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Update key_colnames, revision_summary #540

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@brookslogan brookslogan commented Oct 10, 2024

Checklist

Please:

  • Make sure this PR is against "dev", not "main" (unless this is a release
    PR).
  • Request a review from one of the current main reviewers:
    brookslogan, nmdefries.
  • Makes sure to bump the version number in DESCRIPTION. Always increment
    the patch version number (the third number), unless you are making a
    release PR from dev to main, in which case increment the minor version
    number (the second number).
  • Describe changes made in NEWS.md, making sure breaking changes
    (backwards-incompatible changes to the documented interface) are noted.
    Collect the changes under the next release number (e.g. if you are on
    1.7.2, then write your changes under the 1.8 heading).
  • See DEVELOPMENT.md for more information on the development
    process.

Change explanations for reviewer

  • Make key_colnames.epi_archive output its unique key colnames (including version).
  • Make key_colnames.data.frame require other_keys to be passed.
  • Remove key_colnames.default.
  • Require exclude = to be passed by name in key_colnames.
  • Require dots to be empty in key_colnames.
    • Note: this triggers some errors in epipredict tests. See below.
  • Update revision_summary to use new key_colnames.epi_archive.
  • Fix&tweak some tidyeval stuff in revision_summary.
  • Tweak some naming in revision_summary.

epipredict errors

Originally, I misread and thought these were from passing other_keys = hopefully-redundantly into key_colnames.epi_df and having them be ignored. I was planning to do something like

  expected_other_keys <- attr(x, "metadata")$other_keys
  if (is.null(other_keys)) {
    other_keys <- expected_other_keys
  } else {
    if (!identical(other_keys, expected_other_keys)) {
      cli_abort(c(
        "`other_keys` was provided, but didn't match expectations from inspecting `x`",
        "*" = "`other_keys` was {format_chr_with_quotes(other_keys)}",
        "*" = "`expected_other_keys` was {format_chr_with_quotes(expected_other_keys)}",
        "i" = "If you resolve this discrepancy by adjusting the metadata of `x`, you
               shouldn't have to pass `other_keys =` here anymore unless you want to
               continue to perform this check."
      ))
    }
  }

However, the error is actually from passing extra_keys = (which was also previously ignored, but it sounds like it has a different meaning). I am looking a bit more into this.

  • todo: decide what to do re. extra_keys =
    • idea for now: forbid + PR to epipredict to specify other_keys = instead. If current behavior of other_keys = with epi_dfs breaks later, then decide whether to change things here or adjust any offending steps/layers.
  • todo: check whether epipredict#410 is caught... requiring other_keys = in key_colnames.data.frame should be flagging this, right?
    • It is. Also need to include fix in epipredict PR before merging this.
  • todo: prepare epipredict PR and get it merged

Other work

  • todo: tests for additional revision_summary() adjustments
  • todo: break into 2 dependent PRs

Magic GitHub syntax to mark associated Issue(s) as resolved when this is merged into the default branch

* Make `key_colnames.epi_archive` output epikey-time-version rather than just
  epikey-time.
* Make `key_colnames.data.frame` require `other_keys` be provided.
* Remove `key_colnames.default`.
* Make `key_colnames` forbid passing `exclude` positionally.
* Update downstream `revision_summary`.
* Produce error rather than default selection when user provides a tidyselection
  in ... but it selects zero columns.
* Change time_within_x_latest to take `values` as a vector
* Use `.data` instead of `pick` etc. in some places
So it is not misinterpreted as "the amount of time that it has been near the latest".
@brookslogan brookslogan force-pushed the lcb/update-key_colnames.epi_archive branch from 97fdc29 to 052854f Compare October 10, 2024 19:27
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