Releases · SysBioChalmers/RAVEN

fix:
- avoid the use of git-lfs as introduced in 2.11.0, as this resulted in *.mat files being excluded from the release source ZIP (solves #602)
feat:
- distribute keggGenes.mat as separate download (automatically fetched by getGenesFromKEGG) due to size

fix:
- predictLocalization and parseScores to correctly handle output from CELLO
- setParam report reactions not found in model
- mergeModels will only make new metFrom, rxnForm and geneFrom fields if none of the initial models have these fields
- handling of subSystems in various functions, RAVEN supports both cell arrays and nested cell arrays
- YAML file I/O for models without genes
- runINIT retains params as flag for optimizeProb input
- copyToComps does not add or modify metFrom, rxnForm or geneFrom fields
- addRxns makes sure that subSystems are nested cell arrays
- fitTasks parses correct arguments to fillGaps
refactor:
- exportModel speed-up subSystems handling
chore:
- updated BLAST+, DIAMOND, MAFFT and HMMER binaries
- update KEGG to release 116.0, retrained HMMs
feat:
- runRAVENtests runs RAVEN unit tests
- findRAVENroot stores RAVEN root as MATLAB preference during checkInstallation, to avoid problems when running on HPC clusters
doc:
- parseTaskList clarifies that it can handle both *.txt and *.xlsx as input

fix:
- importModel parsing of model notes in MATLAB R2025a (solves #586)
- readYAMLmodel can read files where entries were broken over more than 2 lines.
- readYAMLmodel recognizes '' as an empty string.
doc:
- getExchangeRxns correct 'out' flag definition
refactor:
- setParam and solveLP speed improvements
- optimizeProb parses Threads=1 to gurobi if run in parallel
feat:
- checkModelStruct will throw error if a grRules entry starts/end with AND/OR, example: or geneA and geneB

fix:
- importModel prevent colon operands warning
- importModel parsing of model notes in MATLAB R2025a (solves #586)
- randomSampling uses real reaction bounds and not the model.rev field to identify reversible reactions, and filters from goodRxns those reactions that cannot carry flux
feature:
- setParam checks if the new LB and UB values are not invalid
- randomSampling recognizes if a model is a GECKO v3+ ecModel, in which case the usage_prot reactions are not sampled
refactor:
- importModel parsing of LB and UB values, minor speed improvements
documentation:
- remove traces of getMILPParams, which has been obsolete since 2.7.10

fix:
- closeModel if model only contained one compartment
- generateNewIds returns by default 1 identifier
- readYAMLmodel if the model contains multiple annotations of the same type (e.g. CHEBI) for the same entity (e.g. metabolite)
- readYAMLmodel and writeYAMLmodel if an essential field is empty but should still be imported/exported
- generateNewIds can handle if the model already contains identifiers that start with the prefix (e.g. r_) but is not followed by a number.

fix:
- addMets if metNames and not mets identifiers are given
- addRxns when adding empty subSystems if the model uses cell arrays of cells for subSystems
- importModel properly parsing of annotations if identifiers.org/name:value is used instead of identifiers.org/name/value
features:
- changeGrRules can change the same grRule for multiple reactions simultaneously
- replaceMets can use metabolite identifiers instead of metabolite names
refactor:
- use getGenesFromGrRules in checkModelStruct, changeGrRules and importModel, to correctly split and/or relationships
documentation:
- checkRxn clarify what the output represents (solves #572)

fix:
- readYAMLmodel will correctly construct the ec.rxnEnzmat matrix
- exportForGit will not search for COBRA if it is not in MATLAB path
feature:
- unit-tests for YAML in/output, now also included in checkInstallation
docs:
- exportForGit correctly describe neverPrefix option

fix:
- importModel only removes identifier prefixes (like R_ for reactions) when present in all entries of a certain type; gives a warning that this happened; and has a removePrefix flag that can be set to false if desired
- exportModel only adds identifier prefixes (like R_ for reactions) when one or more entries of a certain type are not compatible with SBML (i.e. do not start with a letter or _); gives a warning that this happened; and has a neverPrefix flag that can be set to true if desired. Previously, prefixes were always added
- importModel allows for empty parameters when not specified
- constructS gives correct error message when a metabolite is missing
- importExcelModel can ignore faulty MIRIAM entries (note: import of Excel models is strongly discouraged!)
- checkModelStruct to determine if reaction is reversible, consider all combinations of LB and UB, not just whether LB < 0 or not
- checkModelStruct checks that all genes in grRules field are also in genes field (solves #556)
feature:
- checkModelStruct queries if the model has any identifiers that are not SBML compatible (i.e. do not start with a letter or _)
- new removeIdentifierPrefix function can remove identifier prefixes like R_ for reactions if desired
- new addIdentifierPrefix function can add identifier prefixes like R_ for reactions if required
- support for model.proteins as field, which matches model.genes and is also supported by SBML and YAML
- getExchangeRxns has more options to select reactions based on their reaction bounds, whether they represent uptake, excretion etc. (solves #555)
docs:
- getKEGGModelForOrganism explicitly refers to the correct dataDir options (i.e. prok90_kegg105 or euk90_kegg105 at this time)

fix:
- ravenCobraWrapper handle empty rxnReferences from COBRA => RAVEN
- replaceMets should not contract the whole model, only for the replaced metabolites
- getBlast can handle paths containing spaces, or makes a custom temp path if required (solves #506)
- importModel with empty confidenceScores entries
- constructS avoid warning about "Colon operands must be real scalars"
- randomSampling should output the solutions as full matrix, as sparse matrices occassionally acts weird when using functions like mean
feature:
- getIndexes supports ecenzymes, ecrxns and ecgenes types, to query GECKO3 model.ec fields
refactor:
- speedup readYAMLmodel
docs
- update badges and refer to GitHub Discussions instead of Gitter

fix:
- checkInstallation finding RAVEN when installed as MATLAB Add-On

Releases: SysBioChalmers/RAVEN

v2.11.1

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v2.11.0

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v2.10.5

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v2.10.4

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v2.10.3

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v2.10.2

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v2.10.1

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v2.10.0

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v2.9.3

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v2.9.2

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