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Updates to minimal_media and GrowthResults #188

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merged 4 commits into from
Jul 24, 2024
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@cdiener cdiener commented Jul 24, 2024

Minimal media workflow

The minimal media workflow is now more flexible and supports all options of the minimal_media base function including:

  • specification of a required community growth rate, taxon growth rates, or any combination
  • support for minimizing the number of media metabolites
  • support for weights allowing to minimize mass uptake, carbon uptake etc.
  • returning the growth results obtained by the media minimization

Growth Results

GrowthResults is now a DataClass and gains some new helpers:

  • combining two GrowthResults via the addition operator (r1 + r2)
  • concatenating many growth results via combine_results
  • converting a CommunitySolution to a growth results object

Other

  • renamed fix_medium to complete_db_medium for consistency with complete_db_medium and to make it more clear what is happening
  • some black style fixes across the code base

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codecov bot commented Jul 24, 2024

Codecov Report

Attention: Patch coverage is 92.00000% with 8 lines in your changes missing coverage. Please review.

Project coverage is 81.08%. Comparing base (62a3e4d) to head (efbdba1).

Files Patch % Lines
micom/workflows/media.py 79.16% 3 Missing and 2 partials ⚠️
micom/workflows/results.py 95.23% 2 Missing and 1 partial ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #188      +/-   ##
==========================================
+ Coverage   80.59%   81.08%   +0.49%     
==========================================
  Files          37       38       +1     
  Lines        2159     2221      +62     
  Branches      451      461      +10     
==========================================
+ Hits         1740     1801      +61     
  Misses        285      285              
- Partials      134      135       +1     

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@cdiener cdiener merged commit 9ee0668 into main Jul 24, 2024
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