JP-1791: Initial commit of WFSS contam correction step and INS grism library modules

[hbushouse]

These are the code modules from Nor Pirzkal's various grism repos that we need in order to support the WFSS contamination corrections. These modules do the work of creating simulated spectra for sources identified in direct images. These will all need a lot of clean-up and rearranging to get them to work from within the jwst pipeline environment. Just getting them into the repo to start with. Some of them may end up going away eventually. The functions/methods in these modules will be called by a new calwebb_spec2 step that will do decontamination of WFSS spectra.

Resolves JP-1791
Resolves #5503
Resolves JP-1924
Resolves #5750

[sosey]

for background, the essence of a lot of these are already implemented in jwst as part of the 2b spec processing and reference files

[hbushouse]

for background, the essence of a lot of these are already implemented in jwst as part of the 2b spec processing and reference files

Good to know. I assumed that a lot or all of what these routines are doing with grism Config (calibration) info is already in the WCS work that you did for grisms and anything dealing with that kind of stuff will need to be migrated to make use of the WCS objects.

[sosey]

yah, grismconf and the parts of poly we ended up using are in transforms/models

[codecov]

Codecov Report

Merging #5508 (04385a1) into master (6609329) will decrease coverage by 0.64%.
The diff coverage is 15.77%.

@@            Coverage Diff             @@
##           master    #5508      +/-   ##
==========================================
- Coverage   77.81%   77.17%   -0.65%     
==========================================
  Files         399      405       +6     
  Lines       35354    35740     +386     
==========================================
+ Hits        27512    27583      +71     
- Misses       7842     8157     +315     

Flag	Coverage Δ		*Carryforward flag
nightly	77.82% <50.00%> (ø)		Carriedforward from 6609329
unit	56.49% <15.14%> (-0.38%)	⬇️

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

Impacted Files	Coverage Δ
jwst/lib/suffix.py	98.50% <ø> (+2.50%)	⬆️
jwst/pipeline/calwebb_spec2.py	76.74% <0.00%> (-19.32%)	⬇️
jwst/stpipe/integration.py	100.00% <ø> (ø)
jwst/wfss_contam/observations.py	8.88% <8.88%> (ø)
jwst/wfss_contam/disperse.py	11.90% <11.90%> (ø)
jwst/wfss_contam/wfss_contam.py	21.42% <21.42%> (ø)
jwst/wfss_contam/sens1d.py	25.92% <25.92%> (ø)
jwst/wfss_contam/wfss_contam_step.py	47.05% <47.05%> (ø)
jwst/source_catalog/source_catalog_step.py	89.06% <100.00%> (-1.27%)	⬇️
jwst/step.py	100.00% <100.00%> (ø)
... and 9 more

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[hbushouse]

@jdavies-st thanks for the comments. There's a lot of this that will be reorganized, if not completely rewritten, yet and some of it (e.g. grismconf and poly) will go away once I'm done migrating the rest of the code over to getting everything we need from our WCS objects and ref files, rather than the aXe-style config files. I'll try to incorporate your suggestions as I go.

But hey, at least I finally got the Travis build to succeed!

[hbushouse]

Latest large set of commits contains LOTS of cleanup, removal of unused functions, complete code commentary, and new functions for handling flux calibration (actually inverse flux calibration) where needed. Reopening for review and hope to merge soon. This version has all of the basic mechanics in place. Still needs a couple of enhancements to handle multiple spectral orders and get the scaling of simulated spectra correct. Those changes will follow in a later PR. Just want to get the basics merged in for now.

[hbushouse]

Complete user docs for the new step and unit tests will also follow in subsequent PRs.

Original C module has been replaced, thus there's no longer an issue with the license.

[nden]

LGTM. I left a couple minor comments inline.