Enhance ERA5 Download Function: Direct NetCDF, Flexible Parameters, and Improved Docs

[divine7022]

Description

This PR refactors the download.ERA5_cds function to:

• Download ERA5 data directly in netcdf format (removes grib_to_netcdf conversion dependency).
• Parameters are now passed in the correct vector format to ensure proper API requests.
• Added support for flexible selection of product type, dataset, and time steps (no longer hardcoded).
• Fixed the extent argument to ensure correct spatial subsetting as required by the API.
• Provided clearer, beginner-friendly documentation and example usage.
• Removed the Python dependency( cdsapi via reticulate ) and migrating to the native R ecmwfr package
• added a unit tests for the extraction function(test.download.ERA5_cds.R)

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.

[dlebauer]

Looks great - thanks for these tests.

I'm running one of the examples, and it has been running for ~20 minutes. How long do you expect the examples to take? This seems long for an example / proof of concept.

I've made a few minor suggestions, including one that generally applies to your work - please add your name to the author field when you have made non-trivial changes to functions!

[dlebauer]

Suggested change

	#' @author Dongchen Zhang
	#' @author Dongchen Zhang, Akash BV

[divine7022]

👍

[dlebauer]

As commented elsewhere, we use pkg::fn notation which makes @importFrom not necessary

[dlebauer]

Hi @divine7022 thanks again for this major update to the ERA5 code, it looks great - and is very close!

Mostly there are just a few minor changes to implement, including a number of suggested changes that you 👍🏻 but were not committed. These are now marked 'outdated' but not 'resolved'.

[dlebauer]

As commented elsewhere, we use pkg::fn notation which makes @importFrom not necessary

[divine7022]

this is the current function signature;
auto.create.key = TRUE argument is outdated -- it was used when the function relied on Python via reticulate.
Now that we’ve switched to using ecmwfr.

[infotroph]

Are user and key optional or required here? A NULL default typically means more or less "the function will figure this out if not provided", which would be aligned with the previous getnetrc approach. But on a quick skim below I see an error if user or key are null and didn't see anything that would fill them in before that -- if they're now required arguments that's fine but might as well remove the default value to make that clearer.

[divine7022]

thanks! @infotroph now removed NULL defaults for user/key parameters

[divine7022]

As commented elsewhere, we use pkg::fn notation which makes @importFrom not necessary

@dlebauer thanks! for the catch - now uses base R pipe |> instead of %>%
i hope all the suggestions have been addressed.

[infotroph]

now uses base R pipe |> instead of %>%

Thank you for that change! Note that this means the package now requires a version of R new enough to contain the base pipe, but I don't think the package checks detect this yet. Can you please add Depends: R (>= 4.1) at line 22 of the DESCRIPTION file (between the Description: and Imports: sections)?

[divine7022]

thanks @infotroph now Depends: R (>= 4.1.0) added to DESCRIPTION

[dlebauer]

Thanks for making these changes - looks like all requested changes have been made.

Apologies some of my earlier requests were based outdated code.

[divine7022]

Thanks for approving @dlebauer