pyproject.toml

[tool.uv.workspace]
members = [
  "packages/linkml",
  "packages/linkml_runtime",
]
[tool.uv.sources]
linkml = { workspace = true }
linkml-runtime = { workspace = true }


[tool.codespell]
skip = [
  ".git", "*.pdf", "*.svg", "*.dill",
  "./tests",  # TODO: bring in tests in too
  "pyproject.toml",
  "uv.lock",
  "./notebooks/DistributedModels.ipynb",
  "./docs/LinkML-logo/LinkML-Revised-Round-Logo-MASTER-FILE.ai",
  "./tests/data/hp.ttl",
  "./tests/data/hp_f.ttl",
  "tests/test_generators/input/jsonschema_value_constraints.yaml",
]
# Ignore table where words could be split across rows
ignore-regex = '(\|.*\|.*\|.*\||\[[A-Z][a-z]\][a-z][a-z])'
ignore-words-list = [
  "acsess",
  "AGS",
  "amination",
  "anc",
  "brite",
  "ClassE",
  "CrossReference",
  "crossReference",
  "connexion",
  "EHR",
  "infarction",
  "linke",
  "mater",
  "mor",
  "ser",
  "Stye",
  "TE",
  "thirdparty",
  "Vas",
  # These are temp exemptions because they are coming from
  # upstream repos linkml-runtime and linkml-model
  # we should remove these once the upstream repos are fixed
  # and changes are propagated to linkml
  "GENERARE",
  "re-used",
  "doesnt",
  "crate"
]
quiet-level = 3

[tool.black]
line-length = 120
target-version = ["py310", "py311", "py312", "py313"]
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
  | linkml/linter/config/datamodel
)/
'''

[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",
  "biolink: tests that validate that the biolink model is unchanged",
  "docker: tests that require a running docker server",
  "kroki: tests that use Kroki diagram creation (skipped in CI)",
  "plantumlgen: Tests for the plantuml generator",
  "pydanticgen_split: Split module generation in pydanticgen",
  "pydanticgen_npd: tests for the numpydantic array generator",
  "panderagen: tests for the pandera generator",
  "dataframe_polars_schema: tests for the polars schema dataframe 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",
  "jsonldgen: Test for JSON-LD generator",
  "jsonldcontextgen: Test for JSON-LD context generator",
  "rdfgen: Tests for the RDFGenerator",
  "rustgen: Tests for the RustGenerator",
  "sqlalchemygen: Tests for SQL Alchemy generator",
  "sqlddlgen: Tests for SQL DDL generator",
  "sqlddlpostgresgen: Tests for SQL DDL postgres generator",
  "owlgen: Tests for OWL generator",
  "yamlgen: Tests for the YAML generator",
  "yarrrml: End-to-end tests for the YARRRML generator"
]

# https://docs.astral.sh/ruff/settings/
[tool.ruff]
extend-exclude = [
    "tests/output",
    "tests/**/output",
    "tests/**/__snapshots__",
    "examples/",
    "docs/",
    "notebooks/",
    # Auto-generated files that may not conform to current linting rules
    "linkml/linter/config/datamodel/config.py"
]
force-exclude = true
line-length = 120
target-version = "py310"

[tool.ruff.lint]
extend-ignore = ["E203"]
select = [
  "E",  # pycodestyle errors
  "F",  # Pyflakes
  "I",  # isort
  "UP", # pyupgrade
]

[tool.ruff.lint.isort]
known-first-party = ["linkml", "linkml_runtime"]

[tool.ruff.lint.per-file-ignores]
# These templates can have long lines
"packages/linkml/src/linkml/generators/sqlalchemy/sqlalchemy_declarative_template.py" = ["E501"]
"packages/linkml/src/linkml/generators/sqlalchemy/sqlalchemy_imperative_template.py" = ["E501"]
"packages/linkml/src/linkml/linter/config/datamodel/config.py" = ["E501", "F401", "I001", "UP007", "UP035", "UP045"]

# Auto-generated model files use Optional/Union with string forward references
"packages/linkml_runtime/src/linkml_runtime/linkml_model/*.py" = ["UP007", "UP045"]
"packages/linkml_runtime/src/linkml_runtime/processing/validation_datamodel.py" = ["UP007", "UP045"]
"packages/linkml/src/linkml/workspaces/datamodel/workspaces.py" = ["UP007", "UP045"]
"packages/linkml/src/linkml/reporting/model.py" = ["UP007", "UP045"]

# Notebooks can have unsorted imports
"tests/linkml/test_notebooks/input/*" = ["E402"]

# tests/linkml_runtime follows the original linkml_runtime linting conventions
"tests/linkml_runtime/**/*.py" = ["E402", "E501", "E712", "E731", "E741", "F401", "F811", "F841", "I001", "UP006", "UP007", "UP035", "UP045"]

[tool.tox]
requires = ["tox>=4", "tox-uv"]
env_list = ["lint", "py{310,311,312,313}"]

[tool.tox.env_run_base]
runner = "uv-venv-lock-runner"
deps = ["pytest"]
commands = [
  ["pytest", "{posargs}"],
]

[tool.tox.env.codespell]
description = "Run spell checkers."
runner = "uv-venv-runner"
skip_install = true
deps = [
  "codespell",
  "tomli", # required for getting config from pyproject.toml
]
commands = [
  ["codespell", "{posargs}"]
]

[tool.tox.env.format]
description = "Run code formatter and code-fixing linter."
runner = "uv-venv-runner"
skip_install = true
deps = ["pre-commit"]
commands = [
  ["pre-commit", "run", "--all-files", "--show-diff-on-failure", { replace = "posargs", extend = true }]
]

[tool.tox.env.lint]
description = "Run code linter and formatter (no fixes)."
runner = "uv-venv-runner"
skip_install = true
deps = ["ruff==0.11.13"]
commands = [
  ["ruff", "check", "{posargs:.}"],
  ["ruff", "format", "{posargs:.}"],
]