include-access-model/pyproject.toml at main · include-dcc/include-access-model · 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
[build-system]
requires = [
  "hatchling>=1.32.0",
  "uv-dynamic-versioning"
]
build-backend = "hatchling.build"

[project]
name = "include_access_model"
description = "Internal Access model for the INCLUDE DCC."
authors = [
  {name = "Robert Carroll", email = "robert.carroll@vumc.org"},
]
license = "MIT"
license-files = ["LICENSE"]
readme = "README.md"
requires-python = ">=3.12,<4.0"
dynamic = ["version"]

dependencies = [
  "sqlalchemy",
  "linkml-runtime>=1.11.0"
]

[dependency-groups]
dev = [
    "linkml>=1.11.0",
    "mkdocs-material>=8.2.8",
    "mkdocs-mermaid2-plugin>=1.1.1",
    "mkdocs-pymdownx-material-extras>=2.5.6",
    "jupyter>=1.0.0",
    "mknotebooks>= 0.8.0",
    "the-caddie",
    "term-weaver"
]

# 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"
pattern = "^v?(?P<base>\\d+\\.\\d+\\.\\d+)"
fallback-version = "0.0.0"

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

# https://docs.astral.sh/ruff/configuration/
[tool.ruff]
exclude = [
    "src/include_access_model/_version.py",
]

# Ref.: https://github.com/codespell-project/codespell
[tool.codespell]
skip = [
  "LICENSE",
  "pyproject.toml",
  "uv.lock",
  "_typos.toml",
  "project/*",
  "src/include_access_model/datamodel/include_access_model_pydantic.py",
  "src/include_access_model/datamodel/include_access_model_sqla.py",
  "src/include_access_model/datamodel/include_access_model.py",
  "./src/include_access_model/schema/upstream-models/*.yaml"
]

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

[tool.hatch.build.targets.wheel]
packages = ["src/include_access_model"]
artifacts = ["src/include_access_model/datamodel/*.py"]

[tool.hatch.build.targets.sdist]
artifacts = ["src/include_access_model/datamodel/*.py"]
exclude = [
  ".direnv",
  ".venv",
  "scratch",
  "scripts",
  "helpers"
]

# 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/include_access_model/datamodel/include_access_model_pydantic.py",
  "src/include_access_model/datamodel/include_access_model.py",
]

[tool.uv.sources]
the-caddie = { git = "https://github.com/carrollaboratory/the-caddie" }
term-weaver = { git = "https://github.com/include-dcc/term-weaver" }