Remove all (including pipeline) uses of Step.__call__

[braingram]

This PR removes all uses of Step.__call__ to allow it's deprecation and eventual removal in stpipe. jwst already warns if Step.__call__ is used outside of a pipeline but to remove __call__ this PR also changes all pipeline usage to Step.run.

To check that all Step.__call__ uses were found, regression tests were run where Step.__call__ was intentionally broken: https://github.com/spacetelescope/RegressionTests/actions/runs/11713130815 This had one expected failure for test_dunder_call_warning which is (with this PR) the only remaining use of __call__. I tested locally and the pytest.warns should catch both the existing jwst warning and the new stpipe one added in spacetelescope/stpipe#204

Regression tests all pass with this PR: https://github.com/spacetelescope/RegressionTests/actions/runs/11728357498

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 15.52795% with 136 lines in your changes missing coverage. Please review.

Project coverage is 63.68%. Comparing base (8cc92a2) to head (ba195b9).
Report is 572 commits behind head on main.

Files with missing lines	Patch %	Lines
jwst/pipeline/calwebb_spec2.py	27.41%	45 Missing ⚠️
jwst/pipeline/calwebb_detector1.py	0.00%	29 Missing ⚠️
jwst/pipeline/calwebb_dark.py	0.00%	17 Missing ⚠️
jwst/pipeline/calwebb_spec3.py	0.00%	14 Missing ⚠️
...st/master_background/master_background_mos_step.py	0.00%	8 Missing ⚠️
jwst/pipeline/calwebb_coron3.py	0.00%	6 Missing ⚠️
jwst/pipeline/calwebb_tso3.py	0.00%	6 Missing ⚠️
jwst/pipeline/calwebb_image3.py	50.00%	4 Missing ⚠️
jwst/pipeline/calwebb_ami3.py	0.00%	3 Missing ⚠️
jwst/pipeline/calwebb_guider.py	0.00%	3 Missing ⚠️
... and 1 more

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #8945   +/-   ##
=======================================
  Coverage   63.68%   63.68%           
=======================================
  Files         375      375           
  Lines       38691    38691           
=======================================
  Hits        24640    24640           
  Misses      14051    14051           

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[tapastro]

LGTM