SpatialTranscriptFormer/pyproject.toml at main · BenjaminIsaac0111/SpatialTranscriptFormer · 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
[build-system]
requires = ["setuptools>=61.0"]
build-backend = "setuptools.build_meta"

[project]
name = "spatial-transcript-former"
version = "0.1.0"
description = "A transformer-based model for spatial transcriptomics"
readme = "README.md"
requires-python = ">=3.9"
dependencies = [
    "pandas",
    "h5py",
    "torch",
    "torchvision",
    "numpy",
    "scikit-learn",
    "tqdm",
    "datasets",
    "pyarrow",
    "huggingface-hub",
    "matplotlib",
    "seaborn",
    "nystrom-attention",
    "scipy",
    "PyYAML",
]

[project.optional-dependencies]
dev = [
    "pytest",
    "black",
    "flake8",
]

[project.scripts]
stf-download = "spatial_transcript_former.data.download:main"
stf-split = "spatial_transcript_former.data.splitting:main"
stf-train = "spatial_transcript_former.train:main"
stf-predict = "spatial_transcript_former.predict:main"
stf-extract = "spatial_transcript_former.data.extract_features:main"
stf-build-vocab = "spatial_transcript_former.data.build_vocab:main"

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

[tool.pytest.ini_options]
testpaths = ["tests"]
pythonpath = ["src"]
filterwarnings = [
    "ignore::DeprecationWarning",
    "ignore:FigureCanvasAgg is non-interactive:UserWarning",
    "ignore:os.fork:RuntimeWarning",
    "ignore:torch.utils._pytree._register_pytree_node is deprecated:UserWarning",
]