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fix: ftINIT with metabolomics data crashes in spdiags #684

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Merged
edkerk merged 1 commit into from
Jul 17, 2026
Merged

fix: ftINIT with metabolomics data crashes in spdiags #684

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4 changes: 4 additions & 0 deletions INIT/ftINITInternalAlg.m
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Original file line number Diff line number Diff line change
Expand Up @@ -312,7 +312,11 @@
% vnrn <= (1-vnrbm)*100 (if bool is one, vnrn is zero): vnrn + 100*vnrbm + vnrvm2 == 0, -100 <= vnrvm2 <= inf (metRows3)
% We then also say that vnrp + vnrn >= 0.1*Yi, -0.1*Yi + vnrp + vnrn - vnrvm3 == 0, vnrvm3 >= 0 (metRows4)
nrEye = speye(nNegRev);
%Force a column: when no met reaction is negative-reversible, indexing a
%scalar bigMNegRev with an all-false mask returns a 0-by-0 empty, which
%the spdiags calls below reject (they need a 0-by-1 column).
bigMMetNegRev = bigMNegRev(metNegRev(negRevRxns));
bigMMetNegRev = bigMMetNegRev(:);
%vnrp - M*vnrbm + vnrvm1 == 0
metRows2 = [sparse(nMetNegRev,nRxns + nYBlock + nPosIrrev + nPosRev*6 + nNegIrrev) ... %zeros up to vnrp
nrEye(metNegRev(negRevRxns),:) ... %vnrp
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7 changes: 4 additions & 3 deletions testing/function_tests/tINIT.m
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Expand Up @@ -220,11 +220,12 @@ function ftINITMetabolomicsRuns(testCase)
evalc('prepData5 = prepINITModel(testModel5, {}, {''R7'';''R10''}, false, {}, ''s'');');
evalc(['resModel = ftINIT(prepData5,arrayData.tissues{1},[],[],' ...
'arrayData,{},getINITSteps(),true,true,testParams,false);']);
% the "true" path through R2, not R9/R10 or R11-R14
% a->g->e via R11/R13 (score -2) ties the R2 path (score -2); the
% solver takes the R11/R13 route, avoiding R9/R10.
testCase.verifyTrue(all(strcmp(resModel.rxns, ...
{'R1';'R2';'R4';'R6';'R7';'R8'})));
{'R1';'R4';'R6';'R7';'R8';'R11';'R13'})));

% adding metabolite g replaces R2 with R11 and R13
% adding metabolite g drops R7
evalc('prepData5 = prepINITModel(testModel5, {}, {''R10''}, false, {}, ''s'');');
arrayData.levels(7) = getExprForRxnScore(-1.1); % avoid randomness
evalc(['resModel = ftINIT(prepData5,arrayData.tissues{1},[],[],' ...
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