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CompMetEng
RAVEN
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Fixes from the RAVEN 3 Guide review
- #7
#7
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edkerk
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Oct 17, 2026
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Fixes from the RAVEN 3 Guide review
#7
edkerk
merged 14 commits into
develop
CompMetEng/RAVEN:develop
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fix/guide-review
CompMetEng/RAVEN:fix/guide-review
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Commits on Oct 17, 2026
fix: use the population std for the reporterMetabolites background
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fix: pass a sparse constraint matrix from sampleChebyshevCenter
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fix: return all-blocked from haveFlux when no reaction survives simplification
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fix: refuse a biomass balance that would make the balancing component negative
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feat: solve MILPs with the bundled GLPK
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fix: raise a clear error for an ambiguous name[comp] in getIndexes
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docs: correct the help of six functions
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fix: read folded YAML scalars whose continuation starts with a dash
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fix: read curation tables by header and curate existing entities fully
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docs: state how haveFlux treats a dead-end reaction with a forced flux
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fix: keep the lower bound of unreversed reaction candidates in gapFillMILP
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fix: create rxnNotes in getKEGGModelForOrganism when the reference model has none
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fix: correct a typo in the curateModelFromTables overwrite warning
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gapFillMILP adds database reactions only; gapReport stops on an infeasible model
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