fix: parsing grRules; addMets and addRxns; importModel annotations; replaceMets and changeGrRules options

[edkerk]

Main improvements in this PR:

• fix:
  • addMets if metNames and not mets identifiers are given
  • addRxns when adding empty subSystems if the model uses cell arrays of cells for subSystems
  • importModel properly parsing of annotations if identifiers.org/name:value is used instead of identifiers.org/name/value
• features:
  • changeGrRules can change the same grRule for multiple reactions simultaneously
  • replaceMets can use metabolite identifiers instead of metabolite names
• refactor:
  • use getGenesFromGrRules in checkModelStruct, changeGrRules and importModel, to correctly split and/or relationships
• documentation:
  • checkRxn clarify what the output represents (solves In checkRxn, output arrays canMake and canConsume are mixed #572)

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               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
   > Import YAML format                 Pass
   > Export YAML 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 ***

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.