Fix/do conversions run input typo

[shreyannandanwar]

Fix a consistent copy-paste typo: settings$run$input (singular) → settings$run$inputs (plural) across 4 files.

Evidence

1. Usage count in codebase

• run$input (singular): fewer occurrences, never assigned anywhere
• run$inputs (plural): way more if compared within do_conversions.R alone
• Zero assignments to run$input found across base/, modules/, scripts/

2. Settings schema confirms inputs (plural) is canonical

• base/settings/R/update.settings.R references <inputs> always plural, never singular
• base/settings/ contains zero occurrences of a literal <input> tag as a child of <run>
• This means run$input (singular) has no corresponding schema definition — it would silently return NULL at runtime

3. check.all.settings.R confirms the canonical field name

• base/settings/R/check.all.settings.R validates the settings object and only references run$inputs (plural) throughout
• No validation path, no coercion, and no fallback exists for a singular run$input field
• If run$input were intentional, it would appear in settings validation — it does not

4. Official PEcAn XML documentation uses <inputs> exclusively

• book_source/03_topical_pages/03_pecan_xml.Rmd documents the <run> block and its children
• The <inputs> tag (plural) is the only form shown in all examples and explanations in that section
• Zero mentions of a singular <input> child under <run> anywhere in the XML guide

5. No documentation anywhere defines run$input as intentional

• Searched .Rd, .Rmd, .qmd, .xml across the entire repo
• 0 matches for run$input as a documented or intentional field name

Conclusion

The schema, the validator, the XML documentation, and the overwhelming majority of code all agree: the canonical field is run$inputs. The singular run$input usages are inconsistent legacy copy-paste typos that would silently return NULL at runtime, causing inputs to be
misrouted or skipped without any error or warning.

Files changed

• base/workflow/R/do_conversions.R
• scripts/workflow.bm.R
• scripts/workflow.pda.R
• modules/data.land/R/soil_process.R

Risk

Low — mechanical typo fix, no logic changed.
The field run$input was never assigned anywhere in the codebase, so correcting these references to run$inputs restores intended behavior.

Review Time Estimate

• Immediately
• Within one week
• When possible

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

• My change requires a change to the documentation.
• My name is in the list of CITATION.cff
• I agree that PEcAn Project may distribute my contribution under any or all of
  • the same license as the existing code,
  • and/or the BSD 3-clause license.
• I have updated the CHANGELOG.md.
• I have updated the documentation accordingly.
• I have read the CONTRIBUTING document.
• I have added tests to cover my changes.
• All new and existing tests passed.

[S1DDHEY]

@shreyannandanwar The changes in run.meta.analysis.R appear to include unrelated work that doesn’t match the PR description.

I'd suggest cleaning up the branch (e.g., drop unrelated commits or cherry-pick only the relevant ones) and update the PR accordingly.

[Yeligay8]

In the check (check_modules, 4.4) / check section:
I recommend to open the R file where the function is defined:

meta_analysis_standalone <- function(...) {

Above the function, you should have something like:

#' @param prior_n ...
#' @param prior_cv ...
#' @param tauA ...
#' @param tauB ...
#' @param gamma_tau ...

Update documentation to match function. If these arguments exist in function, ADD missing params:
#' @param prior_n Description here
#' @param prior_cv Description here
#' @param tauA Description here
#' @param tauB Description here

If gamma_tau doesn't exist in function, REMOVE it:

DELETE this line:

#' @param gamma_tau ...

then run this:
devtools::document()

then re-run checks locally
devtools::check()

OR same as CI:

make -j1 check_modules

[Yeligay8]

In , check (check_base, 4.2) / check section, to fix check error (Error = repo changed during CI and Cause = .Rd not synced with .R):
I recommend to run locally, then commit the changes:

Install if needed

install.packages("roxygen2")

Regenerate documentation

roxygen2::roxygenise()

Then commit the updated files:
git add modules/meta.analysis/man/meta_analysis_standalone.Rd
git commit -m "Update Rd docs to match function arguments"
git push

[infotroph]

@Yeligay8 Thanks for jumping in here! But in this case the underlying problem here isn't the out-of-sync Roxygen docs, it's the presence of edits from a different PR -- fixing a typo in do_conversions should not touch the meta-analysis code at all, and we can't merge this until that's fixed.

(As a smaller matter I recommend everyone follow the PEcAn developer guide and use make rather than manually manage Roxygen builds, but that's mostly a matter of preference)

@shreyannandanwar please do whatever combination of git operations you prefer (likely one or more of cherry-pick, rebase, or revert) to make this branch contain all the typo fixes from commit ecfa103 (do_conversions, soil_process, workflow.bm, and workflow.pda) but without adding .Rapp.history. Commits c82d851, 3a72d67, and 603fae2 should be removed.

[shreyannandanwar]

plzzz checkout -> #3932

I apologies for the noise on the previous PR. I accidentally included unrelated commits (c82d851, 3a72d67, 603fae2) and a stray .Rapp.history file that should never have been tracked.

I've cleaned this up by cherry-picking only the intended fix (ecfa103) onto a fresh branch. This PR now contains exactly 1 commit touching exactly 4 files nothing more.

Thank u @infotroph
Thank u @S1DDHEY
Thank u @Yeligay8

[mdietze]

Closing because superseded by #3932

[S1DDHEY]

@shreyannandanwar Instead of opening a new PR, you could rewrite the commit history here using git reset --soft HEAD~x (where x is the number of commits to go back). This keeps your changes staged, allowing you to remove or adjust unnecessary changes before recommitting into a cleaner history.