JP-3728: Deprecate Step.__call__

[braingram]

This PR adds a warning to Step.__call__ uses to target end-users that might use this expecting the step to use reference files.

Note that Step.__call__ is used in pipelines so the warning will only appear if Step.__call__ is used outside a pipeline (it's used on a step that doesn't have a "parent").

If Step.__call__ is removed, some decision will need to be made about what to do for pipeline uses of Step.__call__.

Regression tests show only failures that exist on main:
https://plwishmaster.stsci.edu:8081/job/RT/job/JWST-Developers-Pull-Requests/1694/
and do not show the new warning (so there is no use of Step.__call__ (outside of a pipeline) in jwst.

Resolves JP-3728

Closes #8748

This PR addresses ...

Checklist for PR authors (skip items if you don't have permissions or they are not applicable)

• added entry in CHANGES.rst within the relevant release section
• updated or added relevant tests
• updated relevant documentation
• added relevant milestone
• added relevant label(s)
• ran regression tests, post a link to the Jenkins job below.
  How to run regression tests on a PR
• All comments are resolved
• Make sure the JIRA ticket is resolved properly

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 61.86%. Comparing base (eab0532) to head (758fd97).
Report is 2 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #8761   +/-   ##
=======================================
  Coverage   61.86%   61.86%           
=======================================
  Files         377      377           
  Lines       38911    38917    +6     
=======================================
+ Hits        24071    24077    +6     
  Misses      14840    14840           

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

[braingram]

Requested many reviewers as this will be discussed at the branch meeting tomorrow.

[melanieclarke]

As a self-contained change, this looks good to me. Testing locally, the warning is emitted when __call__ is used, and not when .call or .run is directly used. I don't see it from substeps when running a pipeline.

I think more work is needed to address the differences between .call and .run, but that's outside the scope of the request in JP-3728. I don't see anything wrong with deprecating __call__ in the meantime.

The change log edit needs to be converted to a towncrier fragment, and I'd like to wait to see if anyone else has opinions, so I'll hold off on approval for now.

[tapastro]

I agree with Melanie that this change should do no harm and inform users about their use of a method we don't necessarily recommend. Just need the updates to changelog -> fragment, and I'll approve and merge.

[braingram]

Thanks @melanieclarke and @tapastro for taking a look. I updated the changelog to use towncrier.