Remove the boundary compartment #179
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previously the leftEquation and rightEquation fields became unequal in size
- Since the boundary mets had been removed from model, it is no longer necessary to load them into `unconstrained` field.
haowang-bioinfo
approved these changes
Jun 9, 2020
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Main improvements in this PR:
As described in #172, the boundary compartment
xis non-standard in the modeling community and therefore a source of much confusion (and incompatibility with COBRA).This PR removes the boundary compartment and all metabolites within the boundary compartment from the model, as well as the metabolite annotation JSON.
Furthermore, I noticed that the
importHumanYamlfunction had problems parsing one-sided reactions; i.e., those with only reactants or products. A small fix was made to ensure that such equations are now parsed correctly.I hereby confirm that I have:
develas a target branch