Integrate LPJ-GUESS with SDA module and synchronize with latest upstream

[yinghaoSunn]

Description

This PR implements the coupling of LPJ-GUESS within the PEcAn Sequential Data Assimilation (SDA) workflow. It includes critical updates to state handling, binary data extraction, and ensures full compatibility with the latest PEcAn develop branch:

Motivation and Context

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.

[Yeligay8]

In CI / check (check_models, 4.2) / check (pull_request) error:
Status: BROKEN
Error: Please fix these and resubmit.

Main blocking issue:
checking R files for non-ASCII characters ... WARNING

File: update.state.both.LPJGUESS.R

I suggest to fix to:
grep -n "[^ -~]" models/lpjguess/R/update.state.both.LPJGUESS.R

OR

tools::showNonASCIIfile("models/lpjguess/R/update.state.both.LPJGUESS.R")

Also, maybe replacing characters might help:
“ ” to ", ‘ ’ to ' , — to -, µ to u

Here I guess R doesn't know where str () comes from:
no visible global function definition for ‘str’

I suggest: importFrom(utils, str)

I guess here needs fixing in missing documentation:
checking for missing documentation entries ... WARNING

run:
devtools::document()
then check for missing docs:
devtools::check()

Here needs fixing in empty Rd section:
Dropping empty section \details

you can edit to:
dot-seed_cohort_quick.Rd

Remove empty section:
\details{
}

Fix ASCII:
tools::showNonASCIIfile("models/lpjguess/R/update.state.both.LPJGUESS.R")

Fix import and add:
#' @importFrom utils str

Regenerate docs:
devtools::document()

Re-run checks locally:
devtools::check()

Run Make again:
make -j1 check_models

[yinghaoSunn]

@Yeligay8 Thanks for the detailed review. I’ve addressed the issues you pointed out, including the non-ASCII characters and missing documentation, and the CI / check (check_models, 4.2) check is now passing. The remaining failing checks appear to be non-required Docker builds. Could you please take another look when you have a chance?

Not a dev team member. Issues have been addressed. Likely that the review was LLM generated.