-
Notifications
You must be signed in to change notification settings - Fork 25
/
pyproject.toml
129 lines (119 loc) · 2.91 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
122
123
124
125
126
127
128
129
[tool.black]
line-length = 80
target-version = ['py312']
include = '\.pyi?$'
exclude = '''
(
/(
\.eggs # exclude a few common directories in the
| \.git # root of the project
| \.hg
| \.mypy_cache
| \.tox
| \.venv
| _build
| buck-out
| build
| dist
)/
| foo.py # also separately exclude a file named foo.py in
# the root of the project
)
'''
[tool.interrogate]
ignore-init-method = true
ignore-init-module = false
ignore-magic = false
ignore-semiprivate = false
ignore-private = false
ignore-property-decorators = false
ignore-module = true
fail-under = 100
exclude = [
"setup.py",
"docs",
"build",
"data",
"bin",
"dandelion/external",
"tests",
]
ignore-regex = ["^get$", "^mock_.*", ".*BaseClass.*"]
verbose = 2
quiet = false
whitelist-regex = []
color = true
[tool.pytest.ini_options]
addopts = "--cov --cov-report term-missing"
testpaths = ["tests"]
[build-system]
requires = ["setuptools>=45", "wheel", "setuptools_scm[toml]>=6.0"]
build-backend = "setuptools.build_meta"
[project]
name = "sc-dandelion"
dynamic = ["version"]
authors = [{ name = "zktuong", email = "[email protected]" }]
description = "sc-TCR/BCR-seq analysis tool"
readme = { file = "README.md", content-type = "text/markdown" }
license = { text = "GNU Affero General Public License v3 or later (AGPLv3+)" }
classifiers = [
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)",
]
keywords = ["dandelion", "single-cell", "immune", "TCR", "BCR"]
dependencies = [
"airr",
"setuptools_scm[toml]>=6.0",
"numpy>=1.18.4",
"pandas>=1.0.3,<=2.2.3",
"changeo>=1.0.0",
"anndata>=0.7.1",
"scanpy>=1.4.6",
"scikit-learn>=0.23.0",
"scipy>=1.4.1",
"numba>=0.48.0",
"seaborn>=0.10.1",
"networkx>=2.4",
"leidenalg>=0.8.0",
"polyleven>=0.5",
"h5py>=3.1.0",
"adjustText>=0.7",
"distance>=0.1.3",
"plotnine>=0.6.0",
"palettable>=3.3.0",
"mizani<0.10.0",
]
[project.urls]
homepage = "https://github.com/zktuong/dandelion/"
documentation = "https://sc-dandelion.readthedocs.io/"
[project.optional-dependencies]
docs = [
"airr",
"ipykernel",
"biopython",
"changeo",
"presto",
"pyyaml",
"yamlordereddictloader",
"nbsphinx<=0.9.2",
"sphinx-autodoc-typehints<=3.0.0",
"sphinx_rtd_theme<=3.0.2",
"readthedocs-sphinx-ext<=2.2.5",
"recommonmark<=0.7.1",
]
scirpy = ["scirpy<=0.20.0", "awkward", "mudata"]
[tool.setuptools]
include-package-data = true
package-data = { "dandelion" = [
"bin/tigger-genotype.R",
"bin/MakeDb_gentle.py",
] }
# Use data-files for extra files, if required
data-files = { bin = ["bin/tigger-genotype.R", "bin/MakeDb_gentle.py"] }
[tool.setuptools.packages.find]
where = ["src"]
[tool.setuptools_scm]
version_scheme = "guess-next-dev"
local_scheme = "dirty-tag"