Backward-incompatible changes#

This is the consolidated list of everything a RAVEN 2 script could plausibly break on, or silently produce different output from, when run against RAVEN 3. Items are grouped by how they manifest.

Will error / undefined function#

RAVEN 2 usage	What happens in RAVEN 3
`importExcelModel(...)`	Removed. Use `curation/curateModelFromTables.m` (different input format: `.tsv`, not `.xlsx`; see §6) or convert your template to YAML/SBML and use `importModel`.
`importModel(...)` on SBML Level < 3, Level 3 without FBC v2, or any non-FBC SBML	Errors. Only SBML Level 3 Version 1, FBC package version 2 is accepted (see §6).
`exportToExcelFormat(model, fileName)` where `fileName` is a bare path (no `.xlsx`)	No longer falls back to tab-delimited text export; errors with "only export to xlsx format is supported".
`exportToTabDelimited(...)`	Removed outright (was a dead-code path anyway).
`getWoLFScores(...)` / `parseScores(..., 'wolf', ...)`	WoLF PSORT support is fully removed. `parseScores` now errors on `'predictor','wolf'` with a message pointing to `'deeploc'`, `'mulocdeep'`, `'compartments'`, or `'uniprot'`. No in-toolbox migration path for existing WoLF PSORT output files.
`qMOMA(...)`, `solveQP(...)`	Removed (RAVEN's last `quadprog`/Optimization Toolbox dependency). `findGeneDeletions`'s `analysisType`/`refModel`/`oeFactor` arguments (MOMA-based over-expression analysis) were removed with them; only FBA-based single/double gene deletion (`sgd`/`dgd`) remains.
`checkRxn(...)`	Removed, no direct successor. For debugging why a reaction can't carry flux, use `gapfilling/findLeakMetabolite.m` / `gapfilling/canExchange.m`, or `gapfilling/checkProduction.m`.
`dispEM(...)`, `followFluxes(...)`, `followChanged(...)`, `printModel(...)`, `mapCompartments(...)`, `getExpressionStructure(...)`, `getMetsInComp(...)`, `parallelPoolRAVEN(...)`	All removed (see §4 for what replaces each, where anything does).
Anything under `external/metacyc/`, `pathway/`, `plotting/`, `legacy/`	Entire subsystems removed: MetaCyc-based reconstruction and all visualization/plotting functionality (`drawMap`, `drawPathway`, `markPathwayWithFluxes`, `setOmicDataToRxns`, etc.). No in-toolbox replacement; use COBRA Toolbox or Escher for visualization.
`getGenesFromKEGG`, `getMetsFromKEGG`, `getRxnsFromKEGG`, `constructMultiFasta`, `getWSLpath`, `getBlastFromExcel`	Removed along with the old local-KEGG-FTP-dump workflow (see §7).
`getToolboxVersion(...)`	Removed as a standalone function; folded into an internal helper of `exportForGit`.

Will silently produce different results#

Same call, same input model, different output. Grouped by function; see the linked section for the full explanation of each.

Function	New behavior (default, unless noted)
`getModelFromHomology`, `strictness=3`	Best-hit tie-break now uses bitscore instead of E-value (`"scoreBy","evalue"` restores the old criterion); §7
`getModelFromHomology`, `minLen`	Default lowered from `200` to `100`; §7
`getModelFromHomology`, GPR merging	Gene substitution is exact-token-based instead of regex/`strrep`-based; §7
`getKEGGModelForOrganism`, `cutOff`	Default lowered from `10^-50` to `10^-30`; §7
`getKEGGModelForOrganism`, `minScoreRatioG`	Default raised from `0.8` to `0.9`; §7
`removeGenes`, `expandModel`, `findPotentialErrors`, `addRxns`	grRules are now parsed correctly (exact gene-token matching, structure-aware isozyme/complex handling) instead of via substring/regex matching; §8
`changeGrRules(..., 'replace', false)` onto a gene-less reaction	Produces a valid grRule instead of an unparseable one; §8
`simplifyModel` (used by task-based gap-filling)	No longer drops a task's boundary constraint on a metabolite with no reactions: a task that used to silently pass may now correctly fail; §9
`ftINITInternalAlg`	`allowExcretion` constraint sign corrected
`ravenCobraWrapper`	Gene-ID-to-MIRIAM matching no longer breaks on gene IDs containing regex metacharacters; §6
`permuteModel`, `randomSampling`, `optimizeProb`, `getFluxZ`, `mergeCompartments`, `convertToIrrev`, `replaceMets`, `setExchangeBounds`, `fitParameters`, `guessComposition`	Each had a pre-existing bug fixed; output differs only for models/inputs that triggered it

None of these are API changes; the same call with the same arguments now returns a different, corrected result.

Will warn, but keep working#

Error/warning identifiers changed. dispEM (RAVEN 2's universal error/warning function) always raised errors with an empty identifier (MException('', ...)), so no RAVEN 2 script could have legitimately caught on err.identifier. RAVEN 3 replaces dispEM with native error()/ warning() calls, most (not all) carrying real identifiers, predominantly RAVEN:badInput, plus a handful of specific ones (RAVEN:modelError, RAVEN:badGrRule, RAVEN:sampling, RAVEN:infeasible, RAVEN:grRuleTooComplex). Message text is largely unchanged (many messages are byte-identical to RAVEN 2's), so try/catch blocks that pattern-match on message text keep working; scripts can newly (optionally) match on err.identifier instead.
getINITModel/runINIT now emit a one-time "legacy" notice pointing at ftINIT, silenceable with warning('off','RAVEN:legacyMethod'). This is explicitly not a deprecation; RAVEN's own documentation states these functions "remain supported" indefinitely, to reproduce previously published Human-GEM-derived models. See §9.
makeSomething, consumeSomething, canProduce, canConsume now live in a new deprecated/ folder as thin wrappers around findLeakMetabolite/ canExchange, and emit a one-time RAVEN:deprecated warning stating they "will be removed in the next major release." Unlike the legacy-notice functions above, these are on an actual removal track; migrate call sites before the next major release. See §9.
checkInstallation is now checkRaven, moved from installation/ to the repository root, with an unchanged signature ([currVer, installType] = checkRaven(developMode, checkBinaries)). Existing calls do not break: checkInstallation survives as a forwarding wrapper that passes every argument and output straight through, after emitting a RAVEN:deprecated warning naming checkRaven. It is on the same removal track as the deprecated/ functions above, so switch at the next opportunity.

Environment / installation changes#

KEGG HMM libraries and external command-line binaries (BLAST+, DIAMOND, HMMER, cd-hit, MAFFT, WoLF PSORT) are no longer committed to the repository. RAVEN 3 fetches them on demand from the raven-data GitHub release the first time a function needs one, which means internet access is required on first use, not just at clone/install time. See §11 for what's needed for an air-gapped install, and the full dependency comparison.