JP-3857 cube build code style changes

[jemorrison]

Helps to Resolve JP-3857

Closes #

This PR addresses updates to cube_build code to conform to the code style changes.

Tasks

• If you have a specific reviewer in mind, tag them.
• add a build milestone, i.e. Build 12.0 (use the latest build if not sure)
• Does this PR change user-facing code / API? (if not, label with no-changelog-entry-needed)
  • write news fragment(s) in changes/: echo "changed something" > changes/<PR#>.<changetype>.rst (see changelog readme for instructions)
  • update or add relevant tests
  • update relevant docstrings and / or docs/ page
  • start a regression test and include a link to the running job ([click here for instructions]
    Regression test passed: https://github.com/spacetelescope/RegressionTests/actions/runs/14668760965

(https://github.com/spacetelescope/RegressionTests/blob/main/docs/running_regression_tests.md))
- [ ] Do truth files need to be updated ("okified")?
- [ ] after the reviewer has approved these changes, run okify_regtests to update the truth files

• if a JIRA ticket exists, make sure it is resolved properly

[codecov]

Codecov Report

Attention: Patch coverage is 87.04846% with 147 lines in your changes missing coverage. Please review.

Project coverage is 75.62%. Comparing base (1ae307b) to head (c33e250).
Report is 740 commits behind head on main.

Files with missing lines	Patch %	Lines
jwst/cube_build/cube_build_step.py	56.92%	56 Missing ⚠️
jwst/cube_build/blot_cube_build.py	3.12%	31 Missing ⚠️
jwst/cube_build/cube_build_io_util.py	80.18%	22 Missing ⚠️
jwst/cube_build/cube_build.py	78.65%	19 Missing ⚠️
jwst/cube_build/instrument_defaults.py	98.77%	8 Missing ⚠️
jwst/cube_build/coord.py	20.00%	4 Missing ⚠️
jwst/cube_build/data_types.py	69.23%	4 Missing ⚠️
jwst/cube_build/file_table.py	97.46%	2 Missing ⚠️
jwst/cube_build/cube_build_wcs_util.py	92.85%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #9347      +/-   ##
==========================================
+ Coverage   75.60%   75.62%   +0.01%     
==========================================
  Files         368      368              
  Lines       36916    36908       -8     
==========================================
+ Hits        27911    27912       +1     
+ Misses       9005     8996       -9     

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[jemorrison]

@melanieclarke take a look at this PR.I am re-running the regression test now and will post the link when they are finished. I have lost momentum on this PR so if you see something in general missing let me know and I can fix it before you do a detailed review

[melanieclarke]

@melanieclarke take a look at this PR.I am re-running the regression test now and will post the link when they are finished. I have lost momentum on this PR so if you see something in general missing let me know and I can fix it before you do a detailed review

Thanks @jemorrison - I glanced through and these look like good changes so far. This module could still use even more unit tests, but we don't need to get them all in now.

[melanieclarke]

There's a lot here - I think we're going to have to iterate a few times to get this ready for merge. I'll start by sending some initial comments from read-through, up to the ifu_cube.py file. More later!

[melanieclarke]

Another round of suggestions/requests - I've now done an initial read-through up to but not including the C code and tests.

[jemorrison]

@melanieclarke Let me take another stab at c code. I think I did not fully clean that code up.

[melanieclarke]

@melanieclarke Let me take another stab at c code. I think I did not fully clean that code up.

Sure, just let me know when you're done and I'll come back around.

[jemorrison]

@melanieclarke When you have time look at the c code: cube_match_sky_driz.c
I can apply similar changes you suggest to that code to the other c code.
Then I will have you look at all the c code. But having an idea of how much detail I should have for this one will be helpful

[melanieclarke]

@jemorrison - I started to look through your updates from yesterday, but it looks like GitHub hid a large chunk of comments from you. Can you please check under the fold from yesterday's round of comments?

I'll start looking at cube_match_sky_driz.c.

[melanieclarke]

Comments for cube_match_sky_driz.c:
In general, this looks like a pretty good level of detail. I think the Python signature and parameter descriptions are the most important part of the docs here. It would be helpful to review them and clean them up a bit - make sure all parameters are listed and in the right order. If you can, listing the Python input types is helpful (e.g. "ndarray of float" is better than "double array").

[melanieclarke]

I found a few more minor things on read-through, but I think we're getting close. The extra comments for the C code are very helpful.

The only significant issue is that there's a missing Exception in the IFU offset file handling code, noted below.

[jemorrison]

@melanieclarke See if the way I modified the exception in cube_build_step.py is ok with you.
I think I got all the changes in. I am going to re-run the regression tests now

[melanieclarke]

Almost there, just a couple more small things that keep getting buried:

1. change log should note that there are new exception names
2. there are still some "shepherds" in instrument_defaults that need to be replaced with Shepard

[melanieclarke]

I think we made it! Can you link to the latest regtest run?

[jemorrison]

@melanieclarke added the link to the latests (today) regression test run - all passing

[melanieclarke]

I approve! Thanks for all your hard work on this one. I think it's a significant improvement in maintainability and documentation for this module.