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Replace CUE with a logistic expression#767

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jacobcook1995 merged 11 commits intodevelopfrom
feature/improved_cue_model
May 22, 2025
Merged

Replace CUE with a logistic expression#767
jacobcook1995 merged 11 commits intodevelopfrom
feature/improved_cue_model

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Description

This PR replaces the current expression for CUE with a logistic expression. This is mainly so that the CUE can be parameterised to always be between 0 and 1.

@hrlai I've changed the function and constants so that it fits with the new model you suggested here. Once the data science side is sorted/merged you could add the values for the constants here.

Let me know how that goes! (also don't worry about the broken tests, they are mostly downstream stuff, I can fix them once you've made your changes)

Type of change

  • New feature (non-breaking change which adds functionality)
  • Optimization (back-end change that speeds up the code)
  • Bug fix (non-breaking change which fixes an issue)

Key checklist

  • Make sure you've run the pre-commit checks: $ pre-commit run -a
  • All tests pass: $ poetry run pytest

Further checks

  • Code is commented, particularly in hard-to-understand areas
  • Tests added that prove fix is effective or that feature works
  • Relevant documentation reviewed and updated

@jacobcook1995 jacobcook1995 requested a review from hrlai March 5, 2025 10:45
@hrlai hrlai linked an issue Apr 2, 2025 that may be closed by this pull request
@hrlai
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hrlai commented Apr 2, 2025

@jacobcook1995 would you be able to add this citation to Zotero and then the bibliography file so I can cite the new data? Thanks.

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Looks good to me, should be ready to merge once I update the constants and add a reference.

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hrlai commented Apr 4, 2025

cool, I think I've added everything from this side and it is ready for you to take a final look.

@jacobcook1995
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@hrlai looks good! I'll fix the testing and merge it next week

@jacobcook1995 jacobcook1995 marked this pull request as ready for review May 8, 2025 09:05
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codecov-commenter commented May 8, 2025

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 94.79%. Comparing base (af805f4) to head (35bb8c7).
Report is 128 commits behind head on develop.

Additional details and impacted files
@@           Coverage Diff            @@
##           develop     #767   +/-   ##
========================================
  Coverage    94.79%   94.79%           
========================================
  Files           75       75           
  Lines         5591     5592    +1     
========================================
+ Hits          5300     5301    +1     
  Misses         291      291           

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@jacobcook1995 jacobcook1995 merged commit abd205d into develop May 22, 2025
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@jacobcook1995 jacobcook1995 deleted the feature/improved_cue_model branch May 22, 2025 09:23
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Review microbial carbon use efficiency (CUE)

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