RAVEN 2.10.4

[edkerk]

Main improvements in this PR:

• fix:
  • importModel prevent colon operands warning
  • importModel parsing of model notes in MATLAB R2025a (solves importModel fails to parse SBML notes on MATLAB 2025a #586)
  • randomSampling uses real reaction bounds and not the model.rev field to identify reversible reactions, and filters from goodRxns those reactions that cannot carry flux
• feature:
  • setParam checks if the new LB and UB values are not invalid
  • randomSampling recognizes if a model is a GECKO v3+ ecModel, in which case the usage_prot reactions are not sampled
• refactor:
  • importModel parsing of LB and UB values, minor speed improvements
• documentation:
  • remove traces of getMILPParams, which has been obsolete since 2.7.10

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 as descriped here.

[github-actions]

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

 > Installation type                    Advanced (via git)
 > Installing from location             /home/m/actions-runner/_work/RAVEN/RAVEN
 > Checking RAVEN release               2.10.3
   > You are running the latest RAVEN release
 > 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             5.20.2
 > Checking model import and export
   > Import Excel format                Pass
   > Export Excel format                Pass
   > Import SBML format                 Pass
   > Export SBML format                 Pass
   > Import YAML format                 Pass
   > Export YAML format                 Pass

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

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

 > Checking function uniqueness         Pass

*** checkInstallation complete ***

Gurobi not installed or not functional, some fillGapsLargeTests skipped.
SCIP MEX binary not installed or not functional, some fillGapsLargeTests skipped.
Gurobi not installed or not functional, some fillGapsSmallTests skipped.
SCIP MEX binary not installed or not functional, some fillGapsSmallTests skipped.
No suitable solver (gurobi or scip) was found, ftINIT tests skipped.
Running blastPlusTests
.
Done blastPlusTests

Running cdhitTests
.
Done cdhitTests

Running checkTasksTests
.
Done checkTasksTests

Running diamondTests
.
Done diamondTests

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/testGurobi and it did not run to completion.
    ---------
    Error ID:
    ---------
    ''
    --------------
    Error Details:
    --------------
    Error using solverTests>testGurobi (line 61)
    Gurobi error 10009: License expired 2025-05-03
    Please consult the Gurobi Quick Start Guide for details on setting up a license.
.
Error occurred in solverTests/testSCIP and it did not run to completion.
    ---------
    Error ID:
    ---------
    ''
    --------------
    Error Details:
    --------------
    Error using solverTests>testSCIP (line 77)
    SCIP MEX binary not installed or not functional.
..
Done solverTests

Running tinitTests
.
Done tinitTests

Failure Summary:

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

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