Remove deprecated __call__ method

[melanieclarke]

Resolves JP-3490
Resolves RCAL-nnnn

Remove the deprecated __call__ method from stpipe steps.

Tasks

• update or add relevant tests
• update relevant docstrings and / or docs/ page
• Does this PR change any API used downstream? (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)
  • run regression tests with this branch installed ("git+https://github.com/<fork>/stpipe@<branch>")
    • jwst regression test
    • romancal regression test

news fragment change types...

• changes/<PR#>.feature.rst: new feature
• changes/<PR#>.bugfix.rst: fixes an issue
• changes/<PR#>.doc.rst: documentation change
• changes/<PR#>.removal.rst: deprecation or removal of public API
• changes/<PR#>.misc.rst: infrastructure or miscellaneous change

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 95.34%. Comparing base (0f3e1cf) to head (37c74ed).
⚠️ Report is 30 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #239      +/-   ##
==========================================
+ Coverage   95.32%   95.34%   +0.02%     
==========================================
  Files          37       37              
  Lines        3399     3414      +15     
==========================================
+ Hits         3240     3255      +15     
  Misses        159      159              

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[melanieclarke]

Regtests with this branch + spacetelescope/jwst#9548:
https://github.com/spacetelescope/RegressionTests/actions/runs/15686793575

Regtests are all passing. Downstream CI does not because there is a test that looks for the warning in jwst on main.
The python 3.13 tests are not passing because of the logging issue reported in spacetelescope/jwst#9544

[melanieclarke]

Romancal regtests:
https://github.com/spacetelescope/RegressionTests/actions/runs/15690780947

[tapastro]

LGTM

[tapastro]

Flagging this for Roman attention: @braingram

Discussed this with Eddie, who signed off but was unsure if romancal/RRN would be impacted.

[braingram]

LGTM. __call__ was deprecated in romancal 0.18.0 so any users should have been seeing warnings.

[schlafly]

FWIW, I don't understand the failure of the romancal unit tests, but it seems more like a configuration issue with how they're being called than it does like anything related to this PR.

[melanieclarke]

I don't have permission to merge this because of the failures in the required CI tests. @zacharyburnett - looks like you're the only stpipe maintainer?