Updates for photutils 3+ deprecations

[larrybradley]

Resolves JP-nnnn

This PR makes updates for renamed/deprecated columns and arguments in photutils 3+. This will prevent new deprecation warnings in devdeps tests.

Tasks

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  • update or add relevant tests
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  • start a regression test and include a link to the running job (click here for instructions)
    • Do truth files need to be updated ("okified")?
      • after the reviewer has approved these changes, run okify_regtests to update the truth files
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[codecov]

Codecov Report

❌ Patch coverage is 75.00000% with 10 lines in your changes missing coverage. Please review.
✅ Project coverage is 85.76%. Comparing base (d10b662) to head (1cdece2).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
jwst/tweakreg/tweakreg_catalog.py	73.68%	5 Missing ⚠️
jwst/extract_1d/ifu.py	40.00%	3 Missing ⚠️
jwst/source_catalog/source_catalog.py	75.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main   #10408      +/-   ##
==========================================
- Coverage   85.77%   85.76%   -0.01%     
==========================================
  Files         372      372              
  Lines       40032    40047      +15     
==========================================
+ Hits        34336    34348      +12     
- Misses       5696     5699       +3     

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[mcara]

What is kind of concerning or at least needs discussion is that catalog columns keep changing over time. So a PR like this is needed to modify tweakreg step to recognize the new column names. Instead, shouldn't the pipeline be stable and create catalogs with the same column names? That is, shouldn't the change be made in the source finding part of the step so that catalogs created by the pipeline are not changed?

Also, IMO, it would have been useful if the version of the pipeline and photutils (and maybe astropy) be written to the catalog in some meta if possible. It seems to me this is more important than the installed version of the photutils package.

What will happen (how will this work) if I have the old version of the pipeline and photutils installed and a collaborator uses the new version and sends me the catalog files? If our catalog formats keep changing, there has to be a way for end-users to figure out how they were created and what software is needed to read them.

[larrybradley]

The jwst tweakreg and catalog output column names are unchanged. The photutils column names are changed, but they are gracefully deprecated. Both the old and new photutils column names continue to work, but the old names give a DeprecationWarning. To ease the transition, there will be a long deprecation period (at least until 4.0 in 2027) with plenty of time to adjust.

[melanieclarke]

Regtests with current dependencies:
https://github.com/spacetelescope/RegressionTests/actions/runs/24084390238
All passing.

Regtests with devdeps:
https://github.com/spacetelescope/RegressionTests/actions/runs/24084426765

There are some errors related to centroid columns, for IFU processing, looks like from this line at a minimum:

jwst/extract_1d/ifu.py:662: in extract_ifu
    x_center, y_center = sources[indx]["xcentroid"], sources[indx]["ycentroid"]

@larrybradley - can you please take a look at photutils usage in the extract_1d step?

[larrybradley]

Thanks, @melanieclarke. Indeed, I missed those in ifu.py, but they are fixed now.

The devdeps regtests don't show any remaining failures due to photutils 3+ renamed deprecations. The orientation column differences will need to be okified -- the angles are now wrapped [0, 360).

[melanieclarke]

Looks good to me! Thanks for the future-proofing.