v2.9.3

• 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

v2.9.2

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

v2.9.1

• refactor:
  • when running a unit test and a solver is not installed, report the absence of the solver, not the general failing of the test
• fix:
  • prevent glpk timeout when running selected large FBA calculations
  • avoid an error when running solveLP in parallel and COBRA toolbox is not installed
  • getAllowedBounds returned inconsistent results when running parallelization
  • ⚠️ various changes in relation to solveLP swapping the sign of reported objective function (sol.f), as already announced with RAVEN release 2.7.12, but not actually done at that point
  • ensure that RAVEN provided libSBML binaries are used, by using unique filenames
  • removeMets also considers metNotes field if available
  • setParam error message if incorrect paramType is specified
• feat:
  • checkInstallation reports how RAVEN was installed, as described in the Wiki
• doc:
  • minor changes in formatting of function documentation

v2.9.0

• chore:
  • update libSBML to version 5.20.2, now including support for Apple Silicon .mexmaca64. The macOS Intel .mexmaci64 is kept at version 5.19.0, as the required compiled mex file is not included in the 5.20.2 release.
  • add .mexmaca64 glpk binary for Apple Silicon.
• fix:
  • simplifyModel with irreversible backwards-only reactions (solves #529)
  • writeYAMLmodel do not write lines with empty entries (e.g. reactions without subsystems)
  • getModelFromKEGG includes model.annotation.defaultLB and model.annotation.defaultUB fields
  • getGenesFromGrRules can handle genes with '|'
  • getModelFromHomology remove geneFrom field (solves #533)
  • getMinNrFluxes reduce default verbosity
  • writeYAMLmodel allow empty id and name fields, in line with https://github.com/SysBioChalmers/RAVEN/wiki/RAVEN-Model-Structure
  • ravenCobraWrapper prefers to use grRules in COBRA models if present (solves GECKO issue #367)
  • optimizeProb will throw error when trying to solve MILP with glpk (also if glpk is set via cobra)
  • writeYAMLmodel will throw an informative error if it cannot write the file to the intended directory
  • mapCompartments correct horizontal concatenation of cell array
  • checkInstallation during first installation on unix machines, makeBinaryExecutables threw an error.
  • importModel correctly parses SBML file that has some missing SBO terms
• feat:
  • randomSampling can run in parallel with MATLAB Parallel Computing Toolbox installed
  • setParam has an additional option, 'unc' if a reaction's lower and upper bound should be set as unconstrained. If available, this will use the default bounds in model.annotation (otherwise [-1000, 1000]), and considers reversibility (in which case lower bound = 0)
  • auxiliary parallelPoolRAVEN function to check if function should be running in parallel
  • use alternative ProgressBar, particularly in functions containing parfor calls
  • give execution rights in Terminal for new RAVEN functions
• refactor:
  • remove mentions to soplex (which has been replaced by scip).
  • avoid cmd windows output by parallelPoolRaven.
  • allow randomSampling with nsamples set to 0, to only get goodRxns.

v2.8.7

• fix:
  • ftINIT could have removed metabolites that are required for specific tasks.
  • importModel allows SBML without a specified objective function (this is not valid SBML, but will be tolerated).
  • Swap soplex with scip as solver. The soplex option introduced in release 2.8.5 should not be used for MILP, scip is dedicated for these problems. Precompiled binaries for Windows are provided (downloaded upon request), further installation instructions are mentioned in the Wiki.
  • ravenCobraWrapper properly makes comps and compNames fields when lacking in COBRA model.
  • writeYAMLmodel can deal with mixture of nested and not-nested cell arrays of subsystems (as COBRA models can have).
  • extractMiriam should allow cell array of multiple miriamNames as input.
  • checkInstallation correctly makes binaries executable on Ubuntu (solves #527)
• refactor:
  • Reduce the default verbosity and number of messages to the command window for a few functions.

v2.8.6

• fix:
  • checkInstallation (via solverTests) will not report soplex as fail on Windows when using RAVEN-provided binary (solves #513).

v2.8.5

• feat:
  • Distribute SoPlex binary for Windows with RAVEN, as another open-source alternative, slower than glpk, but suitable for MILP. Installation instructions are updated.
  • readYAMLmodel should always make model.c-field, even if no objective function is specified (solves #509).
  • standardizeGrRules should throw error if no grRules field is found.
• refactor:
  • addRxnsGenesMets more detailed error message if reactions cannot be found.
  • getAllowedBounds use progressbar for reporting status.

v2.8.4

• feat:
  • metDeltaG and rxnDeltaG fields, I/O via YAML. (solves #280)
  • getAllowedBounds has optional runParallel-flag, true by default.
• fix:
  • parseScores and predictLocalization handling of data from DeepLoc 2.0. (solves #310)
  • randomSampling check feasibility after changing bounds to (-)Inf, as suggested in #438.
  • checkModelStruct no longer checks for duplicate metSmiles with different metabolite names, as it often occurs that these canonical SMILES are non-unique due to e.g. stereochemistry.

v2.8.3

• fix:

  • checkFunctionUniqueness on Mac/Unix with non-RAVEN paths.
  • checkInstallation find printOrange on new RAVEN installations (closes #492).
  • readYAMLmodel allows for a model that has gene entries that are not present in any grRules: these are unused genes and should be allowed. This also prevents a bug where gene annotations are wrongly assigned.
  • writeYAMLmodel correct parsing of text to avoid escape characters (e.g. SMILES may contain \C).
  • importModel assigns -Inf and Inf if no LB and/or UB values are defined.
  • ravenCobraWrapper makes empty model.c if COBRA model had no c field (is not necessarily made by readCbModel)

• feat:

  • keggPhylDist.mat includes species names.
  • getMetaCycModelForOrganism input and output of blastStructure (before cutoffs applied), so that function can repeatedly be run with different cutoffs without having to rerun blast/diamond.

v2.8.2

• fix:
  • readYAMLmodel also reads metNotes fields
  • getMetaCycModelForOrganism handling of large genomes
• feat:
  • analyzeSampling no longer requires MATLAB Stats Toolbox
  • detailed error message if MATLAB Text Analytics Toolbox is installed (see #55)
  • checkInstallation has option to only report RAVEN version as output
  • progressbar distributed, will be used to report progress of various functions
  • checkFunctionUniqueness can also take alternative set of paths as input, for use by other toolboxes