What moved, what's gone, and what's renamed#

1. Repository reorganization#

RAVEN 2's top-level layout (core/, external/, hpa/, io/, legacy/, pathway/, plotting/, solver/, struct_conversion/, installation/, utils/) has been replaced with functional folders that group functions by what they do rather than by legacy history:

RAVEN 3 folder	Contents	Mostly came from (RAVEN 2)
`INIT/`	`ftINIT`, `INIT/tINIT/` for `getINITModel`/`runINIT`, and HPA/expression parsing + gene scoring (`parseHPA`, `parseHPArna`, `scoreModel`)	`INIT/`, `hpa/`
`analysis/`	FBA-adjacent analyses: FVA, sampling, FSEOF, OptKnock, robustness, production envelope, flux comparison/tracing	`core/`
`annotation/`	MIRIAM editing, SBO term assignment, ΔG CSV I/O	`struct_conversion/` (+ new)
`biomass/`	Biomass composition fitting/scaling, GAM	`core/` (+ new)
`comparison/`	Multi-model comparison, structured model diffing	`core/` (+ new)
`conditions/`	Applying a data-driven growth/media condition to a model	new folder
`conversion/`	RAVEN⇄COBRA conversion, identifier prefixing, field ordering	`struct_conversion/`
`curation/`	Genome-annotation-driven gene/model curation	new folder
`gapfilling/`	`fillGaps` and its pluggable algorithms, task fitting, leak-metabolite/exchange checks	`core/` (+ new)
`installation/`	Path setup, on-demand binary/data download	`installation/`
`io/`	Model import/export (SBML, YAML, Excel), FASTA I/O	`io/`
`localization/`	Subcellular localization prediction/scoring, compartment assignment	`external/` (+ new)
`manipulation/`	Structural edits: add/remove/change rxns, mets, genes; merge, sort, simplify	`core/`
`queries/`	Non-mutating lookups: indexes, exchange/transport reactions, stoichiometry construction, model checking	`core/`
`reconstruction/`	KEGG- and homology-based draft reconstruction	`external/`
`solver/`	LP/MILP solving	`solver/`
`tasks/`	Metabolic task list parsing/checking	`core/`
`testing/`	`matlab.unittest` suite (`function_tests/`)	`testing/`
`utils/`	Generic helpers, including the new argument-parsing/registry infrastructure	`utils/`
`deprecated/`	Thin backward-compatible wrappers for merged/renamed functions	new folder

Entirely removed (no successor folder): external/metacyc/ (MetaCyc reconstruction), pathway/ and plotting/ (visualization), legacy/ (CellDesigner import and other pre-2.0 code), struct_conversion/'s Excel-POI helpers.

The reorganization affects fewer scripts than the change list suggests. If your scripts call RAVEN functions by name (the normal usage pattern, with the whole RAVEN folder tree, including subfolders, added to the MATLAB path via addRavenToUserPath or addpath(genpath(...))), moving a file to a new subfolder does not break the call: MATLAB resolves functions by name across the whole path, not by a hard-coded relative location. The reorganization only matters if you (a) hard-coded a path to a specific .m file, (b) called one of the functions that was actually removed or merged (see below), or (c) shadowed a RAVEN function name with your own; folder names are irrelevant otherwise.

The full moved-file mapping (RAVEN 2 path → RAVEN 3 path) is not reproduced here because it is large and, as the point above explains, rarely something you need to act on.

2. Removed functionality#

Beyond the items already listed as backward-incompatible above, RAVEN 3 removed a number of functions and whole subsystems as part of a deliberate effort to make the codebase smaller. None of these have call sites left in RAVEN 3 itself.

Removed	What it did	Replacement / notes
`pathway/`, `plotting/` (16 functions: `drawMap`, `drawPathway`, `colorPathway`, `colorSubsystem`, `markPathwayWithFluxes`, `markPathwayWithExpression`, `setOmicDataToRxns`, `plotAdditionalInfo`, etc.)	Metabolic map/pathway visualization	None in RAVEN core. Use COBRA Toolbox, Escher, or export flux/omics data for external plotting.
`external/metacyc/*` (7 functions: `getModelFromMetaCyc`, `getRxnsFromMetaCyc`, `getMetsFromMetaCyc`, `getEnzymesFromMetaCyc`, `addSpontaneousRxns`, `linkMetaCycKEGGRxns`, `combineMetaCycKEGGModels`)	MetaCyc-based draft reconstruction	None; KEGG- and homology-based reconstruction remain the supported paths.
`legacy/*` (CellDesigner import, `changeGeneAssoc`, the bundled `xml_toolbox`)	Pre-2.0 compatibility code	None; considered dead.
`io/importExcelModel.m`, `io/loadWorkbook.m`, `io/loadSheet.m`, `io/writeSheet.m`, `io/SBMLFromExcel.m`, `io/addJavaPaths.m`, `io/startup.m`	Apache-POI-based Excel model I/O	`io/writeExcel.m` (dependency-free OOXML writer) for export; `curation/curateModelFromTables.m` for tabular curation. No full Excel-template import path remains; see §6.
`io/exportModelToSIF.m`, `io/exportToTabDelimited.m`	SIF graph export; tab-delimited model export	Dead/orphaned code with no callers; removed outright.
`io/getFullPath.m`, `io/getMD5Hash.m`, `io/getToolboxVersion.m`	Path canonicalization; file MD5 hashing; toolbox git-version lookup	Inlined where still needed (e.g. MD5 via Java's `MessageDigest` directly inside `getBlast`), or folded into `exportForGit`.
`core/dispEM.m`	Universal error/warning display	Native `warning()`/`error()` + new `utils/ravenList.m` for formatted item lists. See §3.
`core/followFluxes.m`, `core/followChanged.m`	Flux-change reporting relative to a reference solution	`queries/printFluxes.m` covers the cutoff-filtering half; nothing replaces the reference-flux comparison directly.
`core/printModel.m`	Printed reactions to screen/file	`queries/printModelStats.m` / `queries/printFluxes.m` cover related summary/flux printing; no direct one-line-per-reaction dump remains.
`core/getMetsInComp.m`	Returned metabolite indices in a given compartment	Inline it as `model.metComps == compIndex`.
`core/mapCompartments.m`	Remapped compartment labels in a localization-score structure	Superseded by the new predictor-based localization workflow and `localization/defaultCompartmentMap.m`.
`core/getExpressionStructure.m`	Loaded an expression-experiment structure from an ad hoc Excel format	Superseded by `INIT/parseHPA.m`/`INIT/parseHPArna.m` for the supported expression-data workflow.
`core/checkRxn.m`	Per-reaction reactant/product synthesizability debugging	No direct successor; use `gapfilling/findLeakMetabolite.m`, `gapfilling/canExchange.m`, or `gapfilling/checkProduction.m`.
`core/parallelPoolRAVEN.m`	Parallel Computing Toolbox pool setup	Renamed/rewritten as `utils/parallelWorkersRAVEN.m`.
`external/getWoLFScores.m`	WoLF PSORT score parsing	None; see §3.
`external/kegg/{getGenesFromKEGG,getMetsFromKEGG,getRxnsFromKEGG,constructMultiFasta,getWSLpath}.m`, `external/getBlastFromExcel.m`	Local-KEGG-FTP-dump parsing; per-KO multi-FASTA assembly; WSL path translation; Excel-based BLAST import	Superseded by the raven-data-artifact-based KEGG pipeline. See §7.
`solver/qMOMA.m`, `solver/solveQP.m`	MOMA-based analyses (quadratic programming)	Removed; no in-toolbox QP-based replacement. See §3 for `findGeneDeletions` impact.
`testing/unit_tests/*.m` (script-based tests)	Ad hoc test scripts	`testing/function_tests/*.m`, a `matlab.unittest`-class-based suite. Contributor-facing only; `runRAVENtests` usage is unchanged for end users.

3. Renamed, merged, and consolidated functions#

RAVEN 3 introduces a formal deprecated/ folder convention: functions that were merged into a more general replacement stay callable under their old name, as a thin wrapper that emits a one-time RAVEN:deprecated warning ("will be removed in the next major release") and forwards to the new function.

Old function(s)	New function	Notes
`makeSomething(model, ignoreMets, isNames, minNrFluxes, allowExcretion, params, ignoreIntBounds)`	`findLeakMetabolite(model, 'produce', ...)`	Argument order maps 1:1; the wrapper forwards `varargin` unchanged.
`consumeSomething(model, ignoreMets, isNames, minNrFluxes, params, ignoreIntBounds)`	`findLeakMetabolite(model, 'consume', ...)`	Not a verbatim forward: `consumeSomething`'s old positional order has no `allowExcretion` slot, so the wrapper explicitly remaps arguments by name to avoid corrupting `params`/`ignoreIntBounds`.
`canProduce(model, mets)`	`canExchange(model, 'produce', 'mets', mets)`
`canConsume(model, mets)`	`canExchange(model, 'consume', 'mets', mets)`
`compareRxnsGenesMetsComps`	folded into `comparison/compareMultipleModels.m`	Its rxn/gene/met/comp overlap output is now one part of `compareMultipleModels`'s output; no separate function remains.
`INIT/scoreComplexModel.m`	`INIT/scoreModel.m`	Merged, not renamed. RAVEN 2 had both `INIT/scoreComplexModel.m` and `hpa/scoreModel.m`; RAVEN 3 folded them into one `scoreModel`, called with different settings from tINIT than from ftINIT. A RAVEN 2 call to `scoreModel` is unaffected; a call to `scoreComplexModel` has to move to `scoreModel` and pass the settings that reproduce the old behaviour (a single operator for both `and`/`or`, `dataPrecedence` `'reaction'`).
`INIT/ftINITFillGapsMILP.m`	folded into `solver/getMinNrFluxes.m`	Exposed now via `getMinNrFluxes`'s `resolveTies`/`proveAbsGap` options.
`INIT/ftINITFillGapsForAllTasks.m`	folded into `gapfilling/ftINITFillGaps.m` and `fitTasks`'s `'preMerged'` gap-fill mode
`getGenesFromKEGG`/`getMetsFromKEGG`/`getRxnsFromKEGG`	`reconstruction/kegg/readKEGGTable.m` + the raven-data KEGG artifacts	Not a direct signature-compatible rename: the whole data source changed; see §7.
`checkInstallation`	`checkRaven`	Moved from `installation/checkInstallation.m` to repo-root `checkRaven.m`; identical calling signature. `checkInstallation` remains as a deprecated forwarding wrapper, so old calls keep working with a `RAVEN:deprecated` warning.

Separately, getINITModel and runINIT (now under INIT/tINIT/) are marked legacy but indefinitely supported (not on the deprecated/ removal track) via utils/legacyMethodNotice.m, which fires a one-time, silenceable RAVEN:legacyMethod warning pointing at ftINIT. Use ftINIT for new work; keep getINITModel/runINIT only to reproduce models originally built with them.