pyproject.toml

[tool.poetry]
name = "oaklib"
version = "0.0.0"
description = "Ontology Access Kit: Python library for common ontology operations over a variety of backends"
authors = ["cmungall <cjm@berkeleybop.org>"]

readme = "README.md"

[tool.poetry.dependencies]
python = ">=3.9,<4.0.0"
curies = ">=0.6.6"
pronto = ">=2.5.0"
SPARQLWrapper = "*"
SQLAlchemy = ">=1.4.32"
linkml-runtime = ">=1.5.3"
linkml-renderer = ">=0.3.0"
networkx = ">=2.7.1"
sssom = "^0.4.4"
ratelimit = ">=2.2.1"
appdirs = ">=1.4.4"
semsql = ">=0.3.1"
kgcl-schema = "^0.6.9"

funowl = ">=0.2.0"
gilda = {version = ">=1.0.0", optional = true}
semsimian = {version = ">=0.2.18", optional = true}
kgcl-rdflib = "0.5.0"
llm = "^0.14"
html2text = {version = "*", optional = true}
aiohttp = {version = "*", optional = true}
pystow = ">=0.5.0"
class-resolver = ">=0.4.2"
ontoportal-client = ">=0.0.3"
prefixmaps = ">=0.1.2"
ols-client = ">=0.1.1"
airium = ">=0.2.5"
ndex2 = ">=3.5.0"
pysolr = "^3.9.0"
eutils = ">=0.6.0"
requests-cache = "^1.0.1"
click = "*"
urllib3 = {version = "< 2", optional = true}
pydantic = "*"
jsonlines = "*"
tenacity = ">=8.2.3"
defusedxml = ">=0.7.1"


[tool.poetry.dev-dependencies]
pytest = "^7.1.3"
Sphinx = ">=6.1.3"
pandas = ">=1.5.1"
jupyter = ">=1.0.0"
sphinx-rtd-theme = "^1.0.0"
sphinx-click = ">=4.4.0"
myst-parser = ">=1.0.0"
linkml = ">=1.8.0"
sphinxcontrib-mermaid = "^0.8.1"
sphinx-copybutton = "0.5.1"
nbsphinx = "*"
coverage = "^6.3.2"
tox = "*"

[tool.poetry.group.dev.dependencies]
seaborn = "^0.12.2"
pip = "^24.0"

[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"

[tool.poetry.scripts]
runoak = "oaklib.cli:main"
vskit = "oaklib.utilities.subsets.value_set_expander:main"
boomerang = "oaklib.utilities.mapping.boomer_utils:main"

[tool.poetry.extras]
docs = ["Sphinx", "sphinx-rtd-theme", "sphinxcontrib-mermaid", "sphinx-copybutton"]
gilda = ["scipy", "gilda", "urllib3"]
llm = ["llm", "aiohttp", "html2text"]
seaborn = ["seaborn"]
semsimian = ["semsimian"]

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

[tool.isort]
profile = "black"
multi_line_output = 3
include_trailing_comma = true
reverse_relative = true

[tool.codespell]
skip = '.git,*.pdf,*.svg,poetry.lock,*.obo,*.ttl,*.ofn,*.gaf,*.tsv,*.json,input'
ignore-regex = '(^\s*"image/\S+": ".*|[a-z]*\.\.\.)'
ignore-words-list = 'ptd,ot,nd,ser,oger,gard,te,fo,fof,bu,ue,ois,processus,infarction,infarctions,assertIn,morpholgy,formate,HDA'

[tool.ruff]
lint.extend-ignore = [
    "D211",  # `no-blank-line-before-class`
    "D212",  # `multi-line-summary-first-line`
    "E731",  # Do not assign a `lambda` expression, use a `def`
    "B005",  # Using `.strip()` with multi-character strings is misleading the reader
    "S101",  # Use of `assert` detected
    "S607",  # Starting a process with a partial executable path
    "S608",  # Possible SQL injection vector through string-based query construction
    "S603",  # `subprocess` call: check for execution of untrusted input
    "B024",  # XXX is an abstract base class, but it has no abstract methods
    ]
lint.exclude = ["src/oaklib/datamodels/*"]
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