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Upgrade the testmode pipeline script to just pipeline script -- Do not merge #445

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SamuelBrand1
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This Draft PR has the improvements I'm making to the pipeline towards resolving #404. There were quite a number of improvements before I noticed that the forecast function was now broken:

  • pipeline testmode boolean field which is useful for the test running.
  • prefixes also determined by the pipeline.
  • "testmode" pipeline script upgraded to main script.
  • Better end-to-end tests.

This is tested using the updated EpiAware hash 9c52763.

Currently forecast function in pipeline is still broken, but this is a good place to fix from.

@SamuelBrand1 SamuelBrand1 linked an issue Aug 30, 2024 that may be closed by this pull request
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Try this Pull Request!

Open Julia and type:

import Pkg
Pkg.activate(temp=true)
Pkg.add(url="https://github.com/CDCgov/Rt-without-renewal", rev="404-upgrade-the-testmode-pipeline-script-to-just-pipeline-script", subdir="EpiAware")
using EpiAware

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codecov-commenter commented Aug 30, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 89.91%. Comparing base (e660145) to head (5562326).

Additional details and impacted files
@@           Coverage Diff           @@
##             main     #445   +/-   ##
=======================================
  Coverage   89.91%   89.91%           
=======================================
  Files          57       57           
  Lines         734      734           
=======================================
  Hits          660      660           
  Misses         74       74           

☔ View full report in Codecov by Sentry.
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Upgrade the "testmode" pipeline script to just pipeline script
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