SpaDOT/pyproject.toml at main · marvinquiet/SpaDOT · 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
[build-system]
requires = ["setuptools", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "SpaDOT"
version = "1.0.4b"
description = "Package for paper: Optimal transport modeling uncovers spatial domain dynamics in spatiotemporal transcriptomics"
readme = "README.md"
requires-python = ">=3.9"
license = { text = "MIT" }
authors = [
    { name = "Wenjing Ma", email = "mawenjing1993@gmail.com" }
]

classifiers = [
    "Programming Language :: Python :: 3",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent"
]

dependencies = [
    "torch==2.5.0",
    "torchvision",
    "torchaudio",
    "anndata==0.9.1",
    "scanpy==1.9.8",
    "numpy<2.0.0",
    "chi2comb==0.1.0",
    "KDEpy==1.1.12",
    "wot",
    "pandas",
    "scipy",
    "scikit-learn",
    "matplotlib",
    "seaborn",
    "tqdm",
    "pyyaml",
    "louvain"
]

[project.urls]
homepage = "https://marvinquiet.github.io/SpaDOT"

[project.optional-dependencies]
dev = ["pytest", "black", "ruff"]

[project.scripts]
SpaDOT = "SpaDOT.cli:main"

[tool.setuptools.packages.find]
where = ["."]
include = ["SpaDOT*"]

[tool.setuptools.package-data]
"SpaDOT.utils.OT_loss" = ["libot.so"]
"SpaDOT" = ["config.yaml"]