Binette/pyproject.toml at main · genotoul-bioinfo/Binette · 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
[build-system]
requires = ["setuptools>=61.0.0", "setuptools-scm"]
build-backend = "setuptools.build_meta"

[project]
name = "Binette"
description = "Binette: accurate binning refinement tool to constructs high quality MAGs."
dynamic = ["version"]
authors = [
    {name = "Jean Mainguy"},
]
maintainers = [
    {name = "Jean Mainguy"},
]

readme = "README.md"
keywords = ["Bioinformatics", "Prokaryote", "Binning", "Refinement", "Metagenomics"]
classifiers=[
    "Environment :: Console",
    "Intended Audience :: Science/Research",
    "Natural Language :: English",
    "Operating System :: POSIX :: Linux",
    "Programming Language :: Python :: 3",
    "Topic :: Scientific/Engineering :: Bio-Informatics"]
requires-python = ">=3.12"

dependencies = [
    "joblib>=1.0,<2.0",
    "networkx>=3.0,<4.0",
    "numpy>1.24,<3.0",
    "pandas>=2,<3",
    "pyfastx>=2,<3",
    "pyrodigal>=3,<4",
    "pyroaring>=1.0.0,<2.0.0",
    "typer>=0.9.0,<1.0.0",
    "rich>=12.0.0,<14.0.0"
]

[project.optional-dependencies]

doc = [
    "sphinx==6.2.1",
    "sphinx_rtd_theme==1.2.2",
    "readthedocs-sphinx-search==0.3.1",
    "sphinx-autobuild==2021.3.14",
    "myst-parser==1.0.0",
    "docutils==0.18.1", #"myst-nb",
    "nbsphinx==0.9.5",
    "nbsphinx_link==1.3.0",
    "sphinx-book-theme==1.0.1",
    "sphinxcontrib.mermaid",
    "sphinx_togglebutton==0.3.2"
     ]

dev = [
    "pytest>=7.0.0",
    "pytest-cov",
    "ruff>=0.1.0"
]
#
[project.urls]
Repository = "https://github.com/genotoul-bioinfo/Binette"
#Changelog = "https://github.com/me/spam/blob/master/CHANGELOG.md"
Documentation = "https://binette.readthedocs.io"
#
#
[project.scripts]
binette = "binette.main:main"

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


[tool.setuptools.dynamic]
version = {attr = "binette.__version__"}

[tool.ruff]
line-length = 88
target-version = "py312"

# Essential linting rules
lint.select = ["E", "F", "I", "UP", "B"]

# Ignore rules that conflict with scientific code conventions
lint.ignore = ["E501", "E203"]

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

[tool.pytest.ini_options]
markers = [
    "requires_test_data: marks tests that require test dataset path to be provided",
]