MediaIngredientMech/pyproject.toml at main · CultureBotAI/MediaIngredientMech · 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
[project]
name = "mediaingredientmech"
version = "0.1.0"
description = "LLM-assisted curation system for media ingredient ontology mappings"
authors = [
    {name = "MediaIngredientMech Contributors"}
]
readme = "README.md"
license = {text = "CC0-1.0"}
requires-python = ">=3.10"
keywords = [
    "microbiology",
    "growth media",
    "ontology mapping",
    "curation",
    "knowledge graph",
    "linkml"
]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "License :: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
]

dependencies = [
    "linkml>=1.7.0",
    "linkml-runtime>=1.7.0",
    "oaklib>=0.5.0",
    "pyyaml>=6.0",
    "click>=8.1.0",
    "rich>=13.0.0",
]

[project.optional-dependencies]
dev = [
    "pytest>=7.4.0",
    "pytest-cov>=4.1.0",
    "black>=23.0.0",
    "ruff>=0.1.0",
    "mypy>=1.5.0",
]

[project.urls]
Homepage = "https://github.com/KG-Hub/MediaIngredientMech"
Repository = "https://github.com/KG-Hub/MediaIngredientMech"

[build-system]
requires = ["setuptools>=68.0", "wheel"]
build-backend = "setuptools.build_meta"

[tool.setuptools.packages.find]
where = ["src"]

[tool.setuptools.package-data]
mediaingredientmech = ["schema/*.yaml"]

[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py"]
addopts = [
    "--strict-markers",
    "--cov=mediaingredientmech",
    "--cov-report=term-missing",
    "--cov-report=html",
]

[tool.black]
line-length = 100
target-version = ["py310", "py311", "py312"]
include = '\.pyi?$'
exclude = '''
/(
    \.git
  | \.hg
  | \.mypy_cache
  | \.tox
  | \.venv
  | _build
  | buck-out
  | build
  | dist
)/
'''

[tool.ruff]
line-length = 100
target-version = "py310"
select = [
    "E",   # pycodestyle errors
    "W",   # pycodestyle warnings
    "F",   # pyflakes
    "I",   # isort
    "B",   # flake8-bugbear
    "C4",  # flake8-comprehensions
    "UP",  # pyupgrade
]
ignore = [
    "E501",  # line too long (handled by black)
    "B008",  # do not perform function calls in argument defaults
    "C901",  # too complex
]

[tool.mypy]
python_version = "3.10"
warn_return_any = true
warn_unused_configs = true
disallow_untyped_defs = false
disallow_incomplete_defs = false
check_untyped_defs = true
no_implicit_optional = true
warn_redundant_casts = true
warn_unused_ignores = true
strict_equality = true