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fix: drop stale compMiriams in mergeCompartments #685

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

fix: drop stale compMiriams in mergeCompartments #685

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6 changes: 6 additions & 0 deletions manipulation/mergeCompartments.m
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Original file line number Diff line number Diff line change
Expand Up @@ -110,6 +110,12 @@
model.comps={'s'};
model.compOutside={''};
model.metComps=ones(numel(model.mets),1);
%The per-compartment MIRIAM annotations no longer apply once every
%compartment is merged into one, and leaving them would desync compMiriams
%from the rebuilt comps. Drop them.
if isfield(model,'compMiriams')
model=rmfield(model,'compMiriams');
end

%Add exchange mets to another compartment "b" with id "2"
if keepUnconstrained==true
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14 changes: 14 additions & 0 deletions testing/function_tests/tManipulation.m
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Expand Up @@ -236,6 +236,20 @@ function mergeCompartmentsSingleComp(testCase)
testCase.verifyNumElements(m2.comps, 1);
end

function mergeCompartmentsDropsStaleCompMiriams(testCase)
% Merging collapses every compartment into one, so any
% per-compartment MIRIAM annotation must not be left behind at the
% original length (which would desync compMiriams from comps).
m = testCase.model;
m.compMiriams = cell(numel(m.comps),1);
m.compMiriams{1}.name = {'go'};
m.compMiriams{1}.value = {'GO:0005737'};
evalc('m2 = mergeCompartments(m);');
if isfield(m2,'compMiriams')
testCase.verifyNumElements(m2.compMiriams, numel(m2.comps));
end
end

function mergeModelsReturnsStruct(testCase)
modelB = removeReactions(testCase.model, testCase.model.rxns(1:5), true, true, true);
evalc('merged = mergeModels({testCase.model; modelB});');
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