fix: skip tests if solver is absent & glpk timeout

[edkerk]

Main improvements in this PR:

• Refactor:
  • when running a unit test and a solver is not installed, report the absence of the solver, not the general failing of the test.
• Fix:
  • prevent glpk timeout when running selected large FBA calculations.

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 with a merge commit.

[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             5.20.2
 > 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                     glpk

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

 > Checking function uniqueness         Pass

*** checkInstallation complete ***

Gurobi not installed or cannot be found in MATLAB path, some fillGapsLargeTests skipped.
SCIP MEX binary not installed or not functional, some fillGapsLargeTests skipped.
Gurobi not installed or cannot be found in MATLAB path, some fillGapsLargeTests 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/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/testSCIP    X         X       Errored.

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

[mihai-sysbio]

I'm surprised, the SCIP test should have been skipped but the test still shows it as an error.

[edkerk]

No, that test is not skipped on purpose, so that we can see that SCIP is really not working. But as SCIP is already tested in that test, there is no reason to run other SCIP-based tests.