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pyproject.toml
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pyproject.toml
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[project]
name = "cumulus-etl"
requires-python = ">= 3.10"
# These dependencies are mostly pinned to be under the next major version.
# That makes particular sense as long as we don't have official releases yet and our docker
# images are built from main directly every commit.
#
# We mitigate the risk of missing a new release by having a bot watch for them.
#
# But if we ever start releasing on PyPI, we could switch to open-pinned dependencies to be
# less annoying to pip users.
dependencies = [
"ctakesclient >= 5.1, < 6",
"cumulus-fhir-support >= 1.2, < 2",
"delta-spark >= 3.2.1, < 4",
"httpx < 1",
"inscriptis < 3",
"jwcrypto < 2",
"label-studio-sdk < 2",
"nltk >= 3.9, < 4",
"openai < 2",
"oracledb < 3",
"philter-lite < 1",
"pyarrow < 19",
"rich < 14",
"s3fs",
]
authors = [
{ name="Andy McMurry, PhD", email="andrew.mcmurry@childrens.harvard.edu" },
{ name="Michael Terry", email="michael.terry@childrens.harvard.edu" },
]
readme = "README.md"
license = { text="Apache License 2.0" }
classifiers = [
"License :: OSI Approved :: Apache Software License",
"Operating System :: OS Independent",
"Programming Language :: Python :: 3",
"Topic :: Software Development :: Libraries :: Python Modules",
]
dynamic = ["description", "version"]
[project.optional-dependencies]
tests = [
"coverage",
"ddt",
"moto[server,s3] >= 5.0",
"pytest",
"pytest-cov",
"respx",
"time-machine",
]
dev = [
"pre-commit",
# Ruff is using minor versions for breaking changes until their 1.0 release.
# See https://docs.astral.sh/ruff/versioning/
"ruff < 0.9", # keep in rough sync with pre-commit-config.yaml
]
[project.urls]
"Homepage" = "https://github.com/smart-on-fhir/cumulus-etl"
[project.scripts]
cumulus-etl = "cumulus_etl.cli:main_cli"
[build-system]
requires = ["flit_core >=3.4,<4"]
build-backend = "flit_core.buildapi"
[tool.flit.sdist]
include = [
"docs/",
"tests/",
"LICENSE",
]
exclude = [
"**/.pytest_cache",
]
[tool.ruff]
line-length = 100
[tool.ruff.lint]
allowed-confusables = ["’"] # allow proper apostrophes
select = [
"A", # prevent using keywords that clobber python builtins
"E", # pycodestyle
"F", # pyflakes
"I", # isort
"PLE", # pylint errors
"RUF", # the ruff developer's own rules
"S", # bandit security warnings
"UP", # alert you when better syntax is available in your python version
]
ignore = [
# E501 is the line-too-long check.
# Ruff formatting will generally control the length of Python lines for us.
# But it leaves comments alone. And since we used to have a longer line length (120),
# we have a lot of legacy comments over 100 width.
# Just disable the check for now, rather than manually fixing all 300+ lines.
# Hopefully we can address them slowly over time.
"E501",
]
[tool.ruff.lint.per-file-ignores]
"**/__init__.py" = ["F401"] # init files hold API, so not using imports is intentional
"tests/**" = ["S"] # tests do suspicious stuff that's fine, actually