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fix: ravenCobraWrapper variations on cobra fields #522

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merged 2 commits into from
Feb 14, 2024

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@edkerk edkerk commented Feb 13, 2024

Main improvements in this PR:

  • Fixes:
    • ravenCobraWrapper properly makes comps and compNames fields when lacking in COBRA model
    • writeYAMLmodel can deal with mixture of nested and not-nested cell arrays of subsystems (as COBRA models can have)

I hereby confirm that I have:

  • Selected develop as a target branch

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github-actions bot commented Feb 13, 2024

This PR has been automatically tested with GH Actions. Here is the output of the tests:

 > Installing from location             /home/m/actions-runner/_work/RAVEN/RAVEN
> Checking RAVEN release DEVELOPMENT
> Checking MATLAB release 2020b
> Checking system architecture glnxa64
> Set RAVEN in MATLAB path Pass
> Save MATLAB path Pass
> Make binaries executable Pass

> Add Java paths for Excel format Pass
> Checking libSBML version 5.19.0
> Checking model import and export
> Import Excel format Pass
> Export Excel format Pass
> Import SBML format Pass
> Export SBML format Pass

> Checking for LP solvers
> glpk Pass
> gurobi Pass
> scip Fail
> cobra Pass
> Set RAVEN solver gurobi

> Checking BLAST+ Pass
> Checking DIAMOND Pass
> Checking HMMER Pass

> Checking function uniqueness Pass

*** checkInstallation complete ***

Running blastPlusTests
.
Done blastPlusTests

Running cdhitTests
.
Done cdhitTests

Running checkTasksTests
.
Done checkTasksTests

Running diamondTests
.
Done diamondTests

Running fillGapsLargeTests
..
Done fillGapsLargeTests

Running fillGapsSmallTests
...
Done fillGapsSmallTests

Running hmmerTests
.
Done hmmerTests

Running importExportTests
....
Done importExportTests

Running mafftTests
.
Done mafftTests

Running miriamTests
.
Done miriamTests

Running modelAbilitiesTests
........
Done modelAbilitiesTests

Running modelConversionTests
.
Done modelConversionTests

Running modelCurationTests
.......... ........
Done modelCurationTests

Running modelSortingTests
..
Done modelSortingTests

Running solverTests
..
Error occurred in solverTests/testSCIP and it did not run to completion.
---------
Error ID:
---------
''
--------------
Error Details:
--------------
Error using solverTests>testSCIP (line 80)
SCIP MEX binary not installed or not functional, test skipped
..
Done solverTests

Running tinitTests
..........
Done tinitTests

Failure Summary:

Name Failed Incomplete Reason(s)
=====================================================
solverTests/testSCIP X X Errored.

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

@edkerk edkerk linked an issue Feb 13, 2024 that may be closed by this pull request
@edkerk edkerk merged commit 404e34c into develop Feb 14, 2024
1 check passed
@edkerk edkerk deleted the fix/ravenCobraWrapper branch February 14, 2024 20:38
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Unrecognized field name "compNames" with ravenCobraWrapper error
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