Add GCAFS forecast-only mode to the workflow

[CoryMartin-NOAA]

Description

This PR adds in forecast-only mode for GCAFS and begins to put some of the pieces in place (mainly config files) for cycled mode for GCAFS/GCDAS. This PR also adds a lot of doc strings to places where they were missing. While I am opening this PR, a large portion of the work was done by @bbakernoaa

Partially addresses #3565

Type of change

• Bug fix (fixes something broken)
• New feature (adds functionality)
• Maintenance (code refactor, clean-up, new CI test, etc.)

Change characteristics

• Is this a breaking change (a change in existing functionality)? NO
• Does this change require a documentation update? YES
• Does this change require an update to any of the following submodules? NO
  • EMC verif-global
  • GDAS
  • GFS-utils
  • GSI
  • GSI-monitor
  • GSI-utils
  • UFS-utils
  • UFS-weather-model
  • wxflow

How has this been tested?

• Clone and build on Hera
• Forecast-only on Hera

Checklist

• Any dependent changes have been merged and published
• My code follows the style guidelines of this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have documented my code, including function, input, and output descriptions
• My changes generate no new warnings
• New and existing tests pass with my changes
• This change is covered by an existing CI test or a new one has been added
• Any new scripts have been added to the .github/CODEOWNERS file with owners
• I have made corresponding changes to the system documentation if necessary

[Copilot]

Pull Request Overview

This PR introduces a forecast‐only mode for GCAFS into the global workflow while updating and adding comprehensive docstrings across multiple modules. Key changes include:

• Adding new GCAFS-specific command-line arguments and configuration logic.
• Registering new GCAFS task and XML generators in the Rocoto workflow.
• Enhancing documentation and consistency in application configuration classes.

Reviewed Changes

Copilot reviewed 85 out of 90 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
dev/workflow/setup_expt.py	Updated docstrings and added GCAFS forecast-only parser support
dev/workflow/rocoto/tasks_factory.py	Registered GCAFSTasks for GCAFS
dev/workflow/rocoto/tasks.py	Included GCAFS in forecast hours calculation
dev/workflow/rocoto/rocoto_xml_factory.py	Registered GCAFSForecastOnlyRocotoXML
dev/workflow/rocoto/gfs_forecast_only_xml.py	Docstring updates for GFS forecast-only XML generation
dev/workflow/rocoto/gfs_cycled_xml.py	Docstring enhancements in cycled XML generator
dev/workflow/rocoto/gcafs_forecast_only_xml.py	New module for generating GCAFS forecast-only cycle definitions
dev/workflow/applications/sfs.py	Enhanced documentation for SFS application config
dev/workflow/applications/gfs_forecast_only.py	Updated docstrings for GFS forecast-only configuration
dev/workflow/applications/gfs_cycled.py	Improved documentation in GFS cycled configuration
dev/workflow/applications/gefs.py	Enhanced GEFS configuration docstrings
dev/workflow/applications/gcafs_forecast_only.py	New GCAFS forecast-only app config with configuration adjustments
dev/workflow/applications/applications.py	Updated abstract base and initialization docstrings
dev/workflow/applications/application_factory.py	Registered GCAFS forecast-only app configuration
dev/ci/cases/yamls/gcafs_defaults_ci.yaml	Added CI YAML file for GCAFS default configuration

Files not reviewed (5)

• docs/source/development.rst: Language not supported
• docs/source/gcafs.rst: Language not supported
• docs/source/index.rst: Language not supported
• jobs/JGLOBAL_OFFLINE_ATMOS_ANALYSIS: Language not supported
• parm/chem/chem_emission.yaml.j2: Language not supported

Comments suppressed due to low confidence (2)

dev/workflow/applications/gcafs_forecast_only.py:11

• The logic for setting app_config.configs['base']['RUN'] to 'gcafs' appears redundant with multiple if/else branches; consider simplifying this block to improve clarity.

if 'base' in app_config.configs:

dev/workflow/applications/gcafs_forecast_only.py:139

• [nitpick] There is commented-out code in the get_task_names method; if it is no longer needed, please remove it to reduce clutter.

// if options['do_archcom']:
//     tasks += ['arch_tars']
//     if options['do_globusarch']:
//         tasks += ['globus_arch']

[DavidHuber-NOAA]

I think a few of the parm/config/gcafs files should be links rather than standalone. Otherwise, I think this is pretty close.

[DavidHuber-NOAA]

Should this be a link?

[CoryMartin-NOAA]

Anything else to change/fix before kicking off testing?

[DavidHuber-NOAA]

Looks good. One question about future testing.

[DavidHuber-NOAA]

Starting CI on C6.

[DavidHuber-NOAA]

@CoryMartin-NOAA All tests passed on C6. Could you please resolve the conflicts in your branch? Also, you may need to move parm/config/gcafs/* to dev/parm/config/gcafs. Once complete, I think this PR is ready to merge.

[CoryMartin-NOAA]

Done. Thanks @DavidHuber-NOAA