JP-3769: Add code style F, E, W rules

[emolter]

Partially resolves JP-3769

Closes #

This PR adds basic code style rules to the repository using ruff. In particular, the "F", "E", and "W" rules are the same as those in default flake8. No changes to the pre-commit workflow are necessary, as it is already set up to do a style check with ruff, and it reads pyproject.toml to figure out which rules to use. See e.g. the CI run for this commit to verify that is the case.

I decided to blanket-ignore Jupyter notebooks because they lack any tests, but this could be revisited in the future.

Additional rules should be added in the future but it made sense to split them up in order to keep the number of changes tractable on each PR.

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

[codecov]

Codecov Report

Attention: Patch coverage is 56.25000% with 42 lines in your changes missing coverage. Please review.

Project coverage is 76.91%. Comparing base (24cfbcb) to head (2525dfc).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
jwst/ami/mask_definition_ami.py	66.66%	10 Missing ⚠️
jwst/fits_generator/input_file_types.py	0.00%	7 Missing ⚠️
jwst/ami/oifits.py	37.50%	5 Missing ⚠️
jwst/ami/ami_analyze_step.py	0.00%	4 Missing ⚠️
jwst/fits_generator/create_data.py	0.00%	4 Missing ⚠️
jwst/cube_build/ifu_cube.py	60.00%	2 Missing ⚠️
jwst/extract_1d/soss_extract/pastasoss.py	0.00%	2 Missing ⚠️
jwst/fits_generator/main.py	0.00%	2 Missing ⚠️
jwst/associations/lib/rules_level2_base.py	0.00%	1 Missing ⚠️
jwst/associations/lib/rules_level3_base.py	0.00%	1 Missing ⚠️
... and 4 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #9076      +/-   ##
==========================================
- Coverage   76.92%   76.91%   -0.01%     
==========================================
  Files         498      498              
  Lines       45810    45800      -10     
==========================================
- Hits        35240    35229      -11     
- Misses      10570    10571       +1     

Flag	Coverage Δ		*Carryforward flag
nightly	77.39% <ø> (+0.01%)	⬆️	Carriedforward from 9e46aa8

*This pull request uses carry forward flags. Click here to find out more.

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[emolter]

regression tests started https://github.com/spacetelescope/RegressionTests/actions/runs/12791535797

[stscirij]

I looked at the FITS generator changes, and they look good to me

[melanieclarke]

These changes all look quite benign to me. I'd suggest a slightly broader exception for the os.remove catches, but since that change is in the fits_generator, it probably isn't too important.

[melanieclarke]

Looks like skymatch needs an update, but otherwise I think this looks ready to go. Did you want to wait for more reviews for the association code? The changes don't look at all controversial to me.

[emolter]

Looks like skymatch needs an update, but otherwise I think this looks ready to go. Did you want to wait for more reviews for the association code? The changes don't look at all controversial to me.

Thanks, the skymatch changes just got merged so I missed them. Fixed now. No, I don't think it's necessary to wait for the review of the ASN stuff if you and I and the test suite all think it looks fine.

[melanieclarke]

Thanks for taking this on!