Open edkerk opened 1 week ago
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
> 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.
Main improvements in this PR:
model.proteinNames
field as also defined in COBRA toolbox, supported by SBML and YAML file formats (solves #558)ravenCobraWrapper
handles newproteinNames
field and previously introducedmetSmiles
fieldimportModel
can handle paths that contain non-ASCII characters (solves #562)Instructions on merging this PR:
develop
as target branch, and will be resolved with a squash-merge.main
as target branch, and will be resolved with a merge commit.