.0.0",
    "wheel>=0.38.0",
]
test = [
    "pytest>=7.0.0",
    "pytest-cov>=4.0.0",
    "pytest-xdist>=3.0.0",
]

[project.scripts]
# run_cnaster_sim = "cnaster.sim.scripts.run_cnaster_sim:main"
run_cnaster = "cnaster.scripts.run_cnaster:main"
run_cnaster_tumor_prop = "cnaster.scripts.run_cnaster_tumor_prop:main"
prep_snps = "cnaster.scripts.prep_snps:main"
create_allele_matrices = "cnaster.scripts.create_allele_matrices:main"

[tool.hatch.build.targets.sdist]
include = ["python/cnaster"]

[tool.hatch.build.targets.wheel]
include = ["python/cnaster"]

[tool.hatch.build.targets.wheel.sources]
"python/cnaster" = "cnaster"

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

[tool.ruff.lint]
ignore = [
  "G004", # f-string in logger
  "T201", # print statements
  "PLR2004", # magic value in assert
  "NPY002", # legacy numpy calls
  "ANN",  # Ignore all type annotation rules
  "I002",  # Ignore the rule that requires `from __future__ import annotations`
]

extend-select = [
  "B",           # flake8-bugbear
  "I",           # isort
  "ARG",         # flake8-unused-arguments
  "C4",          # flake8-comprehensions
  "EM",          # flake8-errmsg
  "ICN",         # flake8-import-conventions
  "ISC",         # flake8-implicit-str-concat
  "G",           # flake8-logging-format
  "PGH",         # pygrep-hooks
  "PIE",         # flake8-pie
  "PL",          # pylint
  "PT",          # flake8-pytest-style
  "PTH",         # flake8-use-pathlib
  "RET",         # flake8-return
  "RUF",         # Ruff-specific
  "SIM",         # flake8-simplify
  "T20",         # flake8-print
  "UP",          # pyupgrade
  "YTT",         # flake8-2020
  "EXE",         # flake8-executable
  "NPY",         # NumPy specific rules
  "PD",          # pandas-vet
]
extend-ignore = [
  "PLR09",    # Too many <...>
  "ISC001",   # Conflicts with formatter
]
unfixable = [
  "T20",  # Removes print statements
  "F841", # Removes unused variables
]
isort.required-imports = ["from __future__ import annotations"]

[tool.ruff.lint.per-file-ignores]
"tests/**" = ["ALL"]
"python/cnaster/sandbox/**" = ["ALL"]