Add fre_cli_version to model YAML and enforce version compatibility by Copilot · Pull Request #768 · NOAA-GFDL/fre-cli

Copilot · 2026-03-11T14:34:07Z

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 · 2026-03-11T15:21:32Z

@copilot small bug with fre list introduced, fix

Copilot · 2026-03-11T15:26:58Z

@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 · 2026-03-11T15:39:35Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 84.30%. Comparing base (a17b3f0) to head (83733d3).
⚠️ Report is 27 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #768      +/-   ##
==========================================
+ Coverage   84.24%   84.30%   +0.05%     
==========================================
  Files          71       71              
  Lines        4984     5000      +16     
==========================================
+ Hits         4199     4215      +16     
  Misses        785      785

Flag	Coverage Δ
unittests	`84.30% <100.00%> (+0.05%)`	⬆️

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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 · 2026-03-11T15:49:09Z

ready for actual review

fre/yamltools/helpers.py

docs/usage/yaml_dev/model_yaml.rst

singhd789 · 2026-03-11T16:46:34Z

fre/make/tests/null_example/wrong_model/wrong_null_model.yaml

@@ -1,3 +1,5 @@
+fre_version: "2025.04"


Just a note (forward looking) - I think if/when we adopt uw tools for yaml combining things, this might be better under fre_properties (I think they'll turn into more key:value pairs versus just being defined as yaml anchors used elsewhere)

IMO fre_properties should be optional instead of first-class configuration. fre properties in Bronx are user-specified variables, and we mostly have that style in ours now.

singhd789 · 2026-03-11T16:48:38Z

fre/yamltools/info_parsers/cmor_info_parser.py

        # Clean the yaml, the key exists, delete
        keys_clean=["name", "platform", "target", # these are needed to create the final parsed dictionary fed to cmor
-                    "fre_properties", "directories", "experiments",
+                    "fre_properties", "fre_version", "directories", "experiments",


Hm, it might be beneficial for this to stay and not be cleaned (for more information when troubleshooting maybe?). In that case though, it'll probably have to be added to the gfdl_msd_schema.

Another forward looking thought previously discussed was not doing as much cleaning, so users/workflows have more information to find.

Agree it would be better to keep it, but the compile/pp schemas (fre_make.json, fre_pp.json) have "additionalProperties": false at the top level, so fre_cli_version in the combined YAML would currently fail schema validation. Left it in keys_clean for now with fre_cli_version (renamed). Adding it to the schemas can be a follow-up.

singhd789 · 2026-03-11T16:49:45Z

fre/yamltools/helpers.py

    return y


+def check_fre_version(yamlfile):


type hints might need to be added to this file - just noticed this

Added -> None return type hint to check_fre_version in a7f048b.

singhd789 · 2026-03-11T16:50:40Z

fre/yamltools/helpers.py

    # Clean the yaml
    # If keys exists, delete:
-    keys_clean=["fre_properties", "experiments"]
+    keys_clean=["fre_properties", "fre_version", "experiments"]


same clean note as above

ilaflott · 2026-03-12T18:10:01Z

@copilot understand feedback, implement changes based on it

Copilot · 2026-03-12T18:16:39Z

@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 · 2026-03-16T14:47:53Z

fre/yamltools/tests/esm4_cmip6_ex/esm4_cmip6.yaml

 ##   fre -v cmor yaml -y fre/yamltools/tests/esm4_cmip6_ex/esm4_cmip6.yaml \
 ##                    -e ESM4_TOAR_2014climo_2050ozone_v2 -p gfdl.ncrc5-intel22 -t prod-openmp

+fre_cli_version: "2025.04"


Are these fre_cli_version references in the test yamls used?

The new test test_helpers.py test the fre-cli version check functionality without this file.

Yes, they're used. When consolidate_yamls() runs in tests, it calls check_fre_version() first, which reads fre_cli_version from these model YAMLs. Without the key, every test that calls consolidate_yamls() would log a warning about missing fre_cli_version. The key also now persists in the resolved YAML output (as of 8991fb0), so it's part of the combined output that tests validate.

Removed them in 83733d3. The hardcoded version "2025.04" caused ValueError in CI where fre.version is "2026.01.alpha1". The version check logic is fully covered by test_helpers.py using dynamic temp files with fre.version, so the test YAMLs don't need fre_cli_version.

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 · 2026-03-16T14:51:40Z

fre/yamltools/helpers.py

    # Clean the yaml
    # If keys exists, delete:
-    keys_clean=["fre_properties", "experiments"]
+    keys_clean=["fre_properties", "fre_cli_version", "experiments"]


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?

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.

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.

ilaflott · 2026-03-25T14:14:34Z

@copilot

update the branch
examine feedback and develop code in response, if-needed
respond to the feedback in kind
if you find you have a strong and confident opinion on what should happen, express yourself

Copilot · 2026-03-25T14:25:37Z

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.

- Add check_fre_version() function to fre/yamltools/helpers.py - Call check_fre_version() in consolidate_yamls() before YAML combining - Update clean_yaml() in helpers.py and cmor_info_parser.py to remove fre_version - Add fre_version to all model YAML test files - Add tests for version checking logic - Update model_yaml.rst documentation Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>

… test Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>

…caplog assertions The test_exp_list test in test_list_pp_components_script.py asserts all captured log records are INFO level. The debug-level log emitted on successful version check was captured by caplog, causing the assertion 'DEBUG' == 'INFO' to fail. Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>

@singhd789

… YAMLs Per reviewer consensus (@singhd789, @ceblanton): rename the YAML key from fre_version to fre_cli_version to distinguish it from fre-workflows version. Also adds type hint (-> None) to check_fre_version function. Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>

@ceblanton

Per @ceblanton's feedback: - Remove fre_cli_version from keys_clean in helpers.clean_yaml() and cmor_info_parser.clean_yaml() so it persists in resolved YAMLs - Add fre_cli_version as allowed property in fre_make.json schema (fre_pp.json already has additionalProperties: true) - Update CMOR comparison test fixture to include fre_cli_version Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com> Agent-Logs-Url: https://github.com/NOAA-GFDL/fre-cli/sessions/0cd76d05-84ab-4f72-8691-f09098df07f5

ilaflott · 2026-03-25T15:37:44Z

@copilot fix the tests and describe your changes

@ceblanton

…r missing version The test YAML fixtures had fre_cli_version: "2025.04" hardcoded, but fre.version is dynamic (from GIT_DESCRIBE_TAG env var, default "2026.01.alpha1"). This caused ValueError in CI when the versions didn't match. Changes: - Remove fre_cli_version from all 7 test YAML fixtures and CMOR comparison fixture. The version check is already tested in test_helpers.py with dynamic temp files. - Change missing fre_cli_version log from WARNING to INFO — it's a recommendation, not a warning. WARNING broke test_exp_list which asserts all records are INFO. - Add fre_cli_version back to keys_clean in helpers.clean_yaml() — needed because fre_make.json schema has "additionalProperties": false without fre_cli_version. Once the schema submodule is updated, this can be removed per @ceblanton's preference to keep fre_cli_version in resolved YAMLs. - Update test_check_fre_version_missing to check at INFO level. Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com> Agent-Logs-Url: https://github.com/NOAA-GFDL/fre-cli/sessions/dfdb6e5f-a996-4db1-b6d5-1c3ed1cfc2bf

Copilot · 2026-03-25T15:48:46Z

@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.

Copilot AI assigned Copilot and ilaflott Mar 11, 2026

Copilot started work on behalf of ilaflott March 11, 2026 14:34 View session

ilaflott requested review from ceblanton, ilaflott, laurenchilutti and singhd789 March 11, 2026 14:48

Copilot AI changed the title ~~[WIP] Add FRE_VERSION to model yaml and enforce it~~ Add fre_version to model YAML and enforce version compatibility Mar 11, 2026

Copilot finished work on behalf of ilaflott March 11, 2026 14:50

ilaflott marked this pull request as ready for review March 11, 2026 15:05

ilaflott added new functioning New feature or request priority: HIGH labels Mar 11, 2026

Copilot started work on behalf of ilaflott March 11, 2026 15:21 View session

Copilot finished work on behalf of ilaflott March 11, 2026 15:27

singhd789 added the beta1 label Mar 11, 2026

laurenchilutti reviewed Mar 11, 2026

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ilaflott force-pushed the copilot/add-fre-version-to-model-yaml branch from 092d7e5 to 31216f4 Compare March 12, 2026 18:08

Copilot started work on behalf of ilaflott March 12, 2026 18:10 View session

Copilot AI changed the title ~~Add fre_version to model YAML and enforce version compatibility~~ Add fre_cli_version to model YAML and enforce version compatibility Mar 12, 2026

Copilot finished work on behalf of ilaflott March 12, 2026 18:18

ceblanton reviewed Mar 16, 2026

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ceblanton requested changes Mar 16, 2026

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singhd789 linked an issue Mar 19, 2026 that may be closed by this pull request

Add FRE_VERSION to the model yaml and enforce it #737

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Copilot started work on behalf of ilaflott March 25, 2026 14:14 View session

Copilot finished work on behalf of ilaflott March 25, 2026 14:28

Copilot AI and others added 5 commits March 25, 2026 10:37

Address code review feedback: use debug logging and verify warning in…

b16234e

… test Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>

ilaflott force-pushed the copilot/add-fre-version-to-model-yaml branch from 8991fb0 to 5d1eca6 Compare March 25, 2026 14:37

Update gfdl_msd_schemas submodule to faee9976

72884ce

Copilot started work on behalf of ilaflott March 25, 2026 15:37 View session

Copilot finished work on behalf of ilaflott March 25, 2026 15:52

singhd789 added alpha1 alpha2 and removed beta1 alpha1 labels Mar 26, 2026

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