pyproject.toml

[tool.poetry]
name = "kg-microbe-merge"
version = "0.0.0"
description = "kg-microbe-merge"
authors = ["Harshad Hegde <hhegde@lbl.gov>"]
license = "MIT"
readme = "README.md"

[tool.poetry.dependencies]
python = "^3.9"
click = ">=8.1.7"
importlib-metadata = ">=8.2.0"
kghub-downloader = "^0.3.9"
kgx = ">=2.4.2"
koza = ">=0.6.0"
biolink-model = ">=4.2.1"
linkml = "^1.8.1"
sphinx = {version = "^7.4.7", extras = ["docs"], optional = true }
sphinx-rtd-theme = {version = "^2.0.0", extras = ["docs"], optional = true }
sphinx-autodoc-typehints = {version = "^2.2.3", extras = ["docs"], optional = true }
sphinx-click = {version = "^6.0.0", extras = ["docs"], optional = true }
myst-parser = {version = "^3.0.1", extras = ["docs"], optional = true }
kg-chat = {version = ">=0.1.2", extras = ["chat"], optional = true }

[tool.poetry.group.dev.dependencies]
pytest = ">=8.3.1"
tox = ">=4.16.0"
pre-commit = ">=3.7.1"
parameterized = ">=0.9.0"

[tool.poetry.extras]
docs = ["sphinx", "sphinx-rtd-theme", "sphinx-autodoc-typehints", "sphinx-click", "myst-parser"]
chat = ["kg-chat"]

[tool.poetry.scripts]
kg = 'kg_microbe_merge.run:main'

[tool.poetry-dynamic-versioning]
enable = true
vcs = "git"
style = "pep440"

[tool.black]
line-length = 100
target-version = ["py38", "py39", "py310"]

[tool.ruff]
lint.extend-ignore = [
    "D211",  # `no-blank-line-before-class`
    "D212",  # `multi-line-summary-first-line`
    "S608" , # Possible SQL injection vector through string-based query construction"
    "S202",  # Uses of `tarfile.extractall()`
    ]
line-length = 120

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

# Select or ignore from https://beta.ruff.rs/docs/rules/
lint.select = [
    "B",  # bugbear
    "D",  # pydocstyle
    "E",  # pycodestyle errors
    "F",  # Pyflakes
    "I",  # isort 
    "S",  # flake8-bandit
    "W",  # Warning
]

lint.unfixable = []
target-version = "py310"

[tool.ruff.lint.mccabe]
# Unlike Flake8, default to a complexity level of 10.
max-complexity = 10

[tool.codespell]
skip = "*.po,*.ts,.git,pyproject.toml"
count = ""
quiet-level = 3
# ignore-words-list = ""

[build-system]
requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"]
build-backend = "poetry_dynamic_versioning.backend"