JP-3562: Shower flagging enhancement

[mwregan2]

Resolves JP-3562

Closes spacetelescope/jwst#8333

This PR addresses several effects that lead to inaccurate flagging of showers. These change improve the estimate of the median difference by using all the integrations. It also masks reference pixels to avoid them being used in the convolution used to detect faint emission.

Checklist

• added entry in CHANGES.rst (either in Bug Fixes or Changes to API)
• updated relevant tests
• updated relevant documentation
• updated relevant milestone(s)
• added relevant label(s)

[codecov]

Codecov Report

Attention: Patch coverage is 81.65138% with 20 lines in your changes are missing coverage. Please review.

Project coverage is 84.95%. Comparing base (af5aefb) to head (b87ba51).
Report is 1 commits behind head on main.

Files	Patch %	Lines
tests/test_jump.py	65.85%	14 Missing ⚠️
src/stcal/jump/jump.py	91.17%	6 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #248      +/-   ##
==========================================
- Coverage   85.18%   84.95%   -0.23%     
==========================================
  Files          35       35              
  Lines        6797     6846      +49     
==========================================
+ Hits         5790     5816      +26     
- Misses       1007     1030      +23     

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[hbushouse]

@mwregan2 The description above refers to JP-3560, but that Jira ticket concerns updates to the charge_migration step. Is there another JP ticket that this should refer to?

[hbushouse]

Needs a change log entry, in addition to specific code comments/questions.

[mwregan2]

Howard, It should be JP-3562 Sorry, Mike From: Howard Bushouse ***@***.***> Reply-To: spacetelescope/stcal ***@***.***> Date: Thursday, March 14, 2024 at 1:12 PM To: spacetelescope/stcal ***@***.***> Cc: Michael Regan ***@***.***>, Mention ***@***.***> Subject: Re: [spacetelescope/stcal] Shower flagging enhancement (PR #248) @mwregan2<https://urldefense.com/v3/__https:/github.com/mwregan2__;!!CrWY41Z8OgsX0i-WU-0LuAcUu2o!0klFnl0lH0AfMInlyZIf9LIVL1EnraDg4-ZbAu18eP7GaLZFk9JAnX0b_HGVwlO7z9zlemuL8oDJ-lv-3Ey59hE$> The description above refers to JP-3560, but that Jira ticket concerns updates to the charge_migration step. Is there another JP ticket that this should refer to? — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https:/github.com/spacetelescope/stcal/pull/248*issuecomment-1997945313__;Iw!!CrWY41Z8OgsX0i-WU-0LuAcUu2o!0klFnl0lH0AfMInlyZIf9LIVL1EnraDg4-ZbAu18eP7GaLZFk9JAnX0b_HGVwlO7z9zlemuL8oDJ-lv-yKo4bmw$>, or unsubscribe<https://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/AF6KJLSM2SKCK6IUIWBYUL3YYHK63AVCNFSM6AAAAABEJRSCQWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOJXHE2DKMZRGM__;!!CrWY41Z8OgsX0i-WU-0LuAcUu2o!0klFnl0lH0AfMInlyZIf9LIVL1EnraDg4-ZbAu18eP7GaLZFk9JAnX0b_HGVwlO7z9zlemuL8oDJ-lv-6dy4zg4$>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[mwregan2]

I think I've addressed all the comments.

[hbushouse]

@mwregan2 Several unit tests are failing in the CI test suite. They need fixing.

[hbushouse]

CI tests are all passing now. Code updates look OK to me.