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fix: add "G_" prefix when exporting model to SBML

Open simas232 opened this issue 3 months ago • 1 comments

Main improvements in this PR:

  • Fix:
    • exportModel now adds the "G_" prefix to gene IDs. It is needed for the genes which begin with numeral chars

I hereby confirm that I have:

  • [x] Selected develop as a target branch

simas232 avatar Mar 14 '24 11:03 simas232

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.

github-actions[bot] avatar Mar 14 '24 11:03 github-actions[bot]