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kevin218 / Eureka

Eureka! is a data reduction and analysis pipeline intended for time-series observations with JWST.
https://eurekadocs.readthedocs.io/
MIT License
60 stars 47 forks source link

Upgrading to `jwst==1.14.0` and `Python>=3.10`, and bug fixes #640

Closed taylorbell57 closed 6 months ago

taylorbell57 commented 6 months ago

This gives us access to the EMI correction step for MIRI data in Stage 1 (introduced in jwst v1.13.4) but requires us to use Python>=3.10. After initial testing on my end, the change in Python version seems to have no consequences, but someone with an Apple Silicon computer should probably run a check. I've also added an extra testing suite: now the code will be tested with and without the PyMC3 optional install which is important as that option continues to fall behind because of that hard upper-limit on the jwst version caused by theano's deprecation and the resulting numpy upper limit.

I also added bug fixes in a couple places. Fixed an incorrect self-import style used in S1, fixed the chi-squared calculation in the case of no masked points (in which case ~lc.flux.mask just gives True which gets treated as a 1 which in turn gives a deeply negative reduced chi-squared value), and added the ability to continue an emcee chain with a subset of the parameters that had been used before.

codecov[bot] commented 6 months ago

Codecov Report

Attention: Patch coverage is 57.14286% with 3 lines in your changes are missing coverage. Please review.

Project coverage is 58.49%. Comparing base (ee4570c) to head (6629d15).

Files Patch % Lines
src/eureka/S1_detector_processing/s1_process.py 50.00% 2 Missing :warning:
src/eureka/S5_lightcurve_fitting/fitters.py 0.00% 1 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #640 +/- ## ========================================== - Coverage 58.49% 58.49% -0.01% ========================================== Files 101 101 Lines 12638 12646 +8 ========================================== + Hits 7393 7397 +4 - Misses 5245 5249 +4 ```

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taylorbell57 commented 6 months ago

@kevin218, just had to deal with a merge conflict, and now this is good to go again