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JP-3697: Jump Step Refactor #9039

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Resolves JP-3697

Closes #

This PR refactors the jump step using the refactored jump step interface in STCAL. Due to the simplified interface of the STCAL jump step jump.py and therun_detect_jumps function have been eliminated. All tests based on this function were consolidated into test_jump_step.py.

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

Adding JumpData class to running jump.

Prepping for JumpData class.

Updating import functions.

Removing the dqflags parameter.

The file jump.py is no longer needed, but there is a test suite that still uses the deprectaed run_detect_jumps function directly.

Refactoring out run_detect_jumps in favor of using JumpData.

Refactored jump step.

Updating setting the parameters of the JumpData instance.
…The 'test_detect_jump.py' test suite needs to be integrated into 'test_jump_step.py' and the 'jump.py' needs to be deleted, since it is now unnecessary.
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codecov bot commented Dec 31, 2024

Codecov Report

Attention: Patch coverage is 5.08475% with 56 lines in your changes missing coverage. Please review.

Project coverage is 76.29%. Comparing base (bb62f0c) to head (1c11848).
Report is 9 commits behind head on main.

Files with missing lines Patch % Lines
jwst/jump/jump_step.py 5.08% 56 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main    #9039      +/-   ##
==========================================
- Coverage   76.90%   76.29%   -0.62%     
==========================================
  Files         498      498              
  Lines       45761    46127     +366     
==========================================
  Hits        35194    35194              
- Misses      10567    10933     +366     
Flag Coverage Δ *Carryforward flag
nightly 77.37% <ø> (-0.03%) ⬇️ Carriedforward from bb62f0c

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

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@kmacdonald-stsci
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Here is the regression test run that passed the jump tests.

https://github.com/spacetelescope/RegressionTests/actions/runs/12628208541

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