-
Notifications
You must be signed in to change notification settings - Fork 507
/
pyproject.toml
78 lines (71 loc) · 2.32 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
[tool.poetry]
name = "colabfold"
version = "1.5.5"
description = "Making protein folding accessible to all. Predict proteins structures both in google colab and on your machine"
authors = [
"Milot Mirdita <[email protected]>",
"Sergey Ovchinnikov <[email protected]>",
"Martin Steinegger <[email protected]>",
"Kostantin Schütze <[email protected]>",
"Yoshitaka Moriwaki",
"Lim Heo",
]
readme = "README.md"
license = "MIT, but separate licenses for the trained weights"
repository = "https://github.com/sokrypton/ColabFold"
classifiers = [
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Topic :: Scientific/Engineering :: Artificial Intelligence"
]
[tool.poetry.dependencies]
python = ">=3.9"
absl-py = "^1.0.0"
jax = { version = "^0.4.20", optional = true }
matplotlib = "^3.2.2"
tensorflow-macos = { version = "<2.14.0", markers = "sys_platform == 'darwin'" }
tensorflow-cpu = { version = "^2.12.1", markers = "sys_platform != 'darwin' and platform_machine != 'aarch64'" }
tensorflow = { version = "^2.12.1", markers = "sys_platform != 'darwin' and platform_machine == 'aarch64'" }
biopython = "<1.83"
numpy = "^1.22.0"
pandas = "^1.3.4"
alphafold-colabfold = { version = "v2.3.7", optional = true }
#alphafold-colabfold = { path = "../alphafold", develop = true, optional = true }
requests = "^2.26.0"
tqdm = "^4.62.2"
appdirs = "^1.4.4"
py3Dmol = "^2.0.1"
dm-haiku = "^0.0.12"
importlib-metadata = "^4.8.2"
[tool.poetry.dev-dependencies]
# The latest version conflicts with tensorflow over typing-extensions
black = "^23.1.0"
jupyter = "^1.0.0"
pytest = "^6.2.5"
[tool.poetry.extras]
alphafold = ["alphafold-colabfold", "jax"]
alphafold-minus-jax = ["alphafold-colabfold"]
[tool.pytest.ini_options]
addopts = "--tb=short"
[tool.poetry.scripts]
colabfold_batch = 'colabfold.batch:main'
colabfold_search = 'colabfold.mmseqs.search:main'
colabfold_split_msas = 'colabfold.mmseqs.split_msas:main'
colabfold_relax = 'colabfold.relax:main'
[tool.black]
# Format only the new package, don't touch the existing stuff
include = '''
/(
| colabfold
| tests
)/
'''
# The colabfold.py exclude doesn't work, but the "fmt: off" inside of it does
extend-exclude = '''
/(
| __pycache__
| colabfold/colabfold.py
)/
'''
[build-system]
requires = ["poetry-core>=1.0.0,<2.0.0"]
build-backend = "poetry.core.masonry.api"