JP-3102: NIRSpec combined MOS/FS processing

[melanieclarke]

Resolves JP-3102

Closes #7769

Process fixed slits defined in MSA metafiles, alongside standard MOS slits.

Checklist for maintainers

• 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
• Make sure the JIRA ticket is resolved properly

[codecov]

Codecov Report

Attention: Patch coverage is 56.80934% with 111 lines in your changes missing coverage. Please review.

Project coverage is 59.01%. Comparing base (b7e0b10) to head (fe37e37).
Report is 9 commits behind head on master.

❗ Current head fe37e37 differs from pull request most recent head 2bf2875

Please upload reports for the commit 2bf2875 to get more accurate results.

Files	Patch %	Lines
jwst/pipeline/calwebb_spec2.py	5.33%	71 Missing ⚠️
jwst/master_background/nirspec_utils.py	50.00%	13 Missing ⚠️
jwst/nsclean/nsclean.py	0.00%	9 Missing ⚠️
jwst/master_background/expand_to_2d.py	63.63%	8 Missing ⚠️
jwst/wavecorr/wavecorr.py	82.85%	6 Missing ⚠️
jwst/pipeline/calwebb_spec3.py	0.00%	3 Missing ⚠️
jwst/assign_wcs/nirspec.py	98.61%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #8467      +/-   ##
==========================================
+ Coverage   58.02%   59.01%   +0.98%     
==========================================
  Files         388      388              
  Lines       38977    39136     +159     
==========================================
+ Hits        22617    23095     +478     
+ Misses      16360    16041     -319     

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

[melanieclarke]

@hbushouse @hayescr - I think this is ready for an initial code review. I will leave it at draft status because I still need to update documentation, but would appreciate any thoughts you have about the code changes in the meantime.

Also - this PR will have conflicts with #8376. I'll resolve them when that one goes in.

[melanieclarke]

Started regression tests here:
https://plwishmaster.stsci.edu:8081/job/RT/job/JWST-Developers-Pull-Requests/1505/

I expect many changes for NIRSpec MOS tests: the order of slit processing has changed, which rearranges all the extensions in the products. It was previously processing slitlet IDs from an unordered set; it will now process them in the order they appear in the MSA file.

[melanieclarke]

Okay, I've added documentation everywhere I could think of, and I have merged in the wavecorr changes, so I'm going to take this out of draft now.

New regression test run started here:
https://plwishmaster.stsci.edu:8081/job/RT/job/JWST-Developers-Pull-Requests/1511/

Testing locally, I see the changes I expected for test_nirspec_mos_spec2, due to rearranging the slit order. After my last update, I now see no changes for test_nirspec_fs_spec2, except some pixel_replace differences that also appear when testing with master. I see no changes for test_nirspec_fs_spec3 or test_nirspec_mos_spec3.