forked from lucidrains/alphafold3-pytorch
-
Notifications
You must be signed in to change notification settings - Fork 0
/
pyproject.toml
116 lines (104 loc) · 2.41 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
[project]
name = "alphafold3-pytorch"
version = "0.6.7"
description = "Alphafold 3 - Pytorch"
authors = [
{ name = "Phil Wang", email = "[email protected]" },
{ name = "Alex Morehead", email = "[email protected]"}
]
readme = "README.md"
requires-python = ">= 3.9"
license = { file = "LICENSE" }
keywords = [
'artificial intelligence',
'deep learning',
'protein structure prediction',
]
classifiers=[
'Development Status :: 4 - Beta',
'Intended Audience :: Developers',
'Topic :: Scientific/Engineering :: Artificial Intelligence',
'License :: OSI Approved :: MIT License',
'Programming Language :: Python :: 3.9',
]
dependencies = [
"adam-atan2-pytorch>=0.0.8",
"awscliv2>=2.3.1",
"beartype",
"biopython>=1.83",
"cachetools",
"click>=8.1",
"CoLT5-attention>=0.11.0",
"einops>=0.8.0",
"einx>=0.2.2",
"ema-pytorch>=0.7.0",
"environs",
"lion-pytorch>=0.2.2",
"joblib",
"gemmi>=0.6.6",
"fair-esm",
"fastapi",
"frame-averaging-pytorch>=0.0.18",
"gradio",
"gradio_molecule3d",
"huggingface_hub>=0.21.4",
"jaxtyping>=0.2.28",
"lightning>=2.2.5",
"multimolecule",
"nimporter",
"numpy>=1.23.5",
"polars>=1.1.0",
"pdbeccdutils>=0.8.5",
"pydantic>=2.8.2",
"pyyaml",
"rdkit>=2023.9.6",
"retrying",
"scikit-learn>=1.5.0",
"scipy==1.13.1",
"sentencepiece",
"sh>=2.0.7",
"shortuuid",
"tensorboard",
"taylor-series-linear-attention>=0.1.12",
"torchtyping>=0.1.5",
"timeout_decorator>=0.5.0",
'torch_geometric',
"torch>=2.1",
"tqdm>=4.66.4",
"transformers[torch]",
"loguru",
]
[project.urls]
Homepage = "https://pypi.org/project/alphafold3-pytorch/"
Repository = "https://github.com/lucidrains/alphafold3-pytorch"
[project.optional-dependencies]
examples = []
test = [
"ruff>=0.4.2",
"pytest",
"pytest-shard",
]
[project.scripts]
alphafold3_pytorch = "alphafold3_pytorch.cli:cli"
alphafold3_pytorch_app = "alphafold3_pytorch.app:app"
[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"
[tool.pytest.ini_options]
pythonpath = [
"."
]
[tool.ruff]
line-length = 1000
lint.ignore = [
"F722", # for jaxtyping shape annotation
"F401",
"F821"
]
lint.extend-select = [
"W291"
]
[tool.hatch.metadata]
allow-direct-references = true
[tool.hatch.build.targets.wheel]
packages = ["alphafold3_pytorch"]