pyproject.toml

[build-system]
requires = ["setuptools"]
build-backend = "setuptools.build_meta"

[tool.setuptools.packages.find]
include = ["netmedex*", "webapp*"]

[tool.setuptools.package-data]
webapp = [
  "assets/*.js",
  "assets/*.svg",
  "assets/*.css",
  "assets/*.ico",
  "assets/*.png",
]

[project]
name = "netmedex"
version = "0.1.0"
authors = [{ name = "Zheng-Xiang Ye", email = "r12b48005@ntu.edu.tw" }]
description = "A tool to extract BioConcept entities (e.g., genes, diseases, chemicals, and species) from Pubtator3 and generate a co-mention network for interactive use."
readme = "README.md"
requires-python = ">=3.11"
dependencies = [
  "requests",
  "tqdm",
  "networkx[default]~=3.3",
  "lxml",
  "python-dotenv",
  "dash[diskcache]~=2.17",
  "dash-cytoscape",
  "dash-bootstrap_components",
]
classifiers = [
  "Development Status :: 5 - Production/Stable",
  "Programming Language :: Python :: 3",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "License :: OSI Approved :: MIT License",
  "Operating System :: OS Independent",
]

[project.optional-dependencies]
dev = [
  "pytest~=8.3.2",
  "pytest-xdist",
  "pytest-cov",
  "requests-mock",
  "pytest-mock",
  "ruff==0.8.0",
  "pre-commit",
]

[project.scripts]
netmedex = "netmedex.cli:main"

[tool.ruff]
line-length = 99
target-version = "py311"
# exclude = [""]

[tool.ruff.lint]
select = [
  "E",  # pycodestyle errors
  "W",  # pycodestyle warnings
  "F",  # pyflakes
  "I",  # isort
  "B",  # flake8-bugbear
  "C4", # flake8-comprehensions
  "UP", # pyupgrade
  # "ARG001", # unused arguments in functions
]
ignore = [
  "E402", # module level import not at top of file
  "E501", # line too long, handled by black
  "B008", # do not perform function calls in argument defaults
  "W191", # indentation contains tabs
  "B904", # Allow raising exceptions without from e, for HTTPException
]

[tool.ruff.format]
quote-style = "double"