Closed edkerk closed 1 year ago
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
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:
---------
''
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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.
Main improvements in this PR:
metDeltaG
andrxnDeltaG
fields, I/O via YAML. (solves #280)getAllowedBounds
has optional runParallel-flag, true by default.parseScores
andpredictLocalization
handling of data from DeepLoc 2.0. (solves #310)randomSampling
check feasibility after changing bounds to (-)Inf, as suggested in #438.checkModelStruct
no longer checks for duplicate metSmiles with different metabolite names, as it often occurs that these canonical SMILES are non-unique due to e.g. stereochemistry.I hereby confirm that I have:
main
as a target branch