fix: getModelFromHomology

[edkerk]

Main improvements in this PR:

• fix:
  • getModelFromHomology correct handling of OLD_ genes and "or" relationships (solves RAVEN >= v2.7.7 getModelFromHomology generates invalid GPRs from Recon3D #481)
  • find soplex on PATH when MATLAB is opened via Launcher on Mac.

I hereby confirm that I have:

• Tested my code on my own machine
• Followed the development guidelines.
• Selected develop as a target branch
• If needed, asked first in the Gitter chat room about this PR

[github-actions]

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]

getModelFromHomology fix reviewed in #482, soplex fix did not work and is removed again from this PR.