JP-3900: Tests, clean up, and code style for residual_fringe

[melanieclarke]

Resolves JP-3900

Add test coverage for residual_fringe and update code style to new standards. Also, increase the minimum pin for BayesicFitting to make sure it's compatible with numpy 2.

While writing unit tests, I noticed some minor bugs, inefficiencies, and unused code, so I cleaned these out as well. None of these changes are likely to have any impact on the user -- this is just a maintainability improvement.

The truth files for the new regression test were generated with the code on the main branch, to make sure this PR does not introduce any regresssions.

Tasks

• request a review from someone specific, to avoid making the maintainers review every PR
• add a build milestone, i.e. Build 11.3 (use the latest build if not sure)
• Does this PR change user-facing code / API? (if not, label with no-changelog-entry-needed)
  • write news fragment(s) in changes/: echo "changed something" > changes/<PR#>.<changetype>.rst (see below for change types)
  • update or add relevant tests
  • update relevant docstrings and / or docs/ page
  • 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
• if a JIRA ticket exists, make sure it is resolved properly

news fragment change types...

• changes/<PR#>.general.rst: infrastructure or miscellaneous change
• changes/<PR#>.docs.rst
• changes/<PR#>.stpipe.rst
• changes/<PR#>.datamodels.rst
• changes/<PR#>.scripts.rst
• changes/<PR#>.set_telescope_pointing.rst
• changes/<PR#>.pipeline.rst

stage 1

• changes/<PR#>.group_scale.rst
• changes/<PR#>.dq_init.rst
• changes/<PR#>.emicorr.rst
• changes/<PR#>.saturation.rst
• changes/<PR#>.ipc.rst
• changes/<PR#>.firstframe.rst
• changes/<PR#>.lastframe.rst
• changes/<PR#>.reset.rst
• changes/<PR#>.superbias.rst
• changes/<PR#>.refpix.rst
• changes/<PR#>.linearity.rst
• changes/<PR#>.rscd.rst
• changes/<PR#>.persistence.rst
• changes/<PR#>.dark_current.rst
• changes/<PR#>.charge_migration.rst
• changes/<PR#>.jump.rst
• changes/<PR#>.clean_flicker_noise.rst
• changes/<PR#>.ramp_fitting.rst
• changes/<PR#>.gain_scale.rst

stage 2

• changes/<PR#>.assign_wcs.rst
• changes/<PR#>.badpix_selfcal.rst
• changes/<PR#>.msaflagopen.rst
• changes/<PR#>.nsclean.rst
• changes/<PR#>.imprint.rst
• changes/<PR#>.background.rst
• changes/<PR#>.extract_2d.rst
• changes/<PR#>.master_background.rst
• changes/<PR#>.wavecorr.rst
• changes/<PR#>.srctype.rst
• changes/<PR#>.straylight.rst
• changes/<PR#>.wfss_contam.rst
• changes/<PR#>.flatfield.rst
• changes/<PR#>.fringe.rst
• changes/<PR#>.pathloss.rst
• changes/<PR#>.barshadow.rst
• changes/<PR#>.photom.rst
• changes/<PR#>.pixel_replace.rst
• changes/<PR#>.resample_spec.rst
• changes/<PR#>.residual_fringe.rst
• changes/<PR#>.cube_build.rst
• changes/<PR#>.extract_1d.rst
• changes/<PR#>.resample.rst

stage 3

• changes/<PR#>.assign_mtwcs.rst
• changes/<PR#>.mrs_imatch.rst
• changes/<PR#>.tweakreg.rst
• changes/<PR#>.skymatch.rst
• changes/<PR#>.exp_to_source.rst
• changes/<PR#>.outlier_detection.rst
• changes/<PR#>.tso_photometry.rst
• changes/<PR#>.stack_refs.rst
• changes/<PR#>.align_refs.rst
• changes/<PR#>.klip.rst
• changes/<PR#>.spectral_leak.rst
• changes/<PR#>.source_catalog.rst
• changes/<PR#>.combine_1d.rst
• changes/<PR#>.ami.rst

other

• changes/<PR#>.wfs_combine.rst
• changes/<PR#>.white_light.rst
• changes/<PR#>.cube_skymatch.rst
• changes/<PR#>.engdb_tools.rst
• changes/<PR#>.guider_cds.rst

[melanieclarke]

Regression tests here:
https://github.com/spacetelescope/RegressionTests/actions/runs/13662806122

No failures, including the new test, checked against truth files from main.

[codecov]

Codecov Report

Attention: Patch coverage is 96.87500% with 9 lines in your changes missing coverage. Please review.

Project coverage is 75.30%. Comparing base (e2f4801) to head (c018352).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
jwst/residual_fringe/utils.py	89.70%	7 Missing ⚠️
jwst/residual_fringe/residual_fringe.py	98.87%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #9242      +/-   ##
==========================================
+ Coverage   73.67%   75.30%   +1.62%     
==========================================
  Files         369      369              
  Lines       36407    36326      -81     
==========================================
+ Hits        26824    27356     +532     
+ Misses       9583     8970     -613     

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[melanieclarke]

FYI @drlaw1558 - while implementing tests for residual_fringe, I noticed some TODOs in the code, to remove the contrast and quality calculations and output table. I think they were leftover from some of your work on residual fringe correction. I went ahead and removed the unused code here.

[emolter]

Looks much cleaner Melanie, thanks for this! I added a few small comments.

[melanieclarke]

Thanks for reviewing @emolter! I'll get those fixes in shortly.

[drlaw1558]

FYI @drlaw1558 - while implementing tests for residual_fringe, I noticed some TODOs in the code, to remove the contrast and quality calculations and output table. I think they were leftover from some of your work on residual fringe correction. I went ahead and removed the unused code here.

Thanks- given its heritage some of this code is pretty convoluted.

[melanieclarke]

Thanks- given its heritage some of this code is pretty convoluted.

Yes, it looks like it could use a more general assessment and refactor. In particular, it would be nice to see if we can either replace or reimplement the BayesicFitting dependency with something less fragile.