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fix: readYAMLmodel always make c-field #508

Merged
merged 5 commits into from
Oct 19, 2023
Merged

fix: readYAMLmodel always make c-field #508

merged 5 commits into from
Oct 19, 2023

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edkerk
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@edkerk edkerk commented Aug 19, 2023

Main improvements in this PR:

  • fix:
    • readYAMLmodel should always make model.c-field, even if no objective function is specified.
    • standardizeGrRules should throw error if no grRules field is found.
  • doc:
    • addRxnsGenesMets more detailed error message if reactions cannot be found.

I hereby confirm that I have:

  • Selected develop as a target branch

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github-actions bot commented Aug 19, 2023

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
Writing problem data to `outpb.lp'...
271 lines were written
> glpk Pass
> gurobi Pass
> soplex 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
..Writing problem data to `outpb.lp'...
271 lines were written

Error occurred in solverTests/testSoplex and it did not run to completion.
---------
Error ID:
---------
''
--------------
Error Details:
--------------
Error using solverTests>testSoplex (line 100)
Solver not working
..
Done solverTests

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

Failure Summary:

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

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

@edkerk edkerk linked an issue Aug 19, 2023 that may be closed by this pull request
1 task
@edkerk edkerk force-pushed the fix/YAML-io_c-field branch from 55cd760 to 2028181 Compare October 18, 2023 07:51
@edkerk edkerk merged commit 8eeb1d3 into develop Oct 19, 2023
1 check passed
@edkerk edkerk deleted the fix/YAML-io_c-field branch October 19, 2023 08:54
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bug: model loaded from YAML has no c-field
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