RAVEN 2.9.0

[edkerk]

Main improvements in this PR:

• fix:
  • simplifyModel with irreversible backwards-only reactions (solves bug: simplifyModel with irreversible backwards-only reactions #529)
  • writeYAMLmodel do not write lines with empty entries (e.g. reactions without subsystems)
  • getModelFromKEGG includes model.annotation.defaultLB and model.annotation.defaultUB fields
  • getGenesFromGrRules can handle genes with '|'
  • getModelFromHomology remove geneFrom field (solves Error in getModelFromHomology function #533)
  • getMinNrFluxes reduce default verbosity
  • writeYAMLmodel allow empty id and name fields, in line with https://github.com/SysBioChalmers/RAVEN/wiki/RAVEN-Model-Structure
  • ravenCobraWrapper prefers to use grRules in COBRA models if present (solves GECKO issue #367)
  • optimizeProb will throw error when trying to solve MILP with glpk (also if glpk is set via cobra)
  • writeYAMLmodel will throw an informative error if it cannot write the file to the intended directory
  • mapCompartments correct horizontal concatenation of cell array
  • checkInstallation during first installation on unix machines, makeBinaryExecutables threw an error.
  • importModel correctly parses SBML file that has some missing SBO terms
• feat:
  • randomSampling can run in parallel with MATLAB Parallel Computing Toolbox installed
  • setParam has an additional option, 'unc' if a reaction's lower and upper bound should be set as unconstrained. If available, this will use the default bounds in model.annotation (otherwise [-1000, 1000]), and considers reversibility (in which case lower bound = 0)
  • auxiliary parallelPoolRAVEN function to check if function should be running in parallel
  • use alternative ProgressBar, particularly in functions containing parfor calls
  • give execution rights in Terminal for new RAVEN functions
• chore:
  • update libSBML to version 5.20.2, now including support for Apple Silicon .mexmaca64. The macOS Intel .mexmaci64 is kept at version 5.19.0, as the required compiled mex file is not included in the 5.20.2 release.
• refactor:
  • remove mentions to soplex (which has been replaced by scip).
  • avoid cmd windows output by parallelPoolRaven.
  • allow randomSampling with nsamples set to 0, to only get goodRxns.

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 ***

Running blastPlusTests
.
Done blastPlusTests

Running cdhitTests
.
Done cdhitTests

Running checkTasksTests
.
Done checkTasksTests

Running diamondTests
.
Done diamondTests

Running fillGapsLargeTests
.
Error occurred in fillGapsLargeTests/testLargeSCIP and it did not run to completion.
    ---------
    Error ID:
    ---------
    ''
    --------------
    Error Details:
    --------------
    Error using setRavenSolver (line 35)
    SCIP not found. RAVEN only provides the precompiled SCIP MEX binary for Windows. Instructions on how to compile the SCIP MEX file are found at
    https://github.com/scipopt/MatlabSCIPInterface
    
    Error in fillGapsLargeTests>testLargeSCIP (line 56)
    setRavenSolver('scip');
.
Done fillGapsLargeTests

Running fillGapsSmallTests

Error occurred in fillGapsSmallTests/testSmallSCIP and it did not run to completion.
    ---------
    Error ID:
    ---------
    ''
    --------------
    Error Details:
    --------------
    Error using setRavenSolver (line 35)
    SCIP not found. RAVEN only provides the precompiled SCIP MEX binary for Windows. Instructions on how to compile the SCIP MEX file are found at
    https://github.com/scipopt/MatlabSCIPInterface
    
    Error in fillGapsSmallTests>testSmallSCIP (line 16)
    setRavenSolver('scip');
..
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, test skipped
..
Done solverTests

Running tinitTests
.
Error occurred in tinitTests/testftINIT_T0001 and it did not run to completion.
    ---------
    Error ID:
    ---------
    ''
    --------------
    Error Details:
    --------------
    Error using dispEM (line 49)
    Failed to find good enough solution within the time frame. MIPGap: Inf
    
    
    Error in ftINIT (line 281)
            dispEM(['Failed to find good enough solution within the time frame. MIPGap: ' num2str(mipGap)]);
    
    Error in tinitTests>testftINIT_T0001 (line 237)
        [~,tst1ResModel1] = evalc('ftINIT(prepDataTest1,arrayData1.tissues{1},[],[],arrayData1,[],getINITSteps(),true,true,testParams,false);');
.
Error occurred in tinitTests/testftINIT_T0002 and it did not run to completion.
    ---------
    Error ID:
    ---------
    ''
    --------------
    Error Details:
    --------------
    Error using dispEM (line 49)
    Failed to find good enough solution within the time frame. MIPGap: Inf
    
    
    Error in ftINIT (line 281)
            dispEM(['Failed to find good enough solution within the time frame. MIPGap: ' num2str(mipGap)]);
    
    Error in tinitTests>testftINIT_T0002 (line 277)
        [~,tst1ResModel1] = evalc('ftINIT(prepDataTest1,arrayData1.tissues{1},[],[],arrayData1,[],getINITSteps(),true,true,testParams,false);');
.....
Error occurred in tinitTests/testftINIT_T0008 and it did not run to completion.
    ---------
    Error ID:
    ---------
    ''
    --------------
    Error Details:
    --------------
    Error using dispEM (line 49)
    Failed to find good enough solution within the time frame. MIPGap: Inf
    
    
    Error in ftINIT (line 281)
            dispEM(['Failed to find good enough solution within the time frame. MIPGap: ' num2str(mipGap)]);
    
    Error in tinitTests>testftINIT_T0008 (line 377)
        [~,tst1ResModel1] = evalc('ftINIT(prepDataTest1,arrayData1.tissues{1},[],[],arrayData1,[],getINITSteps(),true,true,testParams,false);');
..
Error occurred in tinitTests/testftINIT_T0050 and it did not run to completion.
    ---------
    Error ID:
    ---------
    ''
    --------------
    Error Details:
    --------------
    Error using dispEM (line 49)
    Failed to find good enough solution within the time frame. MIPGap: Inf
    
    
    Error in ftINIT (line 281)
            dispEM(['Failed to find good enough solution within the time frame. MIPGap: ' num2str(mipGap)]);
    
    Error in tinitTests>testftINIT_T0050 (line 543)
        [~,mres] = evalc('ftINIT(prepDataL,arrayDataL.tissues{1},[],[],arrayDataL,[],getINITSteps(),true,true,testParams,false);');
.
Done tinitTests

Failure Summary:

     Name                              Failed  Incomplete  Reason(s)
    =================================================================
     fillGapsLargeTests/testLargeSCIP    X         X       Errored.
    -----------------------------------------------------------------
     fillGapsSmallTests/testSmallSCIP    X         X       Errored.
    -----------------------------------------------------------------
     solverTests/testSCIP                X         X       Errored.
    -----------------------------------------------------------------
     tinitTests/testftINIT_T0001         X         X       Errored.
    -----------------------------------------------------------------
     tinitTests/testftINIT_T0002         X         X       Errored.
    -----------------------------------------------------------------
     tinitTests/testftINIT_T0008         X         X       Errored.
    -----------------------------------------------------------------
     tinitTests/testftINIT_T0050         X         X       Errored.

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