NSAPH Utils python package

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There are open questions about how best to structure this package that we can address (i.e. do we do multiple modules within this module, 1 single module, etc).

Overview of Utilities

The nsaph_utils package is intended to hold python code that will be useful across multiple portions of the NSAPH pipelines.

The included utilities are developed to be as independent of specific infrastructure and execution environment as possible.

Included utilities:

• Interpolation code

• Reading FST files from Python The pyfst Module

• Reading FWF files The fwf Module

• various I/O wrappers The io_utils Module

• An API and CLI framework The context Module

• QC Framework

• Documentation utilities to simplify creation of consistent documentation for NSAPH platform

Current Development

Updated 2/26/2021, Ben Sabath

• Interpolatation code: We have re-implemented the logic used for the initial moving average interpolation used in the R based pipelines. Developing better metholdologies remains to be done. Based on spot checks the results match those from the previous version.

TODO

Updated 2/26/2021, Ben Sabath

• Generic Data object that other NSAPH modules can inherit from.

• Creation of list of other useful general features

• Review of already done development to see what would make sense to port to this package

Documentation Indices

• Index

• Module Index