8000 Apply code style rules to pipelines by emolter · Pull Request #9144 · spacetelescope/jwst · GitHub
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Apply code style rules to pipelines #9144

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Merged
merged 12 commits into from
Feb 14, 2025
Merged

Apply code style rules to pipelines #9144

merged 12 commits into from
Feb 14, 2025

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emolter
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@emolter emolter commented Feb 5, 2025 •
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Partially Resolves JP-3860

This PR applies code style and documentation fixes to the pipeline/ submodule.

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#>.stpi 8000 pe.rst
  • changes/<PR#>.datamodels.rst
  • changes/<PR#>.scripts.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

@emolter
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emolter commented Feb 5, 2025 •
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regression tests started here https://github.com/spacetelescope/RegressionTests/actions/runs/13163158711

edit: all passing except the ones also failing on main

@emolter emolter added this to the Build 11.3 milestone Feb 5, 2025
@emolter emolter requested review from melanieclarke, tapastro, jemorrison, kmacdonald-stsci, stscirij and penaguerrero February 5, 2025 17:50
@codecov Codecov
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codecov bot commented Feb 5, 2025 •
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Codecov Report

Attention: Patch coverage is 33.95225% with 249 lines in your changes missing coverage. Please review.

Project coverage is 73.67%. Comparing base (6f80991) to head (553910c).
Report is 751 commits behind head on main.

Files with missing lines Patch % Lines
jwst/pipeline/calwebb_detector1.py 7.84% 47 Missing ⚠️
jwst/pipeline/calwebb_spec2.py 54.00% 46 Missing ⚠️
jwst/pipeline/calwebb_spec3.py 13.95% 37 Missing ⚠️
jwst/pipeline/calwebb_ami3.py 14.28% 24 Missing ⚠️
jwst/pipeline/calwebb_coron3.py 7.69% 24 Missing ⚠️
jwst/pipeline/calwebb_dark.py 11.11% 24 Missing ⚠️
jwst/pipeline/calwebb_tso3.py 20.83% 19 Missing ⚠️
jwst/pipeline/calwebb_guider.py 23.07% 10 Missing ⚠️
jwst/pipeline/calwebb_image3.py 61.90% 8 Missing ⚠️
jwst/pipeline/calwebb_image2.py 81.57% 7 Missing ⚠️
... and 1 more
Additional details and impacted files 
@@            Coverage Diff             @@
##             main    #9144      +/-   ##
==========================================
- Coverage   73.67%   73.67%   -0.01%     
==========================================
  Files         372      372              
  Lines       37089    37083       -6     
==========================================
- Hits        27327    27321       -6     
  Misses       9762     9762

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

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  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

@stscijgbot-jp stscijgbot-jp mentioned this pull request Feb 5, 2025
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@emolter emolter marked this pull request as ready for review February 5, 2025 23:56
@emolter emolter requested review from a team as code owners February 5, 2025 23:56
melanieclarke
melanieclarke reviewed Feb 6, 2025
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Looks good, just a couple minor requests.

@emolter
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emolter commented Feb 6, 2025 •
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All suggested fixes are in 0f47e5f

restarted the regression tests just in case the hasattr change messed something up (though I doubt it)

https://github.com/spacetelescope/RegressionTests/actions/runs/13163158711

@melanieclarke
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Looks good, thanks! I'll leave this one open for a bit in case anyone else wants to review.

kmacdonald-stsci
kmacdonald-stsci approved these changes Feb 12, 2025
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jwst/pipeline/calwebb_spec2.py
"""
Calibrate WFSS & Grism data.
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I recommend editing these three lines to read:

Apply flat_field to calibrate WFSS and Grism data.

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The intent of the "extended description" appears to be that it clarifies how grism processing differs from other modes. I don't think the proposed edit retains that. Instead, I've expanded the extended description to explicitly state "this differs from other modes because..."

let me know if it looks ok to you: 74df406

tapastro
tapastro approved these changes Feb 14, 2025
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Apart from a typo, looks good to me.

jwst/pipeline/calwebb_spec2.py Outdated
"""
Calibrate WFSS & Grism data.

This pipeline differs from other spectrscopic modes because
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Typo -> spectroscopic

@emolter emolter enabled auto-merge (squash) February 14, 2025 16:20
@emolter emolter merged commit deabb3d into spacetelescope:main Feb 14, 2025
29 of 30 checks passed
@emolter emolter deleted the JP-3860-pipeline branch May 1, 2025 16:04
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Reviewers

@melanieclarke melanieclarke melanieclarke left review comments

@tapastro tapastro tapastro approved these changes

@kmacdonald-stsci kmacdonald-stsci kmacdonald-stsci approved these changes

@jemorrison jemorrison Awaiting requested review from jemorrison

@stscirij stscirij Awaiting requested review from stscirij

@penaguerrero penaguerrero Awaiting requested review from penaguerrero

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ami3 pipeline coron3 pipeline detector1 FGS image2 pipeline image3 pipeline no-changelog-entry-needed pipeline spec2 pipeline spec3 pipeline testing tso3 pipeline
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