Apply code style rules to soss_extract

[emolter]

Partially resolves JP-3860

This PR updates the soss_extract submodule to comply with the new code style rules.

Since soss_extract is nestled inside extract_1d, I had to add some ugly per-file-ignores to .pre-commit-config.yaml and .ruff.toml; these can be removed once the rest of extract_1d is updated to follow the style rules.

As a procedural note, I added a line to the epic labeled soss_extract and assigned it to myself, then removed my name from the assignment list next to extract_1d so someone else could pick up the rest of the step.

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

[emolter]

regression tests https://github.com/spacetelescope/RegressionTests/actions/runs/13204660540

Errors are unrelated and match the FGS guider errors on main.

[codecov]

Codecov Report

Attention: Patch coverage is 61.70732% with 157 lines in your changes missing coverage. Please review.

Project coverage is 73.76%. Comparing base (a4175b4) to head (c8517b9).
Report is 4 commits behind head on main.

Files with missing lines	Patch %	Lines
jwst/extract_1d/soss_extract/soss_extract.py	27.43%	119 Missing ⚠️
jwst/extract_1d/soss_extract/atoca_utils.py	83.50%	16 Missing ⚠️
jwst/extract_1d/soss_extract/pastasoss.py	30.00%	14 Missing ⚠️
jwst/extract_1d/soss_extract/atoca.py	91.22%	5 Missing ⚠️
jwst/extract_1d/soss_extract/soss_boxextract.py	77.77%	2 Missing ⚠️
jwst/extract_1d/soss_extract/soss_syscor.py	80.00%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #9156   +/-   ##
=======================================
  Coverage   73.76%   73.76%           
=======================================
  Files         372      372           
  Lines       37276    37276           
=======================================
  Hits        27498    27498           
  Misses       9778     9778           

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[melanieclarke]

Lots here, thanks for getting it cleaned up. I can take the rest of the extract1d module, when this one is in.

I spotted a few typos and other small things while reading through.

[melanieclarke]

I think these changes are uncontroversial enough we can go ahead and get them merged. We'll follow up on more documentation updates later.