RAVEN 2.8.3

[edkerk]

Main improvements in this PR:

• fix:

  • checkFunctionUniqueness on Mac/Unix with non-RAVEN paths.
  • checkInstallation find printOrange on new RAVEN installations (closes #492).
  • readYAMLmodel allows for a model that has gene entries that are not present in any grRules: these are unused genes and should be allowed. This also prevents a bug where gene annotations are wrongly assigned.
  • writeYAMLmodel correct parsing of text to avoid escape characters (e.g. SMILES may contain \C).
  • importModel assigns -Inf and Inf if no LB and/or UB values are defined.
  • ravenCobraWrapper makes empty model.c if COBRA model had no c field (is not necessarily made by readCbModel)

• feat:

  • keggPhylDist.mat includes species names.
  • getMetaCycModelForOrganism input and output of blastStructure (before cutoffs applied), so that function can repeatedly be run with different cutoffs without having to rerun blast/diamond.

I hereby confirm that I have:

• [x] Selected main as a target branch

[github-actions[bot]]

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               2.8.2
   > Latest RAVEN release available     2.8.3
     Run git pull in your favourite git client
     to get 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             5.19.0
 > 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
Writing problem data to `outpb.lp'...
271 lines were written
   > glpk                               Pass
   > gurobi                             Pass
   > soplex                             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
..Writing problem data to `outpb.lp'...
271 lines were written

Error occurred in solverTests/testSoplex and it did not run to completion.
    ---------
    Error ID:
    ---------
    ''
    --------------
    Error Details:
    --------------
    Error using solverTests>testSoplex (line 100)
    Solver not working
..
Done solverTests

Running tinitTests
..........
Done tinitTests

Failure Summary:

     Name                    Failed  Incomplete  Reason(s)
    =======================================================
     solverTests/testSoplex    X         X       Errored.

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

[edkerk]

@mihai-sysbio The GitHub Action shows to use RAVEN 2.8.2, but should it not use the RAVEN from this PR? checkInstallation should then not show a version, but rather report DEVELOPMENT.

[mihai-sysbio]

@mihai-sysbio The GitHub Action shows to use RAVEN 2.8.2, but should it not use the RAVEN from this PR? checkInstallation should then not show a version, but rather report DEVELOPMENT.

According to this line: https://github.com/SysBioChalmers/RAVEN/blob/0a180fed494b6c38a6ad9433c625898423972336/.github/workflows/tests.yml#L16

it should pick up whatever is in the current branch.

The base branch is main, which has a version - 2.8.2. The branch that is merged in (develop) doesn't change the version.txt file, so RAVEN "thinks" the current code is 2.8.2. The version is then bumped directly only main, after this PR, with 0a180fed494b6c38a6ad9433c625898423972336 . I've re-ran the action, and you can see in the comment that it picked up that a new version exists. Since that is "outside" of this PR, it still thinks it's running 2.8.2.

One way to work around this would be to create a special workflow only for PRs that target main which remove the version.txt file, so the workflow would then report PRs such as this one as DEVELOPMENT.

[edkerk]

As long as we're sure it installs RAVEN fresh from the current PR, then it's fine for me.