ASAP/pyproject.toml at main · BoevaLab/ASAP · 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
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "atac-asap"
version = "0.2.2"
description = "A package for Allele-specific ATAC-seq prediction (ASAP)"
readme = "README.md"
requires-python = ">=3.8"
license = { file = "LICENSE" }
classifiers = [
    "Programming Language :: Python :: 3",
    "Operating System :: OS Independent",
]
authors = [
    { name = "Aayush Grover", email = "aayush.grover@inf.ethz.ch" },
    { name = "Till Muser", email = "till.muser@sdsc.ethz.ch" },
    { name = "Liine Kasak", email = "lkasak@student.ethz.ch" },
    { name = "Lin Zhang", email = "lin.zhang@sdsc.ethz.ch" },
    { name = "Ekaterina Krymova", email = "ekaterina.krymova@sdsc.ethz.ch" },
    { name = "Valentina Boeva", email = "valentina.boeva@inf.ethz.ch" }
]
dependencies = [
    "antlr4-python3-runtime~=4.9.3",
    "dacite",
    "filelock>=3.13.1",
    "fsspec>=2023.12.2",
    "hydra-core~=1.3.2",
    "importlib-metadata~=7.0.1",
    "jinja2~=3.1.3",
    "mpmath~=1.3.0",
    "networkx>=3.1",
    "numpy>=1.12.0,<2.0",
    "omegaconf~=2.3.0",
    "packaging>=23.2",
    "pandas>=2.0",
    "pillow~=10.2.0",
    "pybigwig>=0.3.22",
    "pyfaidx>=0.8.1.1",
    "pysam>=0.22.0",
    "python-dateutil~=2.8.2",
    "pytz~=2023.3.post1",
    "pyyaml~=6.0.1",
    "scipy>=1.10.0",
    "six~=1.16.0",
    "sympy~=1.12",
    "torch==2.1.2",
    "torchaudio==2.1.2",
    "torchinfo~=1.8.0",
    "torchmetrics",  # Unpinned due to frequent updates and backward compatibility
    "torchvision==0.16.2",
    "tqdm>=4.66.1",
    "tzdata~=2023.4",
    "zipp~=3.17.0",
]

[project.optional-dependencies]
dev = [
    "pre-commit",
    "pytest",
    "pytest-xdist",
]

[project.urls]
Homepage = "https://github.com/BoevaLab/ASAP"
Repository = "https://github.com/BoevaLab/ASAP"
Documentation = "https://github.com/BoevaLab/ASAP/wiki"

[tool.setuptools]
packages = ["asap", "asap.snv", "asap.utils", "asap.models", "asap.dataloader", "asap.trainer", "asap.models.layers", "asap.dataloader.utils"]
package-dir = { "" = "src" }