sd-graph/pyproject.toml at master · source-data/sd-graph · 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
[project]
name = "sd-graph"
version = "0.1.0"
description = "Discover refereed preprints in the field of molecular biology."
readme = "README.md"
requires-python = ">=3.11"
dependencies = [
    "connexion[swagger-ui]<3.0.0",
    "flask>=2.2.5",
    "flask-caching>=2.3.1",
    "flask-cors>=6.0.1",
    "flask-dotenv>=0.1.2",
    "gunicorn>=23.0.0",
    "lxml>=5.4.0",
    "neo4j>=5.28.1",
    "python-dotenv>=1.1.1",
    "redis>=6.2.0",
    "requests>=2.32.4",
    "tqdm>=4.67.1",
    "werkzeug>=2.2.3",
]

[dependency-groups]
deploy = [
    "ai",
    "cdlib>=0.1.9",
    "hypothepy",
    "infomap>=1.2.1",
    "jinja2>=3.1.6",
    "networkx<=2.5",
    "openai<1.0.0",
    "pandas>=2.3.0",
    "pytest>=8.4.1",
    "python-igraph>=0.11.9",
    "pyyaml>=6.0.2",
    "scikit-learn>=1.7.0",
    "smtag",
    "tenacity>=9.1.2",
    "wurlitzer>=2.0.1",
]
webserver = []

[tool.uv.sources]
ai = { git = "https://github.com/source-data/ai.git", tag = "2020-05-04_001" }
hypothepy = { git = "https://github.com/embo-press/hypothepy", rev = "dc4e0ba5bcbc46fcb0a9ced97218a388c590228d" }
smtag = { git = "https://github.com/source-data/soda-roberta.git", rev = "938dab016348ae547d6f2663bf307d5470290706" }

[tool.uv]
override-dependencies = [
    "numpy<2.0.0",  # networkx
    "scipy<1.13.0",  # cdlib
    "transformers==4.24.0",

]

[tool.uv.extra-build-dependencies]
infomap = ["setuptools<82.0.0"]