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GECKO 3.2.3#399

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edkerk merged 2 commits into
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May 9, 2025
Merged

GECKO 3.2.3#399
edkerk merged 2 commits into
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@edkerk edkerk commented Apr 7, 2025 •
edited
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Main improvements in this PR:

  • Fixes:
    • flexibilizeEnzConcs could mix-up new lower bounds of flexibilized proteins.
    • GECKOInstaller correctly identify if existing GECKO version should be updated.
    • getStandardKcat should use enzyme_comp specified in the modelAdapter, and not a hard-coded 'c' (solves Compartment hardcoded in getStandardKcat #400)

Instructions on merging this PR:

  • This PR has develop as target branch, and will be resolved with a squash-merge.
  • This PR has main as target branch, and will be resolved with a merge commit.

@edkerk
fix: flexibilizeEnzConcs mix up flexibilized proteins (#398)
5e2ef53 
* fix: flexibilizeEnzConcs correct lower bounds

* fix. GECKOinstaller correct identify version
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github-actions Bot commented Apr 7, 2025 •
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This PR has been automatically tested with GH Actions. Here is the output of the tests:

 
GECKO version 3.2.2 installed
Running geckoCoreFunctionTests
================================================================================
Error occurred in geckoCoreFunctionTests/testKcats_tc0011 and it did not run to completion.
    ---------
    Error ID:
    ---------
    'gurobi:Error'
    --------------
    Error Details:
    --------------
    Error using gurobi
    Gurobi error 10009: License expired 2025-05-03
    Please consult the Gurobi Quick Start Guide for details on setting up a license.
    
    Error in optimizeProb (line 108)
            resG = gurobi(prob,solverparams);
    
    Error in solveLP (line 104)
    res = optimizeProb(prob,params);
    
    Error in geckoCoreFunctionTests>testKcats_tc0011 (line 470)
        res = solveLP(ecModel,1);
================================================================================
================================================================================
Error occurred in geckoCoreFunctionTests/testProteomcisIntegration_tc0013 and it did not run to completion.
    ---------
    Error ID:
    ---------
    'gurobi:Error'
    --------------
    Error Details:
    --------------
    Error using gurobi
    Gurobi error 10009: License expired 2025-05-03
    Please consult the Gurobi Quick Start Guide for details on setting up a license.
    
    Error in optimizeProb (line 108)
            resG = gurobi(prob,solverparams);
    
    Error in solveLP (line 104)
    res = optimizeProb(prob,params);
    
    Error in flexibilizeEnzConcs (line 97)
    [sol,hs] = solveLP(model);
    
    Error in geckoCoreFunctionTests>testProteomcisIntegration_tc0013 (line 515)
        [~, ecModel, flexEnz] =  evalc("flexibilizeEnzConcs(ecModel, 0.4,[],[],adapter,false)");
================================================================================
Done geckoCoreFunctionTests
__________

Failure Summary:

     Name                                                     Failed  Incomplete  Reason(s)
    ========================================================================================
     geckoCoreFunctionTests/testKcats_tc0011                    X         X       Errored.
    ----------------------------------------------------------------------------------------
     geckoCoreFunctionTests/testProteomcisIntegration_tc0013    X         X       Errored.

Note: In the case of multiple test runs, this post will be edited.

@edkerk edkerk merged commit eadb0f0 into main May 9, 2025
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