pyproject.toml

[build-system]
requires = ["hatchling", "uv-dynamic-versioning"]
build-backend = "hatchling.build"

[project]
name = "linkml-runtime"
description = "Runtime environment for LinkML, the Linked open data modeling language"
authors = [
  {name = "Chris Mungall", email = "cjmungall@lbl.gov"},
  {name = "Harold Solbrig", email = "solbrig@jhu.edu"},
  {name = "Sierra Moxon", email = "smoxon@lbl.gov"},
  {name = "Bill Duncan", email = "wdduncan@gmail.com"},
  {name = "Harshad Hegde", email = "hhegde@lbl.gov"},
]
license = "CC0-1.0"
license-files = ["LICENSE"]
homepage = "https://github.com/linkml/linkml-runtime"
repository = "https://github.com/linkml/linkml-runtime"
documentation = "https://github.com/linkml/linkml-runtime"
readme = "README.md"
keywords = ["linkml", "metamodel", "schema visualization", "rdf", "owl", "yaml"]
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Environment :: Console",
    "Intended Audience :: Developers",
    "Intended Audience :: Science/Research",
    "Intended Audience :: Healthcare Industry",
    "Topic :: Software Development :: Libraries :: Python Modules",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
]
include = ["linkml_runtime"]
requires-python = ">=3.9"
dynamic = ["version"]
dependencies = [
    "click",
    "deprecated",
    "hbreader",
    "json-flattener >=0.1.9",
    "jsonasobj2 ==1.*,>=1.0.0,>=1.0.4",
    "jsonschema >=3.2.0",
    "prefixcommons >=0.1.12",
    "pyyaml",
    "rdflib >=6.0.0",
    "requests",
    "prefixmaps >=0.1.4",
    "curies >=0.5.4",
    "pydantic >=2.0.0, <3.0.0",
    "isodate >=0.7.2, <1.0.0; python_version < '3.11'",
]

[dependency-groups]
dev = [
    "coverage >=6.2",
    "requests-cache >=1.2.0",
    "tox>=4",
    "ruff==0.11.13",
]

[project.scripts]
comparefiles = "linkml_runtime.utils.comparefiles:cli"
linkml-normalize = "linkml_runtime.processing.referencevalidator:cli"

[project.optional-dependencies]
dev = [
    "coverage",
    "requests-cache",
]

[tool.codespell]
skip = [
  ".git", "*.pdf", "*.svg", "*.dill",
  "uv.lock",
]
# Ignore table where words could be split across rows
ignore-regex = '(\|.*\|.*\|.*\||\[[A-Z][a-z]\][a-z][a-z])'
ignore-words-list = [
  "CrossReference",
  "ND",
  "MILIARY",
  "Miliary",
  # The two below are from metamodel upstream, should be
  # dropped when upstream is fixed
  "GENERARE",
  "re-used",
  "ot",
  "VRSATILE",
  "vrsatile"
]
quiet-level = 3
# https://docs.astral.sh/ruff/settings/
[tool.ruff]
extend-exclude = []
force-exclude = true
line-length = 120
# Assume Python 3.9
target-version = "py39"

[tool.ruff.lint]

select = [
    "E",  # pycodestyle errors
    "F",  # Pyflakes
    "I", # isort
    "W", # pycodestyle warnings
    "C90", # mccabe +
    "N", # pep8-naming
    # "D", # pydocstyle
    "UP", # pyupgrade
    # extensions
    # "YTT", # flake8-2020
    # "ANN", # flake8-annotations
    # "ASYNC", # flake8-async
    # "S", # flake8-bandit
    # "BLE", # flake8-blind-except
    # "FBT", # flake8-boolean-trap
    # "B", # flake8-bugbear
    # "A", # flake8-builtins
    # "COM", # flake8-commas
    # "CPY", # flake8-copyright
    # "C4", # flake8-comprehensions
    # "DTZ", # flake8-datetimez
    # "T10", # flake8-debugger
    # "DJ", # flake8-django
    # "EM", # flake8-errmsg
    # "EXE", # flake8-executable
    # "FA", # flake8-future-annotations
    # "ISC", # flake8-implicit-str-concat
    # "ICN", # flake8-import-conventions
    # "G", # flake8-logging-format
    # "INP", # flake8-no-pep420
    # "PIE", # flake8-pie
    # "T20", # flake8-print
    # "PYI", # flake8-pyi
    # "PT", # flake8-pytest-style
    # "Q", # flake8-quotes
    # "RSE", # flake8-raise
    # "RET", # flake8-return
    # "SLF", # flake8-self
    # "SLOT", # flake8-slots
    # "SIM", # flake8-simplify
    # "TID", # flake8-tidy-imports
    # "TCH", # flake8-type-checking
    # "INT", # flake8-gettext
    # "ARG", # flake8-unused-arguments
    # "PTH", # flake8-use-pathlib
    # "TD", # flake8-todos
    # "FIX", # flake8-fixme
    # "ERA", # eradicate
    # "PD", # pandas-vet
    # "PGH", # pygrep-hooks
    # "PL", # Pylint
    # "TRY", # tryceratops
    # "FLY", # flynt
    # "NPY", # NumPy-specific rules
    # "AIR", # Airflow
    # "PERF", # Perflint
    # "FURB", # refurb
    # "LOG", # flake8-logging
    # "RUF", # Ruff-specific rules
]

# Allow autofix for all enabled rules (when `--fix`) is provided.
fixable = ["ALL"]
unfixable = []

# D203: one-blank-line-before-class (conflicts with D211)
# D212: multi-line-summary-first-line (conflicts with D213)
# E203: whitespace before ',', ';', or ':'
# E501: line length
# ISC001: conflicts with Ruff's formatter
ignore = [
    "D203",
    "D213",
    "E203",
    "E501",
    "ISC001",
]

[tool.ruff.lint.per-file-ignores]
"tests/**/*.py" = ["S101"] # use of assert

[tool.ruff.lint.mccabe]
# Flag errors (`C901`) whenever the complexity level exceeds 15.
max-complexity = 15

[tool.tox]
requires = ["tox>=4"]
env_list = ["lint", "py{39,310,311,312,313}"]

[tool.tox.env_run_base]
allowlist_externals = ["uv"]
deps = ["pytest"]
commands = [
  ["uv", "sync", "--all-extras", "--dev"],
  ["uv", "run", "pytest", "{posargs}"],
]

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

[tool.tox.env.format]
description = "Run ruff code formatter."
skip_install = true
deps = ["ruff==0.11.13"]
commands = [
  ["ruff", "format", "{posargs:.}"],
]

[tool.tox.env.format_check]
description = "Check that code is correctly formatted by ruff."
skip_install = true
deps = ["ruff==0.11.13"]
commands = [
  ["ruff", "format", "--check", "{posargs:.}"],
]

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

[tool.uv-dynamic-versioning]
vcs = "git"
style = "pep440"
fallback-version = "0.0.0"

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