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Follow-ups from the RAVEN 3 Guide review - #8
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- optimizeProb solves MILPs with the COBRA Toolbox's GLPK as well, with the same RAVEN:glpkMILP warning as the bundled GLPK; getMinNrFluxes no longer refuses it. - scaleBiomassFraction takes a targetTotal for the balanced biomass total. - gapReport always reports the metabolites produced or consumed with the boundary closed, closing the reactions getExchangeRxns returns when the model has no unconstrained field, and stops when that closed model is infeasible. - MILP tests run on the bundled GLPK when neither Gurobi nor SCIP is available. - CONTRIBUTING, the documentation workflow and docs/v3_review.md refer to develop and RAVEN 3; the asset download error points to CompMetEng.
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Function test results422 tests 415 ✅ 2m 12s ⏱️ Results for commit aabdf16. |
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Follow-ups from the RAVEN 3 Guide review.
optimizeProbalso solves MILPs with the COBRA Toolbox's GLPK interface (setRavenSolver('cobra')with GLPK as COBRA's MILP solver), with the sameRAVEN:glpkMILPwarning that recommends Gurobi.getMinNrFluxesaccepts it too.scaleBiomassFraction: atargetTotalname-value argument sets the biomass total thatbalanceOutbrings the components to (default 1 g/gDW), astarget_totaldoes in raven-toolbox'sscale_biomass.gapReport: always reports the metabolites that can be produced or consumed with the boundary closed, as raven-toolbox'sgap_reportdoes. Without anunconstrainedfield it closes the reactionsgetExchangeRxnsreturns; it stops withRAVEN:infeasibleModelwhen the closed model is infeasible.CONTRIBUTING.md, the documentation workflow anddocs/v3_review.mdrefer todevelopand RAVEN 3; the asset-download error links to CompMetEng/RAVEN issues; two comments describe current behaviour only.