RAVEN 2.10.0

[edkerk]

Main improvements in this PR:

• Fixes:
  • importModel only removes identifier prefixes (like R_ for reactions) when present in all entries of a certain type; gives a warning that this happened; and has a removePrefix flag that can be set to false if desired
  • exportModel only adds identifier prefixes (like R_ for reactions) when one or more entries of a certain type are not compatible with SBML (i.e. do not start with a letter or _); gives a warning that this happened; and has a neverPrefix flag that can be set to true if desired. Previously, prefixes were always added
  • importModel allows for empty parameters when not specified
  • constructS gives correct error message when a metabolite is missing
  • importExcelModel can ignore faulty MIRIAM entries (note: import of Excel models is strongly discouraged!)
  • checkModelStruct to determine if reaction is reversible, consider all combinations of LB and UB, not just whether LB < 0 or not
  • checkModelStruct checks that all genes in grRules field are also in genes field (solves checkModelStruct should compare .genes and .grRules #556)
• Features:
  • checkModelStruct queries if the model has any identifiers that are not SBML compatible (i.e. do not start with a letter or _)
  • new removeIdentifierPrefix function can remove identifier prefixes like R_ for reactions if desired
  • new addIdentifierPrefix function can add identifier prefixes like R_ for reactions if required
  • support for model.proteins as field, which matches model.genes and is also supported by SBML and YAML
  • getExchangeRxns has more options to select reactions based on their reaction bounds, whether they represent uptake, excretion etc. (solves getExchangeRxns.m works inconsistently #555)
• Documentation:
  • getKEGGModelForOrganism explicitly refers to the correct dataDir options (i.e. prok90_kegg105 or euk90_kegg105 at this time)

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               2.9.3
   > 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.

[edkerk]

Minor release 2.9.3 -> 2.10.0, as changes in handling of identifier prefixes by importModel and exportModel can cause some changes in SBML files in comparison to earlier versions.