JP-3593: 2nd group saturation part 2

[drlaw1558]

Ready for review: this addresses JP-3593, flagging cosmic ray saturation in group 2 data in a consistent manner between both IRS2 and non-IRS2 modes using the new use_readpatt keyword. This PR is tied to STCAL PR spacetelescope/stcal#283

Checklist for PR authors (skip items if you don't have permissions or they are not applicable)

• 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
• All comments are resolved
• Make sure the JIRA ticket is resolved properly

[codecov]

Codecov Report

Attention: Patch coverage is 93.33333% with 1 line in your changes missing coverage. Please review.

Project coverage is 61.76%. Comparing base (da9691d) to head (0fd2201).

Files with missing lines	Patch %	Lines
jwst/saturation/saturation_step.py	50.00%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #8731   +/-   ##
=======================================
  Coverage   61.75%   61.76%           
=======================================
  Files         377      377           
  Lines       38750    38764   +14     
=======================================
+ Hits        23931    23943   +12     
- Misses      14819    14821    +2     

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[drlaw1558]

@tapastro Should now be ready for review.

[melanieclarke]

This looks good to me, given that Roman is happy with the corresponding changes in stcal, and given your testing across multiple instrument modes. Thanks for the unit tests and documentation updates!

One small documentation request below, for the new function parameters.

I will run regression tests when the system is free.

[melanieclarke]

Thanks for the update! One last small formatting thing - the type annotation should be the Python type (bool).

I started regression tests here:
https://plwishmaster.stsci.edu:8081/job/RT/job/JWST-Developers-Pull-Requests/1709/

[melanieclarke]

In the regtests, I see a difference for NIRISS rate files, which I think is because the corresponding stcal branch is out of date - the difference looks related to the chargeloss readnoise variance calculation change.

I also see one difference for a NIRSpec rate file, to the DQ plane only. It looks like some pixels that were do not use but not flagged as saturated are now also flagged as saturated. Looking at the image in a local run, it certainly looks like they were saturated, so this is a reasonable change.

I think this is good to go from my perspective, pending the merge of the corresponding stcal PR. @tapastro - can you please coordinate on the stcal side?