ms2pip/pyproject.toml at main · CompOmics/ms2pip · 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
[project]
name = "ms2pip"
description = "MS2PIP: Accurate and versatile peptide fragmentation spectrum prediction."
readme = "README.rst"
license = { file = "LICENSE" }
dynamic = ["version"]
keywords = [
    "MS2PIP",
    "proteomics",
    "peptide fragmentation",
    "peak intensity prediction",
    "spectrum prediction",
    "machine learning",
    "spectral library",
    "fasta2speclib",
]
authors = [
    { name = "Ralf Gabriels", email = "ralf@gabriels.dev" },
    { name = "Sven Degroeve" },
    { name = "Arthur Declercq", email = "arthur.declercq@ugent.be" },
    { name = "Kevin Velghe", email = "kevin.velghe@ugent.be" },
    { name = "Ana Sílvia C. Silva" },
]
classifiers = [
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: Apache Software License",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3 :: Only",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Development Status :: 5 - Production/Stable",
]
requires-python = ">=3.11"
dependencies = [
    "numpy>=1.25,<3",
    "pandas[feather]>=1,<3",
    "pyteomics>=3.5,<5",
    "sqlalchemy>=1.4,<3",
    "click>=7,<9",
    "xgboost>=1.3,<3",
    "lxml>=4,<7",
    "rich>=13,<16",
    "pydantic>=2,<3",
    "werkzeug>=2,<4",
    "psm_utils>=1.5,<4",
    "ms2rescore-rs>=0.5.0,<2",
]
[project.optional-dependencies]
plotting = ["matplotlib>=3.0", "spectrum-utils>=0.5"]
rt = ["deeplc>=4.0.0b1,<5"]
im = ["im2deep>=2.0.0,<3"]

[dependency-groups]
notebook = ["ipykernel", "ipywidgets", "pip"]
dev = ["pytest", "ruff", "ty"]
docs = [
    "sphinx",
    "numpydoc>=1,<2",
    "recommonmark",
    "toml",
    "semver>=2",
    "sphinx_rtd_theme",
    "sphinx-autobuild",
    "sphinx-automodapi",
    "sphinx-click",
]

[project.urls]
documentation = "http://compomics.github.io/projects/ms2pip"
source = "https://github.com/compomics/ms2pip"
tracker = "https://github.com/compomics/ms2pip/issues"
webserver = "https://iomics.ugent.be/ms2pip/"
publication = "https://doi.org/10.1093/nar/gkad335/"

[project.scripts]
ms2pip = "ms2pip.__main__:main"

[build-system]
requires = ["setuptools"]
build-backend = "setuptools.build_meta"

[tool.setuptools.packages.find]
include = ["ms2pip*"]

[tool.setuptools.dynamic]
version = { attr = "ms2pip.__version__" }

[tool.black]
line-length = 99
target-version = ['py311']

[tool.ruff]
line-length = 99
target-version = 'py311'