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pyproject.toml
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pyproject.toml
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[tool.poetry]
name = "cycquery"
version = "0.1.7"
description = "A tool to query EHR databases"
authors = ["Vector AI Engineering <[email protected]>"]
license = "Apache-2.0"
repository = "https://github.com/VectorInstitute/cycquery"
documentation = "https://vectorinstitute.github.io/cycquery/"
packages = [
{ include = "cycquery" },
]
readme = "README.md"
[tool.poetry.dependencies]
python = ">=3.9, <3.12"
pandas = ">2.0.0, <2.2.0"
pyarrow = "^14.0.0"
psycopg2 = "^2.9.6"
SQLAlchemy = "^1.4.32, <2.0"
[tool.poetry.group.test]
optional = true
[tool.poetry.group.test.dependencies]
pytest = "^7.1.1"
pre-commit = "^2.17.0"
pytest-cov = "^3.0.0"
codecov = "^2.1.13"
nbstripout = "^0.6.1"
mypy = "^1.0.0"
ruff = "^0.3.0"
nbqa = { version = "^1.7.0", extras = ["toolchain"] }
pip-audit = "^2.7.1"
[tool.poetry.group.docs]
optional = true
[tool.poetry.group.docs.dependencies]
numpydoc = "^1.2"
sphinx = "^7.2.5"
sphinxcontrib-apidoc = "^0.4.0"
sphinx-autodoc-typehints = "^1.24.0"
myst-parser = "^2.0.0"
sphinx-design = "^0.5.0"
sphinx-copybutton = "^0.5.0"
sphinx-autoapi = "^2.0.0"
nbsphinx = "^0.8.11"
ipython = "^8.8.0"
ipykernel = "^6.23.0"
furo = "^2024.01.29"
[tool.mypy]
ignore_missing_imports = true
install_types = true
pretty = true
namespace_packages = true
explicit_package_bases = true
non_interactive = true
warn_unused_configs = true
allow_any_generics = false
allow_subclassing_any = false
allow_untyped_calls = false
allow_untyped_defs = false
allow_incomplete_defs = false
check_untyped_defs = true
allow_untyped_decorators = false
warn_redundant_casts = true
warn_unused_ignores = true
warn_return_any = true
implicit_reexport = false
strict_equality = true
extra_checks = true
plugins = ["sqlalchemy.ext.mypy.plugin"]
[tool.ruff]
include = ["*.py", "pyproject.toml", "*.ipynb"]
select = [
"A", # flake8-builtins
"B", # flake8-bugbear
"COM", # flake8-commas
"C4", # flake8-comprehensions
"RET", # flake8-return
"SIM", # flake8-simplify
"ICN", # flake8-import-conventions
"Q", # flake8-quotes
"RSE", # flake8-raise
"D", # pydocstyle
"E", # pycodestyle
"F", # pyflakes
"I", # isort
"W", # pycodestyle
"N", # pep8-naming
"ERA", # eradicate
"PL", # pylint
]
fixable = ["A", "B", "COM", "C4", "RET", "SIM", "ICN", "Q", "RSE", "D", "E", "F", "I", "W", "N", "ERA", "PL"]
line-length = 88
ignore = [
"B905", # `zip()` without an explicit `strict=` parameter
"E501", # line too long
"D203", # 1 blank line required before class docstring
"D213", # Multi-line docstring summary should start at the second line
"PLR2004", # Replace magic number with named constant
"PLR0913", # Too many arguments
]
# Ignore import violations in all `__init__.py` files.
[tool.ruff.per-file-ignores]
"__init__.py" = ["E402", "F401", "F403", "F811"]
[tool.ruff.pep8-naming]
ignore-names = ["X*", "setUp"]
[tool.ruff.isort]
lines-after-imports = 2
[tool.ruff.pydocstyle]
convention = "numpy"
[tool.ruff.pycodestyle]
max-doc-length = 88
[tool.pytest.ini_options]
markers = [
"integration_test: marks tests as integration tests",
]
[tool.coverage]
[tool.coverage.run]
source=["cycquery"]
omit=["tests/*", "*__init__.py"]
[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"