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pyproject.toml
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[tool.poetry]
name = "linkml"
version = "0.0.0"
description = "Linked Open Data Modeling Language"
authors = [
"Chris Mungall <cjmungall@lbl.gov>",
"Sierra Moxon <smoxon@lbl.gov>",
"Harold Solbrig",
"Sujay Patil <spatil@lbl.gov>",
"Harshad Hegde",
"Mark Andrew Miller <MAM@lbl.gov>",
"Deepak Unni",
"Gaurav Vaidya <gaurav@renci.org>",
"Kevin Schaper <kevin@tislab.org>",
]
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-dbml = "linkml.generators.dbmlgen: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=">=4.6.0", python="<3.12" }
numpydantic = { version=">=1.6.1", python = ">=3.9", optional = true}
[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"
pytest-xdist = "^3.6.1"
numpy = [
{ "version" = ">=1.24.3", "python" = "<3.12" },
{ "version" = ">=1.25.2", "python" = ">=3.12" }
]
requests-cache = "^1.2.0"
mock = "^5.1.0"
testcontainers = "3.7.1"
[tool.poetry.extras]
black = ["black"]
numpydantic = ["numpydantic"]
shacl = ["pyshacl"]
tests = ["black", "numpydantic", "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,./notebooks/DistributedModels.ipynb'
# 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,thirdparty,linke'
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",
"docker: tests that require a running docker server",
"plantumlgen: Tests for the plantuml generator",
"pydanticgen_split: Split module generation in pydanticgen",
"pydanticgen_npd: tests for the numpydantic array generator",
"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"]