8000 JP-1793: Standardize wfs_combine Step by tapastro · Pull Request #6376 · spacetelescope/jwst · GitHub
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JP-1793: Standardize wfs_combine Step #6376

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tapastro
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@tapastro tapastro commented Oct 4, 2021

Closes #5511

Resolves JP-1793

Description

This PR addresses issues with the Step/Pipeline identity crisis that calwebb_wfs-image3 - err, wfs_combine - found itself in.

The step now uses datamodels.open() instead of load_as_level3_asn() - this should allow the step to take a ModelContainer as input, though the formatting will need to follow the level 3 associations, i.e. presence of member pairs under products, expnames provided, etc. Documentation might be on the to-do list to make this clear...

The step now follows a more traditional structure for saving results, though this requires an stpipe PR to be merged that allows for Step instances to access the save_model(format=...) parameter.

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  • Tests
  • Documentation
  • Change log
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codecov bot commented Oct 4, 2021

Codecov Report

Merging #6376 (7ae5b09) into master (5d2613b) will increase coverage by 0.04%.
The diff coverage is 100.00%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #6376      +/-   ##
==========================================
+ Coverage   77.60%   77.65%   +0.04%     
==========================================
  Files         408      408              
  Lines       34881    34941      +60     
==========================================
+ Hits        27068    27132      +64     
+ Misses       7813     7809       -4     
Flag Coverage Δ *Carryforward flag
nightly 77.61% <100.00%> (ø) Carriedforward from 5baafd9
unit 56.40% <100.00%> (+0.11%) ⬆️

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

Impacted Files Coverage Δ
jwst/wfs_combine/wfs_combine_step.py 100.00% <100.00%> (ø)
jwst/saturation/saturation.py 97.89% <0.00%> (-2.11%) ⬇️
jwst/associations/lib/product_utils.py 94.73% <0.00%> (-0.10%) ⬇️
jwst/datamodels/make_header.py 91.36% <0.00%> (-0.03%) ⬇️
jwst/timeconversion/time_conversion.py 11.03% <0.00%> (+0.07%) ⬆️
jwst/fits_generator/template.py 17.25% <0.00%> (+0.26%) ⬆️
jwst/associations/lib/process_list.py 74.07% <0.00%> (+0.58%) ⬆️
jwst/associations/asn_edit.py 67.41% <0.00%> (+0.74%) ⬆️
jwst/saturation/saturation_step.py 82.85% <0.00%> (+6.66%) ⬆️

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LGTM

I am presuming the stpipe issue will need to be implemented before this is merged? Has an issue been filed against stpipe and is it linked to jp-1793?

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tapastro commented Oct 5, 2021

LGTM

I am presuming the stpipe issue will need to be implemented before thi 8000 s is merged? Has an issue been filed against stpipe and is it linked to jp-1793?

The stpipe issue does need to be in first, as this uses the new Step.output_use_format parameter.

I've tried to dot my github i's and cross the JIRA t's, but I'm not sure the linking of the stpipe issue to JP-1793 has gone through - I may need another link somewhere? The stpipe issue is here and the PR here

@stscieisenhamer stscieisenhamer self-requested a review October 8, 2021 12:57
@tapastro tapastro merged commit e083b5e into spacetelescope:master Oct 11, 2021
loicalbert pushed a commit to talensgj/jwst that referenced this pull request Nov 5, 2021
* flake8

* name the model not the container

* Allow for ModelContainer as input

* might as well output a ModelContainer instead of a list of models? not sure

* stpipe changed new Step parameter name
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Standardize wfs_combine
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