Alternate Stage 3 Inputs

[AarynnCarter]

Pull request to allow for non-Eureka! inputs to Stage 4.

• [x] Remove saving of MetaSave.dat file and allocate values to SpecData.h5 file for Stage 3
• [x] Enable Stage 4 to read information from Stage 3 SpecData.h5 file
• [x] Write notebook tutorial for formatting some generic data in the Eureka! SpecData format.
• [x] Get notebook uploaded to documentation
• [ ] Check things are working for photometric data
• [ ] Develop default conversion functions for other pipelines
• [ ] Add documentation on supported pipelines.
• [ ] Stretch goal: Tutorial on how to create a built-in conversion function

This PR resolves part of #404

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 69.04762% with 26 lines in your changes missing coverage. Please review.

Project coverage is 54.28%. Comparing base (a344dbe) to head (ab7a32a). Report is 3 commits behind head on main.

Files	Patch %	Lines
src/eureka/S4_generate_lightcurves/s4_genLC.py	23.80%	16 Missing :warning:
src/eureka/lib/manageevent.py	77.77%	8 Missing :warning:
src/eureka/S3_data_reduction/s3_reduce.py	75.00%	1 Missing :warning:
src/eureka/lib/util.py	95.45%	1 Missing :warning:

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #603      +/-   ##
==========================================
- Coverage   54.29%   54.28%   -0.01%     
==========================================
  Files         101      101              
  Lines       12713    12779      +66     
==========================================
+ Hits         6902     6937      +35     
- Misses       5811     5842      +31     

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

[AarynnCarter]

@kevin218 , @taylorbell57 Okay I made some tweaks based on the comments. Sorry if I couldn't get absolutely everything done, I think we at least have a good foundation to build from for more specific custom data inputs and / or changes to the tutorial. I don't think I'll have a chance to put more work into this, so if there's any more tweaks you'd like to make, it would probably be best to checkout my branch and incorporate them directly - I'll be sure to leave it as it currently is! 😄

[kevin218]

@taylorbell57 Do you also want to review changes to this PR before merging into main?

[taylorbell57]

@taylorbell57 Do you also want to review changes to this PR before merging into main?

Yes please, I'll likely do so this weekend or on Monday

[taylorbell57]

I know you're busy right now @AarynnCarter, so I'll try to address my own comments in the next week or so

[AarynnCarter]

Thanks @taylorbell57, sorry to drop the PR on you not quite finished!

[taylorbell57]

Alright, I've fixed most of the known issues with the PR. I still need to review the new tutorial and potentially make some changes to the S4 checks (depending on whether this PR gets merged after or before PR #632).

[taylorbell57]

@AarynnCarter, I fixed some very minor typos in your excellent tutorial, but there was also an error in how you setup the photometry SpecData.h5 file. To be sure that Stage 4 functions properly, the wave_1d array must still be defined, otherwise integrations with ExoTiC-LD and some of the Eureka! code is going to break.

I believe my implemented change should work well, but I need you to re-run the notebook to update all the notebook outputs; hopefully this should take only ~1 minute of your time. It's possible that I should've done wave_1d = np.array([2.1,]) instead of wave_1d = 2.1 - if you get an error message, then try adjusting the code to that.

[AarynnCarter]

@taylorbell57 No worries, I'll aim to update things by the end of next week!

[AarynnCarter]

@taylorbell57 Okay, all done! You were right about it needing to be cast as a numpy array. There was also a typo I fixed in the allocation of the x value.