linkml-reference-validator/pyproject.toml at main · linkml/linkml-reference-validator · 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
[build-system]
requires = ["hatchling", "uv-dynamic-versioning"]
build-backend = "hatchling.build"

[project]
name = "linkml_reference_validator"
description = "Validation of supporting text from references and publications"
authors = [
  {name = "Chris Mungall", email = "cjmungall@lbl.gov"},
]
license = "Apache-2.0"
license-files = ["LICENSE"]
readme = "README.md"
requires-python = ">=3.10,<4.0"
dynamic = ["version"]

dependencies = [
  "typer >= 0.9.0",
  "linkml-runtime >=1.9.4",
  "biopython >= 1.80",
  "beautifulsoup4 >= 4.9.0",
  "lxml >= 4.9.0",
  "requests >= 2.28.0",
  "pydantic >= 2.0.0",
  "ruamel-yaml >= 0.18.0",
  "rapidfuzz >= 3.14.3",
  "jsonpath-ng >= 1.6.0",
]

[dependency-groups]
dev = [
    "linkml>=1.9.3",
    "mypy>=1.17.1",
    "ruff>=0.4.8",
    "mkdocs-material>=8.2.8",
    "mkdocs-mermaid2-plugin>=1.1.1",
    "mkdocs-jupyter>=0.24.0",
    "jupyter>=1.0.0",
    "papermill>=2.4.0",
    "pytest>=7.0.0",
    "pytest-mock>=3.10.0",
    "pytest-cov>=7.0.0",
]

[project.scripts]
linkml-reference-validator = "linkml_reference_validator.cli:main"


# See https://hatch.pypa.io/latest/config/build/#file-selection for how to
# explicitly include files other than default into the build distributions.

[tool.hatch.version]
source = "uv-dynamic-versioning"

# Ref.: https://github.com/ninoseki/uv-dynamic-versioning/
[tool.uv-dynamic-versioning]
vcs = "git"
style = "pep440"
fallback-version = "0.0.0"

# Ref.: https://docs.pytest.org/en/stable/reference/reference.html#configuration-options
[tool.pytest.ini_options]
testpaths = ["tests"]

# Ref.: https://github.com/codespell-project/codespell
[tool.codespell]
skip = [
  "LICENSE",
  "pyproject.toml",
  "uv.lock",
  "project/*",
  "src/linkml_reference_validator/datamodel/linkml_reference_validator_pydantic.py",
  "src/linkml_reference_validator/datamodel/linkml_reference_validator.py",
]

# Reminder: words have to be lowercased for the ignore-words-list
ignore-words-list = "linke"
quiet-level = 3

# Ref.: https://github.com/crate-ci/typos (spell checker)
[tool.typos.default.extend-words]
linke = "linke"
[tool.typos.files]
extend-exclude = [
  "LICENSE",
  "uv.lock",
  "pyproject.toml",
  "project/*",
  "src/linkml_reference_validator/datamodel/linkml_reference_validator_pydantic.py",
  "src/linkml_reference_validator/datamodel/linkml_reference_validator.py",
]