RAVEN 2.9.1

[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
  • avoid an error when running solveLP in parallel and COBRA toolbox is not installed
  • getAllowedBounds returned inconsistent results when running parallelization
  • various changes in relation to solveLP swapping the sign of reported objective function (sol.f), as already announced with RAVEN release 2.7.12
  • ensure that RAVEN provided libSBML binaries are used, by using unique filenames
  • removeMets also considers metNotes field if available
  • setParam error message if incorrect paramType is specified
• feat:
  • checkInstallation reports how RAVEN was installed, as described in the Wiki
• doc:
  • minor changes in formatting of function documentation

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:

 > Installation type                    Advanced (via git)
 > Installing from location             /home/m/actions-runner/_work/RAVEN/RAVEN
 > Checking RAVEN release               2.9.0
   > 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

 > 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 ***

SCIP MEX binary not installed or not functional, some fillGapsLargeTests skipped.
SCIP MEX binary not installed or not functional, some fillGapsSmallTests skipped.
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 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.