forked from linkml/linkml
-
Notifications
You must be signed in to change notification settings - Fork 0
/
pyproject.toml
250 lines (230 loc) · 7.91 KB
/
pyproject.toml
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
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
[tool.poetry]
name = "linkml"
version = "0.0.0"
description = "Linked Open Data Modeling Language"
authors = [
"Chris Mungall <[email protected]>",
"Harold Solbrig <[email protected]>",
"Sujay Patil <[email protected]>",
"Harshad Hegde <[email protected]>",
"Sierra Moxon <[email protected]>",
"Mark Andrew Miller <[email protected]>",
"Deepak Unni <[email protected]>",
"Bill Duncan <[email protected]>",
"Joseph Eugene Flack IV <[email protected]>",
"Gaurav Vaidya <[email protected]>",
"Kevin Schaper <[email protected]>",
]
readme = "README.md"
homepage = "https://linkml.io/linkml/"
repository = "https://github.com/linkml/linkml"
documentation = "https://linkml.io/linkml/"
keywords = ["schema", "linked data", "data modeling", "rdf", "owl", "biolink"]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Environment :: Console",
"Intended Audience :: Developers",
"Intended Audience :: Science/Research",
"Intended Audience :: Healthcare Industry",
"License :: OSI Approved :: Apache Software License",
"Topic :: Software Development :: Libraries :: Python Modules",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
]
packages = [
{ include = "linkml" }
]
[tool.poetry-dynamic-versioning]
enable = true
vcs = "git"
style = "pep440"
[tool.poetry.scripts]
linkml = "linkml.cli.main:linkml"
gen-jsonld-context = "linkml.generators.jsonldcontextgen:cli"
gen-prefix-map = "linkml.generators.prefixmapgen:cli"
gen-csv = "linkml.generators.csvgen:cli"
gen-graphviz = "linkml.generators.dotgen:cli"
gen-golang = "linkml.generators.golanggen:cli"
gen-golr-views = "linkml.generators.golrgen:cli"
gen-graphql = "linkml.generators.graphqlgen:cli"
gen-java = "linkml.generators.javagen:cli"
gen-jsonld = "linkml.generators.jsonldgen:cli"
gen-json-schema = "linkml.generators.jsonschemagen:cli"
gen-markdown = "linkml.generators.markdowngen:cli"
gen-doc = "linkml.generators.docgen:cli"
gen-namespaces = "linkml.generators.namespacegen:cli"
gen-owl = "linkml.generators.owlgen:cli"
gen-plantuml = "linkml.generators.plantumlgen:cli"
gen-proto = "linkml.generators.protogen:cli"
gen-py-classes = "linkml.generators.pythongen:cli"
gen-python = "linkml.generators.pythongen:cli"
gen-pydantic = "linkml.generators.pydanticgen:cli"
gen-rdf = "linkml.generators.rdfgen:cli"
gen-shex = "linkml.generators.shexgen:cli"
gen-shacl = "linkml.generators.shaclgen:cli"
gen-sparql = "linkml.generators.sparqlgen:cli"
gen-typescript = "linkml.generators.typescriptgen:cli"
gen-terminusdb = "linkml.generators.terminusdbgen:cli"
gen-yuml = "linkml.generators.yumlgen:cli"
gen-yaml = "linkml.generators.yamlgen:cli"
gen-erdiagram = "linkml.generators.erdiagramgen:cli"
gen-sqla = "linkml.generators.sqlalchemygen:cli"
gen-sqlddl = "linkml.generators.sqltablegen:cli"
gen-sqltables = "linkml.generators.sqltablegen:cli"
gen-summary = "linkml.generators.summarygen:cli"
gen-project = "linkml.generators.projectgen:cli"
run-tutorial = "linkml.utils.execute_tutorial:cli"
linkml-convert = "linkml.utils.converter:cli"
linkml-lint = "linkml.linter.cli:main"
linkml-sqldb = "linkml.utils.sqlutils:main"
linkml-validate = "linkml.validator.cli:cli"
linkml-jsonschema-validate = "linkml.validators.jsonschemavalidator:cli"
linkml-sparql-validate = "linkml.validators.sparqlvalidator:cli"
linkml-run-examples = "linkml.workspaces.example_runner:cli"
gen-excel = "linkml.generators.excelgen:cli"
gen-sssom = "linkml.generators.sssomgen:cli"
gen-linkml = "linkml.generators.linkmlgen:cli"
linkml-schema-fixer = "linkml.utils.schema_fixer:main"
[tool.poetry.dependencies]
python = "^3.8.1"
antlr4-python3-runtime = "<4.10,==4.*,>=4.9.0"
click = ">=7.0"
graphviz = ">=0.10.1"
hbreader = "*"
isodate = ">=0.6.0"
jinja2 = ">= 3.1.0"
jsonasobj2 = "==1.*,>=1.0.0,>=1.0.3"
jsonschema = {extras = ["format"], version = ">=4.0.0"}
linkml-dataops = "*"
linkml-runtime = "^1.8.1"
openpyxl = "*"
parse = "*"
prefixcommons = ">=0.1.7"
prefixmaps = ">=0.2.2"
pydantic = ">=1.0.0,<3.0.0"
pyjsg = ">=0.11.6"
pyshex = ">=0.7.20"
pyshexc = ">=0.8.3"
python-dateutil = "*"
pyyaml = "*"
rdflib = ">=6.0.0"
requests = ">=2.22"
sqlalchemy = ">=1.4.31"
watchdog = ">=0.9.0"
pyshacl = { version = "^0.25.0", optional = true }
black = { version=">=24.0.0", optional = true }
typing-extensions = { version=">=4.4.0", python="<3.9" }
[tool.poetry.group.dev.dependencies]
chardet = "*"
ipykernel = "*"
ipython-genutils = "*"
nbconvert = "*"
nbformat = "*"
coverage = "^6.4.1"
tox = "^4"
requests-cache = "^1.2.0"
myst-nb = {version=">=1.0.0", python=">=3.9"}
sphinx-design = "^0.5.0"
rich = "^13.7.1"
[tool.poetry.group.tests.dependencies]
pytest = "^7.4.0"
pytest-subtests = "^0.11.0"
numpy = [
{ "version" = ">=1.24.3", "python" = "<3.12" },
{ "version" = ">=1.25.2", "python" = ">=3.12" }
]
requests-cache = "^1.2.0"
mock = "^5.1.0"
[tool.poetry.extras]
black = ["black"]
shacl = ["pyshacl"]
tests = ["black", "pyshacl"]
[tool.poetry.group.docs]
optional = true
[tool.poetry.group.docs.dependencies]
furo = {version = "^2023.03.27", extras = ["docs"]}
sphinxcontrib-mermaid = {version = "^0.7.1", extras = ["docs"]}
sphinx = "*"
sphinx-click = "*"
sphinx-rtd-theme = "*"
myst-parser = "*"
matplotlib = ">=3.7"
sphinx-jinja = "^2.0.2"
sphinxcontrib-programoutput = "^0.17"
[build-system]
requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"]
build-backend = "poetry_dynamic_versioning.backend"
[tool.codespell]
# TODO: bring in tests in too
skip = '.git,*.pdf,*.svg,./tests,pyproject.toml,*.dill,poetry.lock'
# Ignore table where words could be split across rows
# Ignore shortcut specifications like [Ff]alse
ignore-regex = '(\|.*\|.*\|.*\||\[[A-Z][a-z]\][a-z][a-z])'
ignore-words-list = 'mater,connexion,infarction'
quiet-level = 3
[tool.black]
line-length = 120
target-version = ["py38", "py39", "py310", "py311"]
force-exclude = '''
/(
# default exclude
\.direnv|\.eggs|\.git|\.hg|\.ipynb_checkpoints|\.mypy_cache|\.nox|\.pytest_cache|\.ruff_cache|\.tox|\.svn|\.venv|\.vscode|__pypackages__|_build|buck-out|build|dist|venv
# additional exclude
| tests.*/output
| __snapshots__
| docs
| examples
| notebooks
)/
'''
[tool.pytest.ini_options]
filterwarnings = [
# https://github.com/RDFLib/rdflib/issues/1830
"ignore:.*_pytestfixturefunction is not defined in namespace:UserWarning"
]
markers = [
"network: mark tests that make external network requests",
"slow: mark test as slow to run",
"no_asserts: tests that don't have meaningful asserts, but are only snapshot comparisons, or historically had print statements, or other non-erroring behavior",
"strcmp: tests that compare stringified values rather than the values themselves",
"pydanticgen_split: Split module generation in pydanticgen",
"pythongen: Tests for python generator",
"pydanticgen: Tests for pydantic generator",
"javagen: Tests for java generator",
"jsonschemagen: Tests for Json Schema generator",
"shaclgen: Tests for shacl generator",
"shexgen: Tests for shex generator",
"jsonldcontextgen: Test for JSON-LD context generator",
"rdfgen: Tests for the RDFGenerator",
"sqlddlgen: Tests for SQL DDL generator",
"sqlddlpostgresgen: Tests for SQL DDL postgres generator",
"owlgen: Tests for OWL generator"
]
[tool.ruff]
extend-exclude = [
"tests/output",
"tests/**/output",
"tests/**/__snapshots__",
"examples/",
"docs/",
"notebooks/"
]
force-exclude = true
line-length = 120
extend-ignore = ["E203"]
select = [
"E", # pycodestyle errors
"F", # Pyflakes
"I", # isort
]
# Assume Python 3.8
target-version = "py38"
[tool.ruff.per-file-ignores]
# These templates can have long lines
"linkml/generators/sqlalchemy/sqlalchemy_declarative_template.py" = ["E501"]
"linkml/generators/sqlalchemy/sqlalchemy_imperative_template.py" = ["E501"]
# Notebooks can have unsorted imports
"tests/test_notebooks/input/*" = ["E402"]