[WIP] Track deferred features from fre.cmor for future implementation

[Copilot]

Thanks for asking me to work on this. I will get started on it and keep this PR's description up to date as I form a plan and make progress.

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This section details on the original issue you should resolve

<issue_title>Deferred Features from fre.cmor</issue_title>
<issue_description># Phase 3: Deferred Features from fre.cmor

This document tracks features from open fre.cmor pull requests that are intentionally deferred for future implementation in fremorizer. Each item corresponds to a specific PR in the fre-cli repository.

Purpose

Phase 3 features represent enhancements and improvements that were in progress in the fre.cmor submodule. These are deferred to focus on:

1. Establishing a stable, working independent fremorizer package (Phase 1-2)
2. Validating equivalence with existing fre-cli functionality (Phase 2.5)
3. Ensuring CI/CD pipelines are robust and reliable

Once the foundation is solid and equivalence testing is complete, these features can be incorporated systematically.

Phase 3 Items

1. PR ilaflott/fremorizer#826: Replace nccmp with netCDF4 in tests ✅ COMPLETED

• Source: fre.cmor: replace nccmp subprocess calls with netCDF4 in cmor run subtool tests NOAA-GFDL/fre-cli#826
• Description: Replace external nccmp tool dependency with Python netCDF4 library for comparing netCDF files in tests
• Impact: Eliminated external tool dependency, making tests more portable and reliable
• Status: Implemented — nccmp subprocess calls replaced with netCDF4/numpy assertions in test_cmor_run_subtool.py

2. PR ilaflott/fremorizer#832: Harden branded-variable disambiguations

• Source: fre.cmor: harden branded-variable disambiguations NOAA-GFDL/fre-cli#832
• Description: Improve handling of branded variable name disambiguation (e.g., when multiple variables map to same target)
• Impact: More robust variable handling in edge cases
• Priority: Medium

3. PR ilaflott/fremorizer#833: Improved omission tracking

• Source: fre.cmor: improved and comprehensive omission tracking NOAA-GFDL/fre-cli#833
• Description: Better tracking and reporting of variables that are omitted during CMORization
• Impact: Improved user feedback and debugging capabilities
• Priority: Medium

4. PR ilaflott/fremorizer#834: New fremor init command for config fetching

• Source: fre.cmor: new fre cmor init command for config fetching NOAA-GFDL/fre-cli#834
• Description: Add new CLI subcommand to fetch/initialize CMOR configuration files
• Impact: Improved user experience for initial setup
• Priority: Medium - new feature, not a fix

5. PR ilaflott/fremorizer#836: Informative error on mip_era/table format mismatch

• Source: fre.cmor: raise informative error when mip_era config mismatches table format (CMIP6 vs CMIP7) NOAA-GFDL/fre-cli#836
• Description: Provide clear error messages when MIP era and table format don't match
• Impact: Better user experience and faster debugging
• Priority: Medium

6. PR ilaflott/fremorizer#837: Accept CF calendar aliases (noleap/365_day, etc.)

• Source: fre.cmor: accept CF calendar aliases as equivalent (noleap / 365_day, etc.) NOAA-GFDL/fre-cli#837
• Description: Support CF convention calendar aliases (e.g., "noleap" as alias for "365_day")
• Impact: Improved compatibility with various input data conventions
• Priority: Medium

7. PR ilaflott/fremorizer#838: CMIP7 flavored tests

• Source: fre.cmor: create CMIP7 flavored tests of cmor_run_subtool_further_examples NOAA-GFDL/fre-cli#838
• Description: Add test cases specifically for CMIP7 conventions and requirements
• Impact: Ensure CMIP7 compatibility and catch CMIP7-specific issues
• Priority: High - CMIP7 support is important for future-proofing

8. PR ilaflott/fremorizer#846: Variable list semantics (map modeler vars to MIP table names)

• Source: fre.cmor: variable list semantics: map modeler variable names to MIP table names NOAA-GFDL/fre-cli#846
• Description: Improve variable list handling to better map model variable names to MIP table variable names
• Impact: More flexible and intuitive variable mapping
• Priority: Medium

9. PR ilaflott/fremorizer#817: Update cmor to 3.14.2

• Source: fre.cmor: update to 3.14.2 from 3.14.0 NOAA-GFDL/fre-cli#817
• Description: Update the CMOR library dependency from current version to 3.14.2
• Impact: Access to latest CMOR features and bug fixes
• Priority: Medium - should verify compatibility before upgrading

Implementation Strategy

When ready to implement Phase 3 features:

1. Create individual GitHub issues for each item above with:

   • Link to the original fre-cli PR
   • Description of the feature/fix
   • Any fremorizer-specific considerations
   • Testing requirements

2. Prioritize based on:

   • User impact (e.g., PR ilaflott/fremorizer#826 fixes current test failures)
   • Dependencies between features
   • Alignment with CMIP6/CMIP7 timelines

3. Implementation approach:

   • Review the original PR in fre-cli for implementation details
   • Adapt code to fremorizer's independent package structure
   • Ensure all changes maintain test coverage
   • Update documentation as needed
   • Validate no regressions in existing functionality

4. Testing requirements:

   • All existing tests must continue to pass
   • New tests should be added for new features
   • Phase 2.5 equivalence tests should still pass after each feature addition

Notes

• Phase 2.5 (equivalence testing with fre-cli) should be completed before implementing Phase 3 features
• Each Phase 3 feature should be implemented in a separate PR for easier review and rollback if needed
• Consider creating a project board to track Phase 3 implementation progress

References

• Original fre-cli repository: https://github.com/noaa-gfdl/fre-cli
• fre.cmor submodule path: fre/cmor/ in fre-cli
• This fremorizer PR: [WIP] Add independent package fremorizer based on fre.cmor #1</issue_description>

<agent_instructions>focus on easier features to start, like the calendar alias equivalents. don't forget to consult the original PR source for the feature in the notes</agent_instructions>

Comments on the Issue (you are @copilot in this section)

[ilaflott]

this was a good PR??