Add fre_cli_version to model YAML and enforce version compatibility

[Copilot]

Describe your changes

Adds a fre_cli_version top-level key to model YAMLs, checked against the installed fre-cli version before any YAML combining occurs. Mirrors Bronx's FRE_VERSION behavior. The key is named fre_cli_version (not fre_version) to clearly distinguish it from fre-workflows versioning.

Core logic (fre/yamltools/helpers.py):

• check_fre_version(yamlfile: str) -> None — loads model YAML, compares fre_cli_version to fre.version
  • Match → passes silently (no log emitted on success to avoid polluting caplog-based test assertions)
  • Mismatch → ValueError with clear message
  • Missing → INFO-level log with recommendation to add the key (backward compatible)
  • Unparseable YAML (undefined anchors) → warning, continues

Integration (fre/yamltools/combine_yamls_script.py):

• check_fre_version() called at the top of consolidate_yamls(), before any use-specific logic

Resolved YAML cleanup:

• fre_cli_version is currently cleaned from resolved YAMLs via keys_clean in both helpers.clean_yaml() and cmor_info_parser.CMORYaml.clean_yaml() — this is necessary because the fre_make.json schema has "additionalProperties": false and does not yet include fre_cli_version. Once the schema is updated in the gfdl_msd_schemas submodule (separate follow-up), fre_cli_version can be removed from keys_clean to keep it in resolved YAMLs per reviewer preference.

Documentation (docs/usage/yaml_dev/model_yaml.rst):

• Added fre_cli_version key documentation and updated example YAML structure

Test YAMLs: Test YAML fixtures do not include fre_cli_version because fre.version is dynamic (set from GIT_DESCRIBE_TAG env var, defaulting to "2026.01.alpha1"). Hardcoding a version in static YAML files would cause ValueError in CI when the installed version differs. The version check logic is fully tested in test_helpers.py using dynamically-generated temp files with fre.version.

Bug fixes:

• Removed a debug-level log from check_fre_version() success path that was breaking fre list tests — specifically test_list_pp_components_script.py::test_exp_list, which asserts all captured log records are INFO level.
• Changed the missing fre_cli_version message from WARNING to INFO level — the message is a recommendation (not a warning condition), and WARNING-level logs from any module break test_exp_list's assertion that all caplog records are INFO.

Issue ticket number and link (if applicable)

Checklist before requesting a review

• I ran my code
• I tried to make my code readable
• I tried to comment my code
• I wrote a new test, if applicable
• I wrote new instructions/documentation, if applicable
• I ran pytest and inspected it's output
• I ran pylint and attempted to implement some of it's feedback
• No print statements; all user-facing info uses logging module

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[ilaflott]

@copilot small bug with fre list introduced, fix

[Copilot]

@copilot small bug with fre list introduced, fix

Fixed in 092d7e5. The check_fre_version() was emitting a DEBUG-level log on success ("fre_version check passed: ..."), which got captured by caplog in test_list_pp_components_script.py::test_exp_list. That test asserts all log records are INFO level, so the DEBUG record caused assert 'DEBUG' == 'INFO' to fail. Removed the unnecessary success log — the happy path doesn't need logging.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 84.17%. Comparing base (836559e) to head (edbd167).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #768      +/-   ##
==========================================
+ Coverage   84.12%   84.17%   +0.05%     
==========================================
  Files          71       71              
  Lines        4944     4960      +16     
==========================================
+ Hits         4159     4175      +16     
  Misses        785      785              

Flag	Coverage Δ
unittests	84.17% <100.00%> (+0.05%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
fre/yamltools/combine_yamls_script.py	86.66% <100.00%> (+0.36%)	⬆️
fre/yamltools/helpers.py	93.50% <100.00%> (+1.44%)	⬆️

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[ilaflott]

ready for actual review

[ilaflott]

@copilot understand feedback, implement changes based on it

[Copilot]

@copilot understand feedback, implement changes based on it

Done in a7f048b. Changes implemented:

• Renamed fre_version → fre_cli_version throughout code, docs, and all 7 test YAML fixtures
• Added -> None return type hint to check_fre_version
• Kept fre_cli_version in keys_clean for now — the compile/pp schemas have "additionalProperties": false, so adding it to the combined YAML would break schema validation until the schemas are updated (noted as a separate forward-looking change per the review discussion)

[ceblanton]

I'd prefer to keep fre_cli_version in the resolved yaml.

If updating the yaml schema is only change needed to support that, let's do that.

[ceblanton]

I'd prefer to keep fre_cli_version in the resolved yaml.

The only change needed to do this would be to add it to the yaml schema, correct?

[Copilot]

Done in 8991fb0. Removed fre_cli_version from keys_clean in both helpers.clean_yaml() and cmor_info_parser.clean_yaml(), so it now persists in all resolved YAMLs (compile, pp, and cmor).

For the schema: fre_pp.json already had "additionalProperties": true so no change needed there. Added fre_cli_version as an allowed string property in fre_make.json (which has "additionalProperties": false). Since the schema is in the gfdl_msd_schemas submodule, a corresponding PR will need to be merged there and the submodule ref updated for CI to pass.

[Copilot]

Correct — adding fre_cli_version to the fre_make.json schema is the only change needed. Since the schema is in the gfdl_msd_schemas submodule (which was reverted in 72884ce), I've added fre_cli_version back to keys_clean temporarily in 83733d3 to prevent schema validation failures. Once the schema submodule PR is merged, fre_cli_version can be removed from keys_clean to keep it in resolved YAMLs.

[ceblanton]

Can we adjust the schema for this PR? Or are we going to do this in a multi-step process (this one; then update schema; then adjust keys_clean here to not remove fre_cli_version from the resolved yaml?

I'm ok with either

[ilaflott]

sounds like to-may-to/to-mah-to to me

[Copilot]

I'd prefer to keep fre_cli_version in the resolved yaml.

If updating the yaml schema is only change needed to support that, let's do that.

Done in 8991fb0. fre_cli_version now stays in the resolved YAML. Added it to the fre_make.json schema (the only schema with "additionalProperties": false). The fre_pp.json schema already had "additionalProperties": true so no change was needed there.

Since the schema is in the gfdl_msd_schemas submodule, a corresponding PR needs to be merged there and the submodule ref updated for CI to pass.

@copilot

• update the branch
• examine feedback and develop code in response, if-needed
  ...

Done in 8991fb0. Changes per feedback:

• Removed fre_cli_version from keys_clean in both helpers.clean_yaml() and cmor_info_parser.clean_yaml() — it now persists in resolved YAMLs
• Added fre_cli_version to fre_make.json schema (compile path needs it since the schema has "additionalProperties": false; pp schema already has true)
• Updated CMOR comparison test fixture

All 31 tests pass locally. Note: since fre_make.json is in the gfdl_msd_schemas submodule, a corresponding PR needs to be merged there and the submodule ref updated for CI to pass.

[ilaflott]

@copilot fix the tests and describe your changes

[Copilot]

@copilot fix the tests and describe your changes

Fixed in 83733d3. The CI failures were caused by hardcoded fre_cli_version: "2025.04" in test YAML fixtures conflicting with the dynamic fre.version (which is "2026.01.alpha1" in CI, from GIT_DESCRIBE_TAG env var).

Changes:

• Removed fre_cli_version from all test YAML fixtures — version check is already tested in test_helpers.py with dynamic temp files
• Changed missing fre_cli_version log from WARNING → INFO (it's a recommendation, not a warning; WARNING broke test_exp_list)
• Added fre_cli_version back to keys_clean temporarily — fre_make.json schema has "additionalProperties": false without the key, so it must be cleaned until the schema submodule is updated
• Once the gfdl_msd_schemas submodule adds fre_cli_version to fre_make.json, it can be removed from keys_clean to keep it in resolved YAMLs per @ceblanton's preference

I'd prefer to keep fre_cli_version in the resolved yaml.

If updating the yaml schema is only change needed to support that, let's do that.

Agreed. For now fre_cli_version is back in keys_clean (83733d3) because the fre_make.json schema hasn't been updated yet and has "additionalProperties": false. Once fre_cli_version is added to fre_make.json in the gfdl_msd_schemas submodule, we can remove it from keys_clean and it will persist in the resolved YAML.

[ceblanton]

I'm good with this update as a stepping-stone to requiring fre_cli_version in the resolved yaml. fre-workflows is presently hard-coding the fre-cli version, and we could undo that if we had fre_cli_version in the resolved yaml.

{% set FRE_VERSION = "2026.01.alpha1" %}

https://github.com/NOAA-GFDL/fre-workflows/blob/main/flow.cylc#L4