342 benchcab sub command for do meorg

[bschroeter]

Implemented the meorg-transfer subcommand.

I note that there are no real tests for the meorg components of benchcab, so here are the outputs from these efforts after having run the vanilla bench_example with the following config:

realisations:
  - repo:
      git:
        branch: main
    meorg_output_name: True
    name: 123-test

modules: [
  intel-compiler/2021.1.1,
  netcdf/4.7.4,
  openmpi/4.1.0
]

fluxsite:
  pbs:
    storage: [scratch/tm70]

Note, scratch/tm70 was added because that is where I have pixi installed for development.

Stdout (after successful benchcab run on bench_example with no upload):

(benchcab-dev) (base) [REDACTED@gadi-login-07 bench_example]$ benchcab meorg-transfer
2026-02-25 11:52:16,587 - DEBUG - benchcab.benchcab.py:466 - Checking task completion
2026-02-25 11:52:16,724 - DEBUG - benchcab.benchcab.py:469 - 168/168 completed.
2026-02-25 11:52:16,724 - INFO - benchcab.benchcab.py:477 - Submitting job for meorg transfer
2026-02-25 11:52:16,724 - DEBUG - meorg.meorg.py:50 - Inferring meorg bin from /scratch/tm70/REDACTED/pixi_cache/envs/benchcab-dev-10170176265764084219/envs/default/bin/benchcab
2026-02-25 11:52:16,725 - DEBUG - meorg.meorg.py:55 - meorg_bin = /scratch/tm70/REDACTED/pixi_cache/envs/benchcab-dev-10170176265764084219/envs/default/bin/meorg
2026-02-25 11:52:16,726 - INFO - meorg.meorg.py:86 - Uploading outputs to modelevaluation.org
2026-02-25 11:52:16,960 - INFO - meorg.meorg.py:121 - Upload job submitted: 161549238.gadi-pbs

PBS:

PBS Job Id: 161549238.gadi-pbs
Job Name:   meorg_jobscript_WGGXACAG.j2
Execution terminated
Exit_status=0
resources_used.cpupercent=10
resources_used.cput=00:00:38
resources_used.jobfs=0b
resources_used.mem=7753360kb
resources_used.ncpus=1
resources_used.vmem=7753360kb
resources_used.walltime=00:10:54

Outputs uploaded to: https://modelevaluation.org/modelOutput/display/kWaGuDaP2qHpknpF9

In addressing this issue, there were problems identified with the docs. These have been raised in #343.

Feel free to ask any questions.

[codecov]

Codecov Report

❌ Patch coverage is 17.64706% with 14 lines in your changes missing coverage. Please review.
✅ Project coverage is 68.83%. Comparing base (8e0d58f) to head (874ae98).
⚠️ Report is 20 commits behind head on main.

Files with missing lines	Patch %	Lines
src/benchcab/benchcab.py	6.66%	14 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #344      +/-   ##
==========================================
+ Coverage   68.28%   68.83%   +0.55%     
==========================================
  Files          21       21              
  Lines        1157     1232      +75     
==========================================
+ Hits          790      848      +58     
- Misses        367      384      +17     

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[SeanBryan51]

Thanks Ben. This LGTM!