PEPRMT: new parameters, met integration

[abbylewis]

Description

Fairly substantial changes to PEcAn.PEPRMT to incorporate meteorological inputs, update parameter specification, and transition away from using example data:

• Updated met2model.PEPRMT to focus on only meteorological inputs (previously had placeholders for salinity, nitrate, etc)
• Updated model2netcdf.PEPRMT to handle years when data do not start on Jan 1
• Updated write.configs.PEPRMT to accommodate new parameter formulation in PEPRMT.Tidal, as well as to add met inputs. This is a bit involved because the dates differ across sites
• Set up data processing to generate site_info.csv and site-specific driver files from the files Patty Oikawa has sent
• Updated input_demo.qmd to handle new parameter names and run met2model.PEPRMT
• Some tweaks to documentation and plotting in the original demo
  @infotroph

Review Time Estimate

• Immediately
• Within one week
• [ x] When possible

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• [x ] 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
• [x ] 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.
• [x ] I have read the CONTRIBUTING document.
• I have added tests to cover my changes.
• [x ] All new and existing tests passed.

[infotroph]

Thanks for doing this and for your patience with the wait for reviews.

• Code: Looks great! I left one optional suggestion about a line that confused me but appears to work as intended anyway.
• Demos: Ran both with no problem ✅
• Files: Is it necessary to include all three of raw-data/site-data-raw, raw-data/site-data-formatted, and data/PEPRMT_specific_inputs? They're small enough it's OK to commit them all if needed, but big enough to be worth being sure.

[infotroph]

Am I reading right that this is testing whether in.prefix already ends in . or _?
Would this be more readable?

Suggested change

	if(nchar(in.prefix)>0 &
	!substr(in.prefix, nchar(in.prefix), nchar(in.prefix)) %in% c(".", "_")) {
	in.prefix = paste0(in.prefix,".")
	}
	if (nchar(in.prefix) > 0 && !any(endsWith(in.prefix, c(".", "_")))) {
	in.prefix <- paste0(in.prefix, ".")
	}

[infotroph]

A couple more to quiet the CI messages. You'll also need to remove PEPRMT from the Imports: section of DESCRIPTION since it's no longer called anywhere R's package checks can see it. I suggest moving it to a new Enhances: line.

[infotroph]

Suggested change

	run_data <- read.csv(peprmt_specific_input_path) |>
	run_data <- utils::read.csv(peprmt_specific_input_path) |>

[infotroph]

Suggested change

	dplyr::select(-any_of(met_vars)) |>
	dplyr::select(-dplyr::any_of(met_vars)) |>