HuggingfaceTransformer/pyproject.toml at main · Brandes-Lab/HuggingfaceTransformer · 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
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
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "gLM"
version = "0.1.0"
description = "Gene Language Model - A transformer-based package for protein and gene sequence modeling"
readme = "README.md"
license = {file = "LICENSE"}
keywords = ["transformers", "protein", "gene", "language-model", "bert", "bioinformatics"]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
    "License :: OSI Approved :: MIT License",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.8",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
]
requires-python = ">=3.8"
dependencies = [
    "torch>=2.0.0",
    "transformers>=4.30.0",
    "tokenizers>=0.13.0",
    "datasets>=2.10.0",
    "numpy>=1.21.0",
    "pandas>=1.3.0",
    "scikit-learn>=1.0.0",
    "wandb>=0.15.0",
]

[project.optional-dependencies]
dev = [
    "pytest>=7.0.0",
    "pytest-cov>=4.0.0",
    "black>=23.0.0",
    "flake8>=6.0.0",
    "isort>=5.12.0",
    "mypy>=1.0.0",
]
training = [
    "accelerate>=0.20.0",
    "deepspeed>=0.9.0",
]
evaluation = [
    "evaluate>=0.4.0",
    "seqeval>=1.2.0",
]
flash-attn = [
    "flash-attn"
]

[project.urls]
Homepage = "https://github.com/BrandesLab/HuggingfaceTransformer"
Repository = "https://github.com/BrandesLab/HuggingfaceTransformer"
Issues = "https://github.com/BrandesLab/HuggingfaceTransformer/issues"

[tool.setuptools.packages.find]
where = ["."]
include = ["gLM*"]
exclude = ["tests*", "checkpoints*", "slurm_scripts*"]

[tool.setuptools.package-data]
gLM = ["*.json", "*.txt", "*.yaml", "*.yml"]

[tool.black]
line-length = 88
target-version = ["py38", "py39", "py310", "py311"]
include = '\.pyi?$'
extend-exclude = '''
/(
  # directories
  \.eggs
  | \.git
  | \.hg
  | \.mypy_cache
  | \.tox
  | \.venv
  | build
  | dist
  | checkpoints
)/
'''

[tool.isort]
profile = "black"
multi_line_output = 3
line_length = 88
known_first_party = ["gLM"]
skip_glob = ["checkpoints/*"]

[tool.mypy]
python_version = "3.8"
warn_return_any = true
warn_unused_configs = true
disallow_untyped_defs = true
ignore_missing_imports = true
exclude = [
    "checkpoints/",
    "slurm_scripts/",
]

[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py", "*_test.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]
addopts = [
    "--strict-markers",
    "--strict-config",
    "--verbose",
    "--cov=gLM",
    "--cov-report=term-missing",
    "--cov-report=html",
]
markers = [
    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
    "integration: marks tests as integration tests",
    "unit: marks tests as unit tests",
]

[tool.coverage.run]
source = ["gLM"]
omit = [
    "*/tests/*",
    "*/test_*",
    "checkpoints/*",
    "slurm_scripts/*",
]

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "def __repr__",
    "if self.debug:",
    "if settings.DEBUG",
    "raise AssertionError",
    "raise NotImplementedError",
    "if 0:",
    "if __name__ == .__main__.:",
    "class .*\\bProtocol\\):",
    "@(abc\\.)?abstractmethod",
]

[tool.uv.extra-build-dependencies]
flash-attn = ["torch"]