BiasAnalyzerCore/pyproject.toml at main · VACLab/BiasAnalyzerCore · GitHub

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[tool.poetry]
name = "biasanalyzer"
version = "0.1.0"
description = "A python package for health data bias quantification to support visual analytics techniques for tracking and communicating bias in cohort selection"
authors = ["Hong Yi <[email protected]>"]
readme = "README.md"
license="MIT"
keywords=["bias", "healthcare", "cohort", "OMOP", "analytics", "observational research"]
include = [
    {path = "biasanalyzer/sql_templates/*.sql", format=["sdist", "wheel"]}
]
[tool.poetry.dependencies]
python = ">=3.9,<3.13"
duckdb = "^1.1.1"
pandas = "^2.1.4"

scipy = [
    {version = ">=1.10.1,<1.11", markers = "python_version<'3.12'"},
    {version = ">=1.14.1,<1.15", markers = "python_version>='3.12'"}
]
numpy = [
    {version = ">=1.24.4,<1.25", markers = "python_version<'3.12'"},
    {version = ">=1.25.0,<=1.26.4", markers = "python_version>='3.12'"}
]
duckdb-engine = "^0.13.2"
sqlalchemy = "^2.0.35"
pyyaml = "^6.0.2"
pydantic = "^2.9.2"
psycopg2 = "^2.9.9"
ipytree = "^0.2.2"
ipywidgets = "^8.1.5"
jinja2 = "3.1.6"
tqdm = "4.67.1"
networkx = "3.1"

[tool.poetry.group.dev.dependencies]
pytest = "^8.3.3"
pytest-cov = "5.0.0"
ruff = "^0.14.3"

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

# ----------------------------
# Ruff configuration
# ----------------------------
[tool.ruff]
# Linting targets your source and test code
target-version = "py38"
src = ["biasanalyzer", "tests", "scripts"]
line-length = 120

# Enable full linting set roughly equivalent to Flake8 + isort + pyupgrade
lint.select = [
    "E",  # pycodestyle errors
    "F",  # pyflakes
    "I",  # isort-style import sorting
    "B",  # flake8-bugbear
    "UP", # pyupgrade
    "N",  # pep8-naming
    "S",  # security (flake8-bandit subset)
]
lint.ignore = ["S101", "N805", "S701"]

# Automatically fix simple issues on save (optional)
fix = true

# Exclude build/test caches and notebooks
exclude = [
    ".venv",
    ".git",
    "__pycache__",
    "build",
    "dist",
    "notebooks",
]

[tool.ruff.format]
# Ruff's built-in formatter replaces Black
indent-style = "space"
docstring-code-format = true
docstring-code-line-length = "dynamic"