NMD-Scanner/pyproject.toml at main · gagneurlab/NMD-Scanner · GitHub

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

[project]
name = "nmd_scanner"
version = "0.2.0"
description = "A simple scanner package for NMD"
authors = [
    { name = "Carina Hui Schröder", email = "Carina2504@users.noreply.github.com" },
    { name = "Florian R. Hölzlwimmer", email = "git.ich@frhoelzlwimmer.de" },
]
readme = "README.md"
license = "MIT"
requires-python = ">=3.12"
dependencies = [
    "pandas",
    "numpy",
    "pyfaidx",
    "biopython",
    "pyranges",
    "pysam",
    "tqdm>=4.66.5,<5",
    "importlib-metadata",
]

[project.urls]
"Homepage" = "https://github.com/gagneurlab/NMD-Scanner"

[project.scripts]
nmd-scanner = "nmd_scanner.cli:main_cli"

[dependency-groups]
dev = [
    "tox>=4",
    "tox-uv",
]
test = [
    "pytest>=8,<9",
    "pytest-xdist",
    "pytest-mock",
    "pytest-cov",
    "pytest-sugar",
]
lint = [
    "ruff",
    "mypy",
    "pandas-stubs",
]

[tool.hatch.build.targets.wheel]
packages = ["src/nmd_scanner"]

[tool.ruff]
target-version = "py312"
line-length = 120
extend-exclude = ["scripts", "resources", "testdir"]

[tool.ruff.lint]
select = ["E", "F", "W", "I"]
ignore = [
    "E501",  # line-too-long
    "E712",  # comparison-to-true (pandas idiom: df[col == True])
    "F403",  # star imports used intentionally in package
    "F405",  # may-be-undefined-from-star-import
]

[tool.ruff.lint.per-file-ignores]
"tests/*" = ["S", "SIM", "PLR", "F811", "F841"]
"__init__.py" = ["F401"]

[tool.tox]
requires = ["tox>=4", "tox-uv"]
env_list = ["format-check", "lints", "typecheck", "py3.12", "py3.14"]
isolated_build = true

[tool.tox.env_run_base]
runner = "uv-venv-lock-runner"
description = "run unit tests"
dependency_groups = ["test"]
commands = [["pytest", { replace = "posargs", default = ["tests"], extend = true }]]

[tool.tox.env."format-check"]
runner = "uv-venv-lock-runner"
skip_install = true
dependency_groups = ["lint"]
commands = [["ruff", "format", "--check", "."]]

[tool.tox.env."lints"]
runner = "uv-venv-lock-runner"
skip_install = true
dependency_groups = ["lint"]
commands = [["ruff", "check", "."]]

[tool.tox.env."typecheck"]
runner = "uv-venv-lock-runner"
dependency_groups = ["lint"]
commands = [["mypy", "src/nmd_scanner"]]

[tool.mypy]
python_version = "3.12"
ignore_missing_imports = true

[tool.pytest.ini_options]
testpaths = ["tests"]
addopts = ["--import-mode=importlib"]