cumulus-library

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2.0.1 cumulus_library-2.0.1-py3-none-any.whl

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Project: cumulus-library
Version: 2.0.1
Filename: cumulus_library-2.0.1-py3-none-any.whl
Download: [link]
Size: 4641337
MD5: 2a3be99088cd060576f5368c9eaeea1c
SHA256: 0fcb101404c63fd38d501b92918bc916ccebeea57dc4e4b22662696c94a355b2
Uploaded: 2024-04-16 16:14:24 +0000

dist-info

METADATA

Metadata-Version: 2.1
Name: cumulus-library
Version: 2.0.1
Summary: Clinical study SQL generation for data derived from bulk FHIR
Project-Url: Documentation, https://docs.smarthealthit.org/cumulus/
Project-Url: Home, https://smarthealthit.org/cumulus-a-universal-sidecar-for-a-smart-learning-healthcare-system/
Project-Url: Source, https://github.com/smart-on-fhir/cumulus-library
Keywords: FHIR,SQL,Health Informatics
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Python: >= 3.10
Requires-Dist: ctakesclient (>=1.3)
Requires-Dist: cumulus-fhir-support (>=1)
Requires-Dist: duckdb (>=0.9)
Requires-Dist: fhirclient (>=4.1)
Requires-Dist: Jinja2 (>3)
Requires-Dist: pandas (<3,>=2.1.3)
Requires-Dist: psmpy (<1,>=0.3.13)
Requires-Dist: pyarrow (>=11.0)
Requires-Dist: pyathena (>=2.23)
Requires-Dist: pytablewriter (>=1.2)
Requires-Dist: requests (>=2.28)
Requires-Dist: rich (>=13.2)
Requires-Dist: sqlfluff (>=3)
Requires-Dist: sqlparse (>0.4)
Requires-Dist: toml (>=0.10)
Requires-Dist: ruff (==0.2.1); extra == "dev"
Requires-Dist: pre-commit; extra == "dev"
Requires-Dist: freezegun; extra == "test"
Requires-Dist: pytest; extra == "test"
Requires-Dist: requests-mock; extra == "test"
Provides-Extra: dev
Provides-Extra: test
Description-Content-Type: text/markdown
[Description omitted; length: 690 characters]

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Tag: py3-none-any

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entry_points.txt

cumulus-library = cumulus_library.cli:main_cli