JP-3859: Apply code style to clean_flicker_noise and nsclean

[melanieclarke]

Partially addresses JP-3859

Also ignores rule TRY400, which requires log.exception instead of log.error inside an except clause. No need to enforce tracebacks every time we log an error.

Code style updates for clean_flicker_noise and nsclean

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#>.fits_generator.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/13041831981

All passing.

[codecov]

Codecov Report

Attention: Patch coverage is 90.50279% with 17 lines in your changes missing coverage. Please review.

Project coverage is 73.73%. Comparing base (1fa5ca5) to head (d157184).
Report is 6 commits behind head on main.

Files with missing lines	Patch %	Lines
jwst/clean_flicker_noise/lib.py	83.07%	11 Missing ⚠️
jwst/clean_flicker_noise/clean_flicker_noise.py	97.00%	3 Missing ⚠️
jwst/nsclean/nsclean_step.py	25.00%	3 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #9114   +/-   ##
=======================================
  Coverage   73.73%   73.73%           
=======================================
  Files         373      373           
  Lines       37272    37272           
=======================================
  Hits        27482    27482           
  Misses       9790     9790           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[emolter]

Looks great Melanie, just a few very small comments. It looks like the step already had Numpy-style docstrings for the most part

[emolter]

General question: how do you think this process went? To what extent do you feel like the changes improved the readability of the code and/or documentation? Any rules besides TRY400 that you're suspicious of?

[melanieclarke]

General question: how do you think this process went? To what extent do you feel like the changes improved the readability of the code and/or documentation? Any rules besides TRY400 that you're suspicious of?

The process went fine. I ended up cycling between the three command line tools a fair bit -- fixing style, rerunning format, fixing docs, rerunning format, etc.

The one thing I found frustrating was that the formatter didn't let me keep lines at ~88 characters that I felt were more readable that way. It enforced 100 character lines.

But in general I'm very pleased with the changes, and happy to get things cleaned up!

[tapastro]

Looks good!