`fre.cmor`: variable list semantics: map modeler variable names to MIP table names by Copilot · Pull Request #846 · NOAA-GFDL/fre-cli

Copilot · 2026-04-08T18:39:07Z

… names - Change varlist semantics: key = modeler's var name (in filename AND file), value = MIP table variable name - Add validation: error when filename variable != file variable - Read variable data from file using local_var (modeler name) instead of target_var - Update CLI run command to propagate non-zero return status as ClickException - Update test case2 to test error case (filename/file variable mismatch) - Update docstrings, help text, and log messages to reflect new semantics Agent-Logs-Url: https://github.com/NOAA-GFDL/fre-cli/sessions/35f4cd66-b4ff-4394-aa91-d318347d10f1 Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>

Agent-Logs-Url: https://github.com/NOAA-GFDL/fre-cli/sessions/35f4cd66-b4ff-4394-aa91-d318347d10f1 Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>

ilaflott · 2026-04-08T19:31:13Z

@copilot tests are running but we've plenty to do- while you wait for results, find content under docs/ regarding fre.cmor and it's variable list behavior, update the text to match the target behavior we are developing for. if the tests finish unsuccessfully during your iteration, don't stop re-evaluating the docs. we will have another iteration for addressing any test failures if-needed

…ble var Update documentation across docs/usage/cmor_cookbook.rst, docs/tools/cmor.rst, and fre/cmor/README.md to reflect the new variable list semantics where: - key = modeler's variable name (in filename AND inside the file) - value = MIP table variable name - filename var must match file var or fre cmor run errors Agent-Logs-Url: https://github.com/NOAA-GFDL/fre-cli/sessions/5870f988-b97c-4d7b-8b29-e36e63dfb14c Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>

…nsistency Agent-Logs-Url: https://github.com/NOAA-GFDL/fre-cli/sessions/5870f988-b97c-4d7b-8b29-e36e63dfb14c Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>

Copilot · 2026-04-08T19:37:12Z

@copilot tests are running but we've plenty to do- while you wait for results, find content under docs/ regarding fre.cmor and it's variable list behavior, update the text to match...

Updated all documentation under docs/ and fre/cmor/README.md to reflect the new variable list behavior in commit 616d595:

docs/usage/cmor_cookbook.rst: Rewrote "Creating Variable Lists" section with clear key/value semantics (key=modeler var, value=MIP table var), added .. important:: note about filename/file variable matching requirement
docs/tools/cmor.rst: Updated --varlist description from "local to MIP" to "modeler variable names to MIP table variable names"
fre/cmor/README.md: Updated Required User Configuration section with full key/value explanation, updated fre cmor run description to clarify --varlist usage, updated fre cmor varlist section to describe the default identity mapping and editing workflow

codecov · 2026-04-08T20:14:08Z

Codecov Report

❌ Patch coverage is 81.25000% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 84.17%. Comparing base (836559e) to head (bed2b1f).

Files with missing lines	Patch %	Lines
fre/cmor/cmor_finder.py	0.00%	2 Missing ⚠️
fre/cmor/cmor_mixer.py	90.90%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #846      +/-   ##
==========================================
+ Coverage   84.12%   84.17%   +0.05%     
==========================================
  Files          71       71              
  Lines        4944     4949       +5     
==========================================
+ Hits         4159     4166       +7     
+ Misses        785      783       -2

Flag	Coverage Δ
unittests	`84.17% <81.25%> (+0.05%)`	⬆️

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

Files with missing lines	Coverage Δ
fre/cmor/frecmor.py	`100.00% <100.00%> (ø)`
fre/cmor/cmor_mixer.py	`90.66% <90.90%> (+0.79%)`	⬆️
fre/cmor/cmor_finder.py	`97.80% <0.00%> (-2.20%)`	⬇️

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…h fixtures - Create CDL file and varlist for mapped variable test (sea_sfc_salinity → sos) - Add conftest.py with shared session-scoped fixtures for ncgen, paths, file setup - Refactor test_cmor_run_subtool.py to use conftest fixtures and tmp_path - Add case3 tests: success, data comparison, and metadata comparison - Fix CLI error propagation in frecmor.py (check cmor_run_subtool return status) Agent-Logs-Url: https://github.com/NOAA-GFDL/fre-cli/sessions/80cfd2fa-1f68-407c-b0d7-cde17e9e4b1b Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>

…e tests - Add conftest.py for fre/tests/ with shared CLI fixtures - Refactor test_fre_cmor_cli.py to use conftest fixtures and tmp_path - Add case3 mapped-variable tests for both CMIP6 and CMIP7 - All 35 CLI tests pass, all 116 cmor tests pass, all 144 fre/tests pass Agent-Logs-Url: https://github.com/NOAA-GFDL/fre-cli/sessions/80cfd2fa-1f68-407c-b0d7-cde17e9e4b1b Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>

Agent-Logs-Url: https://github.com/NOAA-GFDL/fre-cli/sessions/80cfd2fa-1f68-407c-b0d7-cde17e9e4b1b Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>

ilaflott · 2026-04-13T18:56:14Z

this is about right.

i want to adjust fre cmor varlist too for the new approach, but this PR is already bloated, so i'm cutting myself off.

ilaflott · 2026-04-14T20:12:46Z

fremorizer is still poking at this, keep for now

Initial plan

184868a

Copilot AI assigned Copilot and ilaflott Apr 8, 2026

Copilot started work on behalf of ilaflott April 8, 2026 18:39 View session

Copilot AI linked an issue Apr 8, 2026 that may be closed by this pull request

fre.cmor: adjust current variable list usage to map modeler variable names to MIP ones #845

Open

4 tasks

Copilot AI and others added 4 commits April 8, 2026 19:02

revert test-modified exp config files to their original state

014cd9d

Agent-Logs-Url: https://github.com/NOAA-GFDL/fre-cli/sessions/35f4cd66-b4ff-4394-aa91-d318347d10f1 Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>

address code review: improve assertion message with f-string

d91cdaf

Agent-Logs-Url: https://github.com/NOAA-GFDL/fre-cli/sessions/35f4cd66-b4ff-4394-aa91-d318347d10f1 Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>

revert test-modified exp config files to original state (from main)

0037b53

Agent-Logs-Url: https://github.com/NOAA-GFDL/fre-cli/sessions/35f4cd66-b4ff-4394-aa91-d318347d10f1 Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>

Copilot AI changed the title ~~[WIP] Adjust current variable list usage to map modeler variable names to MIP~~ Adjust fre.cmor variable list semantics: map modeler variable names to MIP table names Apr 8, 2026

Copilot finished work on behalf of ilaflott April 8, 2026 19:05

Copilot AI requested a review from ilaflott April 8, 2026 19:05

Copilot started work on behalf of ilaflott April 8, 2026 19:31 View session

Copilot AI and others added 2 commits April 8, 2026 19:35

docs: minor style fixes, replace em-dashes with double hyphens for co…

616d595

…nsistency Agent-Logs-Url: https://github.com/NOAA-GFDL/fre-cli/sessions/5870f988-b97c-4d7b-8b29-e36e63dfb14c Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>

Copilot finished work on behalf of ilaflott April 8, 2026 19:39

ilaflott changed the title ~~Adjust fre.cmor variable list semantics: map modeler variable names to MIP table names~~ fre.cmor: variable list semantics: map modeler variable names to MIP table names Apr 8, 2026

ilaflott added 3 commits April 9, 2026 17:30

more graceful try/except behavior

d65cc25

additional logging for transparency

2535db1

remove some unneeded lines

2814e35

Copilot started work on behalf of ilaflott April 13, 2026 16:55 View session

Copilot AI and others added 3 commits April 13, 2026 17:13

address code review: strengthen nccmp and varlist assertions

07724af

Agent-Logs-Url: https://github.com/NOAA-GFDL/fre-cli/sessions/80cfd2fa-1f68-407c-b0d7-cde17e9e4b1b Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>

Copilot finished work on behalf of ilaflott April 13, 2026 17:20

restore input configs in test files

bed2b1f

ilaflott marked this pull request as ready for review April 13, 2026 18:55

ilaflott mentioned this pull request Apr 13, 2026

fre.cmor: update fre cmor varlist for new modeler name -> mip table name mapping #860

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ilaflott approved these changes Apr 13, 2026

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ilaflott added new functioning New feature or request priority: HIGH labels Apr 13, 2026

ilaflott requested review from ceblanton, meteorologist15 and singhd789 April 13, 2026 19:48

Copilot AI mentioned this pull request Apr 13, 2026

[WIP] Update fre cmor varlist for new modeler name to mip table name mapping #863

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ilaflott mentioned this pull request Apr 14, 2026

Deferred Features from fre.cmor ilaflott/fremorizer#27

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Copilot AI mentioned this pull request Apr 14, 2026

[WIP] Track deferred features from fre.cmor for future implementation ilaflott/fremorizer#28

Closed

Claude AI mentioned this pull request Apr 14, 2026

[WIP] Add deferred features from fre.cmor for future implementation ilaflott/fremorizer#31

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ilaflott mentioned this pull request Apr 14, 2026

new features: Variable list semantics (map modeler vars to MIP table names) ilaflott/fremorizer#48

Open

Copilot AI mentioned this pull request Apr 14, 2026

[WIP] Improve variable list semantics for MIP table names ilaflott/fremorizer#74

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`fre.cmor`: variable list semantics: map modeler variable names to MIP table names#846

`fre.cmor`: variable list semantics: map modeler variable names to MIP table names#846
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