help with getting testAll to run without fails.

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Ronan M.T. Fleming

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Nov 7, 2024, 11:12:40 AM11/7/24

to COBRA Toolbox

Dear All,

we are trying to establish a new CI system to test all the cobra toolbox code with each PR. This needs to be established before we launch the call for contributions to the COBRA Toolbox v4 Nature Protocol paper. We need help to fix the code where these tests are failing. Could some of yee help as a contribution to the aforementioned paper?

Below are the tests that fail with my local version of https://github.com/opencobra/cobratoolbox/tree/develop

Regards,

Ronan

The following tests failed:
testMinimizeModelFlux.m
testFVA.m
testCreatePanModels.m
testJoinModelsPairwiseFromList.m
testSimulatePairwiseInteractions.m
testRobustnessAnalysis.m
testSampleCbModelRHMC.m
testExtremePathways.m
testExtremePools.m
testLrsInterface.m
testpFBA.m
testdynamicRFBA.m
testLoadBiGGModel.m
testReadSBML.m
testChangeIBMCplexParams.m
testDuals.m
testOptimizeTwoCbModels.m
testAnalyzeGCdesign.m
testMultiProductionEnvelope.m
testMultiProductionEnvelopeInorg.m
testProductionEnvelope.m
testSingleProductionEnvelope.m
testOptEnvelope.m

The reasons were as follows:
------------------------------------------------
testMinimizeModelFlux.m:
Warning: Colon operands must be real scalars. This warning will become an error in a future release.
> In testAll (line 244)

Error using assert
Assertion failed.
Error in testMinimizeModelFlux (line 40)
assert(abs(sol.x(end)) < tol);
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in run (line 112)
evalin('caller', strcat(scriptStem, ';'));
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
------------------------------------------------
------------------------------------------------
testFVA.m:
Warning: Colon operands must be real scalars. This warning will become an error in a future release.
> In testAll (line 244)

Error using gurobi
Incorrect size(model.rhs)
Error in solveCobraLP (line 839)
resultgurobi = gurobi(gurobiLP,gurobiParam);
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in optimizeCbModel (line 652)
solution = solveCobraLP(optProblem2, param);
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in processingLLCs>preprocessLLCs (line 151)
sFeas = optimizeCbModel(model2, 'max', 'one');
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in processingLLCs (line 36)
loopInfo = preprocessLLCs(varargin{1:5});
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in fluxVariability (line 232)
[solveLP, MILPproblem, loopInfo] = processingLLCs('preprocess', loopInfo, LPproblem, model, nRxns, osenseStr, MILPproblem);
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in testFVA (line 230)
[minFluxT, maxFluxT, Vmin, Vmax] = fluxVariability(model, 90, 'max', rxnNamesForV, j, 0, 'threads', threads);
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in run (line 112)
evalin('caller', strcat(scriptStem, ';'));
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
------------------------------------------------
------------------------------------------------
testCreatePanModels.m:
Warning: Colon operands must be real scalars. This warning will become an error in a future release.
> In testAll (line 244)

Error using getDistributedModel (line 38)
Requested Model not present in the Model directory.
This is either due to the model not being downloaded, or not being part of the distributed models.
Error in testCreatePanModels (line 32)
model = getDistributedModel([modelList{i} '.mat']);
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in run (line 112)
evalin('caller', strcat(scriptStem, ';'));
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
------------------------------------------------
------------------------------------------------
testJoinModelsPairwiseFromList.m:
Warning: Colon operands must be real scalars. This warning will become an error in a future release.
> In testAll (line 244)

Error using getDistributedModel (line 38)
Requested Model not present in the Model directory.
This is either due to the model not being downloaded, or not being part of the distributed models.
Error in testJoinModelsPairwiseFromList (line 35)
model = getDistributedModel([modelList{i} '.mat']);
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in run (line 112)
evalin('caller', strcat(scriptStem, ';'));
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
------------------------------------------------
------------------------------------------------
testSimulatePairwiseInteractions.m:
Warning: Colon operands must be real scalars. This warning will become an error in a future release.
> In testAll (line 244)

Error using getDistributedModel (line 38)
Requested Model not present in the Model directory.
This is either due to the model not being downloaded, or not being part of the distributed models.
Error in testSimulatePairwiseInteractions (line 37)
model = getDistributedModel([modelList{i} '.mat']);
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in run (line 112)
evalin('caller', strcat(scriptStem, ';'));
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
------------------------------------------------
------------------------------------------------
testRobustnessAnalysis.m:
Warning: Colon operands must be real scalars. This warning will become an error in a future release.
> In testAll (line 244)

Error using assert
Assertion failed.
Error in testRobustnessAnalysis (line 61)
assert(all(abs(controlFlux - controlExpected) < tol))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in run (line 112)
evalin('caller', strcat(scriptStem, ';'));
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
------------------------------------------------
------------------------------------------------
testSampleCbModelRHMC.m:
Warning: Colon operands must be real scalars. This warning will become an error in a future release.
> In testAll (line 244)

Unrecognized property 'extraHessian' for class 'TwoSidedBarrier'.
Error in Polytope (line 111)
o.barrier.extraHessian = opts.extraHessian;
^^^^^^^^^^^^^^^^^^^^^^
Error in sample (line 69)
polytope = Polytope(problem, opts);
^^^^^^^^^^^^^^^^^^^^^^^
Error in sampleCbModel (line 309)
o = sample(P, nPointsReturned, opts);
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in testSampleCbModelRHMC (line 30)
[modelSampling, samples, volume] = sampleCbModel(model, '', 'RHMC', options);
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in run (line 112)
evalin('caller', strcat(scriptStem, ';'));
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
------------------------------------------------
------------------------------------------------
testExtremePathways.m:
Warning: Colon operands must be real scalars. This warning will become an error in a future release.
> In testAll (line 244)

Error using lrsOutputReadRay (line 23)
Could not read lrs output file.
Error in extremePathways (line 114)
[R, V] = lrsOutputReadRay([filename '_' suffix '.ext']);
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in testExtremePathways (line 41)
[P, V] = extremePathways(minimalModel);
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in run (line 112)
evalin('caller', strcat(scriptStem, ';'));
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
------------------------------------------------
------------------------------------------------
testExtremePools.m:
Warning: Colon operands must be real scalars. This warning will become an error in a future release.
> In testAll (line 244)

Error using lrsReadRay (line 70)
Could not read lrs output file.
Error in extremePools (line 176)
[Q, vertexBool, fileNameOut] = lrsReadRay(modelName,param);
^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in testExtremePools (line 50)
[CalculatedPools]=extremePools(model);
^^^^^^^^^^^^^^^^^^^
Error in run (line 112)
evalin('caller', strcat(scriptStem, ';'));
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
------------------------------------------------
------------------------------------------------
testLrsInterface.m:
Warning: Colon operands must be real scalars. This warning will become an error in a future release.
> In testAll (line 244)

Error using lrsReadRay (line 70)
Could not read lrs output file.
Error in testLrsInterface (line 46)
[Q, vertexBool, fileNameOut] = lrsReadRay(modelName,param);
^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in run (line 112)
evalin('caller', strcat(scriptStem, ';'));
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
------------------------------------------------
------------------------------------------------
testpFBA.m:
Warning: Colon operands must be real scalars. This warning will become an error in a future release.
> In testAll (line 244)

Error using assert
Assertion failed.
Error in testpFBA (line 103)
assert(min(t_fg) == 1)
^^^^^^^^^^^^^^^^^^^^^^
Error in run (line 112)
evalin('caller', strcat(scriptStem, ';'));
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
------------------------------------------------
------------------------------------------------
testdynamicRFBA.m:
Warning: Colon operands must be real scalars. This warning will become an error in a future release.
> In testAll (line 244)

Error using -
Arrays have incompatible sizes for this operation.
Error in testdynamicRFBA (line 46)
assert(any(any(abs(concentrationMatrixtest-concentrationMatrix) < tol)))
^
Error in run (line 112)
evalin('caller', strcat(scriptStem, ';'));
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
------------------------------------------------
------------------------------------------------
testLoadBiGGModel.m:
Warning: Colon operands must be real scalars. This warning will become an error in a future release.
> In testAll (line 244)

Error using assert
Assertion failed.
Error in testLoadBiGGModel (line 102)
assert(abs(FBA.f - modelArr{i,5}) < tol);
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in run (line 112)
evalin('caller', strcat(scriptStem, ';'));
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
------------------------------------------------
------------------------------------------------
testReadSBML.m:
Warning: Colon operands must be real scalars. This warning will become an error in a future release.
> In testAll (line 244)

Error using assert
Assertion failed.
Error in testReadSBML (line 76)
assert(abs(FBA.f - modelFBAf_min(i)) < tol);
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in run (line 112)
evalin('caller', strcat(scriptStem, ';'));
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
------------------------------------------------
------------------------------------------------
testChangeIBMCplexParams.m:
Warning: Colon operands must be real scalars. This warning will become an error in a future release.
> In testAll (line 244)

Error using assert
The condition input argument must be convertible to a scalar logical.
Error in testChangeIBMCplexParams (line 42)
assert(isempty(sol.full) & sol.origStat == 11)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in run (line 112)
evalin('caller', strcat(scriptStem, ';'));
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
------------------------------------------------
------------------------------------------------
testDuals.m:
Warning: Colon operands must be real scalars. This warning will become an error in a future release.
> In testAll (line 244)

Error using -
Arrays have incompatible sizes for this operation.
Error in testDuals (line 83)
assert(norm(solQP.rcost - solLP.rcost,inf) < tol)
^
Error in run (line 112)
evalin('caller', strcat(scriptStem, ';'));
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
------------------------------------------------
------------------------------------------------
testOptimizeTwoCbModels.m:
Warning: Colon operands must be real scalars. This warning will become an error in a future release.
> In testAll (line 244)

Error using assert
Assertion failed.
Error in testOptimizeTwoCbModels (line 51)
assert(all(abs(sol1.x) < objtol));
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in run (line 112)
evalin('caller', strcat(scriptStem, ';'));
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
------------------------------------------------
------------------------------------------------
testAnalyzeGCdesign.m:
Warning: Colon operands must be real scalars. This warning will become an error in a future release.
> In testAll (line 244)

Error using assert
Assertion failed.
Error in testAnalyzeGCdesign (line 54)
assert(isequal({'EX_akg(e)', 'EX_co2(e)'}, improvedRxns));
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in run (line 112)
evalin('caller', strcat(scriptStem, ';'));
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
------------------------------------------------
------------------------------------------------
testMultiProductionEnvelope.m:
Warning: Colon operands must be real scalars. This warning will become an error in a future release.
> In testAll (line 244)

Error using assert
Assertion failed.
Error in testMultiProductionEnvelope (line 45)
assert(isequal((abs(refData_x-biomassValues) < 1e-4), true(20, 1)));
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in run (line 112)
evalin('caller', strcat(scriptStem, ';'));
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
------------------------------------------------
------------------------------------------------
testMultiProductionEnvelopeInorg.m:
Warning: Colon operands must be real scalars. This warning will become an error in a future release.
> In testAll (line 244)

Error using assert
Assertion failed.
Error in testMultiProductionEnvelopeInorg (line 42)
assert(isequal((abs(refData_x-biomassValues) < 1e-4), ones(20, 1)));
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in run (line 112)
evalin('caller', strcat(scriptStem, ';'));
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
------------------------------------------------
------------------------------------------------
testProductionEnvelope.m:
Warning: Colon operands must be real scalars. This warning will become an error in a future release.
> In testAll (line 244)

Error using assert
Assertion failed.
Error in testProductionEnvelope (line 45)
assert(isequal((abs(refData_biomass-biomassValues) < 1e-4), true(20, 1)));
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in run (line 112)
evalin('caller', strcat(scriptStem, ';'));
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
------------------------------------------------
------------------------------------------------
testSingleProductionEnvelope.m:
Warning: Colon operands must be real scalars. This warning will become an error in a future release.
> In testAll (line 244)

Error using assert
Assertion failed.
Error in testSingleProductionEnvelope (line 32)
assert(isequal(refData_y1, y1));
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in run (line 112)
evalin('caller', strcat(scriptStem, ';'));
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
------------------------------------------------
------------------------------------------------
testOptEnvelope.m:
Warning: Colon operands must be real scalars. This warning will become an error in a future release.
> In testAll (line 244)

Unrecognized field name "peak".
Error in testOptEnvelope (line 40)
assert(abs(main.peak.x - testMain.peak.x) < tol);
^^^^^^^^^^^
Error in run (line 112)
evalin('caller', strcat(scriptStem, ';'));
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
------------------------------------------------

> The exit code is 1.

--
Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.
----------------------------------------------------------------------------
Associate Professor,

Digital Metabolic Twin Center, www.digitalmetabolictwin.org

School of Medicine,
University of Galway.

Ireland.

----------------------------------------------------------------------------

Coordinator of the Horizon Europe project "Reconstruction and Computational Modelling for Inherited Metabolic Diseases" (Recon4IMD)

----------------------------------------------------------------------------
Peer-reviewed publications: https://goo.gl/FZPG23
Mobile: +353 852 109 806
Github: @rmtfleming
----------------------------------------------------------------------------

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