pyAnVIL

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0.1.0 pyAnVIL-0.1.0-py3-none-any.whl

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Project: pyAnVIL
Version: 0.1.0
Filename: pyAnVIL-0.1.0-py3-none-any.whl
Download: [link]
Size: 229230
MD5: 50e56abe62ba70b000a2e7d3111c332f
SHA256: 1fcd8dd8bbc468697921567210e58dd94ace008cb7af75538a55d0c0b46cd16f
Uploaded: 2022-04-21 20:46:47 +0000

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METADATA

Metadata-Version: 2.1
Name: pyAnVIL
Version: 0.1.0
Summary: AnVIL client library. Data harmonization, gen3, terra single sign-on use cases.
Author: The AnVIL project
Author-Email: walsbr[at]ohsu.edu
Home-Page: https://github.com/anvilproject/client-apis/pyAnVIL
Project-Url: Bug Reports, https://github.com/anvilproject/client-apis/issues
Project-Url: Source, https://github.com/anvilproject/client-apis/
Keywords: AnVIL terra gen3 bioinformatics fhir
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Topic :: Software Development :: Build Tools
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.9
Requires-Python: >=3.9, <4
Requires-Dist: gen3 (==4.2.0)
Requires-Dist: firecloud (==0.16.31)
Requires-Dist: xmltodict (==0.12.0)
Requires-Dist: click (==8.1.2)
Requires-Dist: click-loglevel (==0.4.0.post1)
Requires-Dist: attrdict (==2.0.1)
Requires-Dist: google-cloud-storage (==2.0.0)
Requires-Dist: fastavro (==1.2.0)
Requires-Dist: tabulate (~=0.8.9)
Requires-Dist: requests (~=2.27.1)
Requires-Dist: pandas (~=1.4.2)
Requires-Dist: numpy (~=1.22.3)
Requires-Dist: PyYAML (~=5.4.1)
Requires-Dist: setuptools (~=60.2.0)
Requires-Dist: importlib-metadata (~=4.11.3)
Description-Content-Type: text/markdown
[Description omitted; length: 25017 characters]

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top_level.txt

anvil
tests

entry_points.txt

anvil_curl = anvil.clients.fhir_curl:cli
anvil_etl = anvil.etl.anvil_etl:cli