forked from amcdavid/PySnpTools
-
Notifications
You must be signed in to change notification settings - Fork 5
/
Copy pathpyproject.toml
121 lines (108 loc) · 2.92 KB
/
pyproject.toml
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
[build-system]
requires = ["numpy>=1.22.0", "setuptools>=42"]
build-backend = "setuptools.build_meta"
[project]
name = "pysnptools"
version = "0.5.14"
description = "PySnpTools"
readme = "README.md"
requires-python = ">=3.10"
keywords = [
"gwas",
"bioinformatics",
"sets",
"intervals",
"ranges",
"regions",
"plink",
"genomics",
"file-format",
"reader",
"genotype",
"bed-format",
"writer",
"python",
"snps",
]
authors = [{ name = "FaST-LMM Team", email = "[email protected]" }]
license = { text = "Apache 2.0" }
classifiers = [
"Programming Language :: Python",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: 3.13",
]
dependencies = [
"scipy>=1.7.0",
"numpy>=1.22.0",
"psutil>=6.1.0",
"pandas>=1.3.0",
"h5py>=3.12.1",
"cloudpickle>=3.1.0",
"wheel>=0.44.0",
"bed-reader[samples]>=1.0.6",
"more-itertools>=10.5.0",
]
[project.urls]
homepage = "https://fastlmm.github.io/"
bug-tracker = "https://github.com./fastlmm/PySnpTools/issues"
documentation = "http://fastlmm.github.io/PySnpTools"
source-code = "https://github.com./fastlmm/PySnpTools"
[project.optional-dependencies]
bgen = ["cbgen>=1.0.6", "bgen-reader>=4.0.9"]
dev = [
"pytest",
"pytest-cov",
"pytest-doctestplus",
"pytest-datadir",
"limix-sphinx-theme>=0.0.4",
"pytest-sphinx>=0.2.2",
"sphinx>=6.2.1",
"sphinx_rtd_theme>=3.0.1",
"ruff>=0.7.2",
]
[tool.ruff]
line-length = 250
exclude = [
"*.ipynb",
"doc/source/conf.py",
"bed_reader/tests/benchmark/benchmark.py",
]
[tool.ruff.lint]
select = ["E", "F", "W"]
[tool.pytest.ini_options]
addopts = "--doctest-modules --doctest-glob=*.rst --doctest-glob=*.md"
doctest_optionflags = ["ELLIPSIS", "NORMALIZE_WHITESPACE"]
filterwarnings = [
"ignore:Converting float64 to float32 can cause loss of information:UserWarning",
"ignore:'count_A1' was not set.*will default to 'False':FutureWarning",
"ignore:standardizing an ndarray instead of a SnpData is deprecated:DeprecationWarning",
"ignore:.*\\.kernel.*deprecated.*read_kernel.*val:DeprecationWarning",
"ignore:'parent_string' is deprecated. Use 'name':DeprecationWarning",
]
[tool.uv]
dev-dependencies = ["pytest-xdist>=3.6.1", "twine>=5.1.1"]
[tool.setuptools]
packages = [
"pysnptools",
"pysnptools.kernelreader",
"pysnptools.kernelstandardizer",
"pysnptools.pstreader",
"pysnptools.snpreader",
"pysnptools.distreader",
"pysnptools.standardizer",
"pysnptools.util",
"pysnptools.util.filecache",
"pysnptools.util.mapreduce1",
"pysnptools.util.mapreduce1.runner",
]
[tool.setuptools.package-data]
"*" = ["LICENSE.md", "AUTHORS.txt", "*.rst"]
"pysnptools" = [
"util/pysnptools.hashdown.json",
"util/bgen.hashdown.json",
"tests/mintest.py",
]
"doc" = ["*"]
"tests" = ["*"]