fix: metabolite names starting with a number, and a spurious addRxns warning - #682
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…warning Both found by comparing the raven-toolbox test suite against RAVEN's. constructS read the leading number of every "number name" entry as a coefficient, so an equation using a metabolite whose name starts with a digit was silently mis-stoichiometried: "2 oxoglutarate => succinate" produced S = [-2 1] over a metabolite "oxoglutarate" rather than [-1 1] over "2 oxoglutarate". When the caller supplies a metabolite list, an entry that matches it in full is now taken as a name. A list derived from the equations cannot disambiguate, so that path is unchanged, as is the ordinary coefficient reading. addRxns raised its "metabolites both as substrate and product" warning outside any check of whether any equation had that problem, so every call warned, with an empty list of offending reactions.
Function test results243 tests 221 ✅ 1m 1s ⏱️ Results for commit 4d94392. |
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Main improvements in this PR:
constructSread the leading number of a metabolite whose name starts with a digit as a stoichiometric coefficient:2 oxoglutarate => succinategaveS = [-2 1]over a metaboliteoxoglutarate. An entry that matches the supplied metabolite list in full is now taken as a name. Ordinary coefficients are unaffected.addRxnsraised its "metabolites both as substrate and product" warning on every call, with an empty list of reactions, because it never checked whether any equation had the problem.tQueries.mandtManipulation.m.Instructions on merging this PR:
develop3as target branch, and will be resolved with a squash-merge.