forked from scverse/pertpy
-
Notifications
You must be signed in to change notification settings - Fork 0
/
pyproject.toml
121 lines (107 loc) · 2.71 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
[tool.poetry]
name = "pertpy"
version = "0.6.0" # <<COOKIETEMPLE_FORCE_BUMP>>
description = "Perturbation Analysis in the scverse ecosystem."
authors = ["Lukas Heumos <[email protected]>"]
license = "MIT"
readme = "README.md"
homepage = "https://github.com/theislab/pertpy"
repository = "https://github.com/theislab/pertpy"
documentation = "https://pertpy.readthedocs.io"
packages = [
{ include = "pertpy" },
]
classifiers = [
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
]
[tool.poetry.dependencies]
python = ">=3.9.0,<3.11"
rich = ">=10.11.0"
PyYAML = ">=5.4.1"
scanpy = {extras = ["leiden"], version = "^1.9.3"}
muon = ">=0.1.2"
requests = ">=2.27.1"
ipywidgets = ">=7.6.5"
switchlang = ">=0.1.0"
scikit-misc = ">=0.1.4"
plotnine = ">=0.10.1"
scipy = ">=1.9.3"
scvi-tools = ">=0.20.3"
adjusttext = ">=0.7.3"
toytree = "^2.0.1"
arviz = ">=0.14"
numpyro = ">=0.10.1"
statannotations = "^0.5.0"
decoupler = "^1.3.4"
ete3 = {version = "^3.1.2", optional = true}
pyqt5 = {version = "^5.15.9", optional = true}
ott-jax = "^0.4.0"
sparsecca = ">=0.3.0"
numba = "^0.57.1"
remotezip = "^0.12.1"
openpyxl = "^3.1.2"
[tool.poetry.dev-dependencies]
black = ">=22.12.0"
pytest = ">=6.2.5"
coverage = {extras = ["toml"], version = ">=6.2"}
mypy = ">=0.930"
sphinx = ">=4.3.2"
sphinx-autobuild = ">=2021.3.14"
pre-commit = ">=2.16.0"
flake8 = ">=4.0.1"
flake8-bandit = ">=2.1.2"
flake8-bugbear = ">=21.11.29"
flake8-docstrings = ">=1.5.0"
flake8-rst-docstrings = ">=0.2.5"
pep8-naming = ">=0.12.1"
pre-commit-hooks = ">=4.1.0"
Pygments = ">=2.11.1"
types-pkg-resources = ">=0.1.3"
types-requests = ">=2.27.4"
types-attrs = ">=19.1.0"
pyenchant = ">=3.2.1"
nbsphinx = ">=0.8.8"
sphinx-gallery = ">0.6"
sphinx-autodoc-typehints = ">=1.12.0"
sphinx-last-updated-by-git = ">=0.3.0"
sphinx-automodapi = ">=0.14"
nbsphinx-link = ">=1.3.0"
sphinx-copybutton = ">=0.4.0"
pyupgrade = ">=2.31.0"
furo = ">=2022.3.4"
myst-parser = ">=0.17.0"
sphinx-remove-toctrees = ">=0.0.3"
sphinx-design = ">=0.0.13"
sphinxext-opengraph = ">=0.6.2"
[tool.poetry.extras]
ete3 = ["ete3"]
[tool.poetry.scripts]
pertpy = "pertpy.__main__:main"
[tool.black]
line-length = 120
[tool.mypy]
strict = false
pretty = true
show_column_numbers = true
show_error_codes = true
show_error_context = true
ignore_missing_imports = true
no_strict_optional = true
[tool.isort]
multi_line_output=3
include_trailing_comma=true
balanced_wrapping=true
line_length=120
[tool.pytest.ini_options]
testpaths = ["tests"]
[tool.coverage.paths]
source = ["pertpy", "*/site-packages"]
[tool.coverage.run]
branch = true
source = ["pertpy"]
[tool.coverage.report]
show_missing = true
[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"