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

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
[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 = "4.0.2"
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<81",
    "tabulate",
    "textual==8.2.4",
    "trogon",
    "pdiff",
    "ruamel.yaml",
]

[project.optional-dependencies]
dev = [
    "mypy",
    "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-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*"]