tools/pyproject.toml at main · nf-core/tools · GitHub

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[build-system]
build-backend = "setuptools.build_meta"
requires = ["setuptools>=40.6.0", "wheel"]

[tool.setuptools.packages.find]
where = ["."]
include = ["nf_core*"]

[tool.setuptools.package-data]
nf_core = ["**/*"]

[project]
name = "nf-core"
version = "4.2.0"
description = "Helper tools for use with nf-core Nextflow pipelines."
readme = "README.md"
license = "MIT"
keywords = [
    "nf-core",
    "nextflow",
    "bioinformatics",
    "workflow",
    "pipeline",
    "biology",
    "sequencing",
    "NGS",
    "next generation sequencing",
]
authors = [
    {name = "Phil Ewels", email = "phil.ewels@scilifelab.se"}
]
requires-python = ">=3.10, <4"
dependencies = [
    "click",
    "filetype",
    "GitPython",
    "PyGithub",
    "jinja2",
    "jsonschema>=4.0",
    "markdown>=3.3",
    "packaging",
    "pillow",
    "prek",
    "prompt_toolkit<=3.0.52",
    "pydantic>=2.2.1",
    "pyyaml",
    "questionary>=2.0.1",
    "refgenie",
    "requests",
    "requests_cache",
    "rich-click==1.9.*",
    "rich>=13.3.1",
    "rocrate",
    "repo2rocrate",
    "setuptools<84",
    "tabulate",
    "textual==8.2.8",
    "trogon",
    "pdiff",
    "ruamel.yaml",
]

[dependency-groups]
dev = [
    "mypy>=2.0.0",
    "myst_parser",
    "pytest-cov",
    "pytest-datafiles",
    "responses",
    "ruff",
    "Sphinx",
    "sphinx-rtd-theme",
    "textual-dev==1.8.0",
    "types-PyYAML",
    "types-requests",
    "types-jsonschema",
    "types-Markdown",
    "types-setuptools",
    "typing_extensions>=4.0.0",
    "pytest-asyncio",
    "pytest-clarity>=1.0.1",
    "pytest-codspeed>=5.0.3",
    "pytest-sugar>=1.1.1",
    "pytest-textual-snapshot==1.1.0",
    "pytest-workflow>=2.0.0",
    "pytest-xdist>=3.7.0",
    "pytest>=8.0.0",
]

[project.urls]
Homepage = "https://github.com/nf-core/tools"
Documentation = "https://nf-co.re/docs/nf-core-tools"
Repository = "https://github.com/nf-core/tools"
Changelog = "https://github.com/nf-core/tools/blob/master/CHANGELOG.md"

[project.scripts]
nf-core = "nf_core.__main__:run_nf_core"

[project.entry-points."refgenie.hooks.post_update"]
nf-core-refgenie = "nf_core.pipelines.refgenie:update_config"

[tool.pytest.ini_options]
markers = ["datafiles: load datafiles", "integration"]
testpaths = ["tests"]
python_files = ["test_*.py"]
asyncio_mode = "auto"
asyncio_default_fixture_loop_scope = "function"
norecursedirs = [
    ".*",
    "build",
    "dist",
    "*.egg",
    "data",
    "__pycache__",
    ".github",
    "nf_core",
    "docs",
]

[tool.ruff]
line-length = 120
target-version = "py310"
cache-dir = "~/.cache/ruff"

[tool.ruff.lint]
select = [
    "I",                     # isort
    "E1", "E4", "E7", "E9","E902",  # pycodestyle errors (partial)
    "F",                     # pyflakes
    "UP",                    # pyupgrade
    "N",                     # pep8-naming
    "B",                     # flake8-bugbear - catches common bugs and design problems
    "RSE",                   # flake8-raise - unnecessary parentheses on raised exceptions
    "PTH",                   # flake8-use-pathlib - prefer pathlib over os.path
    "SIM",                   # flake8-simplify - simplifies code patterns
    "C4",                    # flake8-comprehensions - better list/dict/set comprehensions
    "BLE",                   # flake8-blind-except - catches blind except clauses
    "W",                     # pycodestyle warnings
    "A",                     # flake8-builtins - catches shadowing of Python builtins
    "PIE",                   # flake8-pie - misc lints for common issues
]
ignore = ["PTH123", "PIE790"]

[tool.ruff.lint.isort]
known-first-party = ["nf_core"]

[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["E402", "F401"]

[tool.ruff.lint.pep8-naming]
extend-ignore-names = ["mocked_*", "*allOf", "*URI*"]