RAVEN 2.8.7

[edkerk]

Main improvements in this PR:

• Fix:
  • ftINIT could have removed metabolites that are required for specific tasks.
  • importModel allows SBML without a specified objective function (this is not valid SBML, but will be tolerated).
  • Swap soplex with scip as solver. The soplex option introduced in release 2.8.5 should not be used for MILP, scip is dedicated for these problems. Precompiled binaries for Windows are provided (downloaded upon request), further installation instructions are mentioned in the Wiki.
  • ravenCobraWrapper properly makes comps and compNames fields when lacking in COBRA model.
  • writeYAMLmodel can deal with mixture of nested and not-nested cell arrays of subsystems (as COBRA models can have).
  • extractMiriam should allow cell array of multiple miriamNames as input.
  • checkInstallation correctly makes binaries executable on Ubuntu (solves bug: make binaries executable on Ubuntu #527)
• Refactor:
  • Reduce the default verbosity and number of messages to the command window for a few functions.

I hereby confirm that I have:

• Selected main as a target branch

[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
   > 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 ***

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 80)
    SCIP MEX binary not installed or not functional, test skipped
..
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.