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Formatting Output For FluSight Submission From Arviz #10

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merged 43 commits into from
Oct 15, 2024

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AFg6K7h4fhy2
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@AFg6K7h4fhy2 AFg6K7h4fhy2 commented Oct 7, 2024

This PR, while made on a branch originally for handling data functions, covers the full reinstantiation of cfa-forecasttools vignette for formatting FluSight submission. The code covered in this PR does not include adding "samples" versus "quantiles", nor does this PR's contents cover scoring (which is cover in #9 ). There are still some fixes needed before this code is as robust as we would like.

#4, #7 , #8, and #1 can be closed when this PR is complete.

Questions

  • One idata per jurisdiction or support more complex posterior_predictive in idata (multiple jurisdictions)?

Tasks

This PR.

  • MVP README.
  • Docstrings w/ all functions.
  • Docstrings w/ all files.
  • PR comments being addressed.
  • Comment & variable name cleaning.
  • Epiweek package integration.
  • Remaining writing in vignette.
  • poetry dependency grouping.

Other PRs & Issues.

@AFg6K7h4fhy2 AFg6K7h4fhy2 self-assigned this Oct 7, 2024
@AFg6K7h4fhy2 AFg6K7h4fhy2 linked an issue Oct 7, 2024 that may be closed by this pull request
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@AFg6K7h4fhy2 AFg6K7h4fhy2 changed the title Re-Create "Formatting Output For FluSight Submission" Vignette Formatting Output For FluSight Submission From Arviz Oct 7, 2024
@AFg6K7h4fhy2 AFg6K7h4fhy2 added the enhancement Enhancement to existing feature or aspect of the project. label Oct 7, 2024
# default horizons
if horizons is None:
horizons = list(range(-1, 4))
reference_date_dt = datetime.strptime(reference_date, "%Y-%m-%d")
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Better to expect reference_date to be a datetime rather than string?

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@AFg6K7h4fhy2 AFg6K7h4fhy2 Oct 7, 2024

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This is what I originally had (because it seemed cleaner to not have to convert to datetime in the function) but opted against, since I have also the impression that most people would prefer passing the a string than a datetime object, hope the function handles converted use adequately. My mind is open to this though. There are date usage patterns that others are more familiar with than I am.

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This is fine, but please document the required date format,

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I still don't see the date format requirement documented.

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Thank you @damonbayer for these comments!

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Approving, but I have suggested a few places to clean up before merging. Thanks @AFg6K7h4fhy2!

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Approving, but I have suggested a few places to clean up before merging. Thanks @AFg6K7h4fhy2!

Thank you Damon. All comments should be addressed via code changes or issues.

@AFg6K7h4fhy2 AFg6K7h4fhy2 merged commit 6b13380 into main Oct 15, 2024
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@AFg6K7h4fhy2 AFg6K7h4fhy2 deleted the 7-data-loading-functions-and-storage branch October 15, 2024 19:55
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Data Loading Functions And Storage
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