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Add fill flag - #893

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Ciheim wants to merge 3 commits into
NOAA-GFDL:mainfrom
Ciheim:892.catalogfill
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Add fill flag#893
Ciheim wants to merge 3 commits into
NOAA-GFDL:mainfrom
Ciheim:892.catalogfill

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@Ciheim

@Ciheim Ciheim commented May 14, 2026

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Describe your changes

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Fixes #XXX (replace XXX with the issue number and GitHub will autolink the PR to the issue)

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

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@Ciheim

Ciheim commented May 14, 2026

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Addresses #892

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codecov Bot commented May 14, 2026

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 82.09%. Comparing base (ad94447) to head (27b5365).

Additional details and impacted files
@@           Coverage Diff           @@
##             main     #893   +/-   ##
=======================================
  Coverage   82.09%   82.09%           
=======================================
  Files          67       67           
  Lines        3736     3737    +1     
=======================================
+ Hits         3067     3068    +1     
  Misses        669      669           
Flag Coverage Δ
unittests 82.09% <100.00%> (+<0.01%) ⬆️

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

Files with missing lines Coverage Δ
fre/catalog/frecatalog.py 94.59% <100.00%> (+0.15%) ⬆️

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Comment thread fre/catalog/frecatalog.py
#, help = 'Specify output filename suffix only. e.g. catalog')
@click.option('--config', required = False, type = click.Path(exists = True), nargs = 1,
help = 'Path to your yaml config, Use the config_template in intakebuilder repo')
@click.option('--fill', '-f', default=True, type=bool, help="Fill all empty CSV column values with 'NA'. Defaults to True. Use --fill=False to disable.")

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To negate the fill option, it's more standard to make it a flag and let it be negated with --no-fill than require an value for the fill option --fill=False.

@ceblanton ceblanton left a comment

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This is ready for the same click updates that went into NOAA-GFDL/CatalogBuilder#159.

Also, please update meta.yaml and enviroment.yaml to specify the new catalogbuilder version. I think it's set to 2025.xx now.

@ilaflott

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@Ciheim how do you feel about this PR?

@Ciheim

Ciheim commented Jul 21, 2026

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Thought this one was already merged @ilaflott Thanks for the reminder. It's mostly ready to go. Just one more update and it should be good.

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3 participants