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

v2.8.1

• fix:
  • checkInstallation throws warnings, not errors, when making binaries executable
  • optimizeProb and readYAMLmodel on MATLAB <2020b (solves #478)
  • getModelFromHomology correct handling of OLD_ genes and "or" relationships (solves #481)
  • prepINITData gets option to skip scaling, as ftINIT will otherwise fail for some models (solves #483)

v2.8.0

• chore:
  • update KEGG and pre-trained HMMs to version 105.
• fix:
  • addRxns correctly defines rev field, only reactions that can go in both directions (LB<0 and UB>0) are reversible (solves #469).
• feat:
  • GitHub updates: Action workflow, rename devel branch to develop, reformat README.md and GH Pages.
  • if Parallel Computing Toolbox is installed, run getAllowedBounds across multiple workers.
  • solveLP checks if lb, ub, c and S fields do not have invalid values (e.g. NaN).

v2.7.12

• fix:

  • checkInstallation failed to find the path for binaries on Mac
  • solveLP report the correct sign of the objective function. .f with objective value was previously inverted (maximization gives negative value). 🚨 If your own code reads the .f field coming from solveLP, it should be updated! 🚨

• feat:

  • setRavenSolver can take 'soplex' as option, which assumes a succesful SCIP installation, and that soplex can be directly called in the terminal. No installation instructions yet, but checkInstallation tests for it.
  • model I/O functions (importModel, exportModel, exportToExcelFormat, writeYAMLmodel and readYAMLmodel) show a dialog box if no file name is specified.
  • convertToIrrev remove warning message

v2.7.11

• fix:
  • fitTasks gave wrongly formatted model.b field
  • checkInstallation -> makeBinaryExecutable on Unix (solves #460).
  • writeYAMLmodel with logical model.ec.geckoLight
  • removeRavenFromPath with unix paths
  • ftINIT and Gurobi version 10: too sensitive to low int tolerances
• feat:
  • checkInstallation highlight when new version is available

v2.7.10

• feat:
  • readYAMLmodel and writeYAMLmodel support I/O of enzyme-constrained models in GECKO3-format
• fix:
  • importModel subSystems bug
  • randomSampling use correct hot-start solution for speed improvement
  • expandModel remove unnecessary warning text
  • full runProductionEnvelope output

v2.7.9

• fix:
  • checkInstallation binary fix on Mac
  • importModel write 0-length chars instead of empty cells if selected reactions do not have subSystem
  • runProductionEnvelope parameter and output parsing
  • runSimpleOptKnock removes duplicate targets if single KO was already sufficient
  • runDynamicFBA plot axes labels
  • contractModel does not contract complete model if it is called by replaceMets
  • removeRavenFromPath removes all RAVEN dirs and warns about MATLAB Add-On installations

v2.7.8

• fix:
  • findGeneDeletions report zero flux and growth ratio for essential genes
  • GitHub workflow parsing of testing output
• feat:
  • removeRavenFromPath can quickly remove RAVEN folders from the MATLAB path
  • graph layout improvements for runPhenotypePhasePlane
  • runRobustnessAnalysis optional reduced cost plot
• refactor:
  • setParam minor speed improvement

v2.7.7

Main improvements in this PR:

• fix:

  • checkInstallation ensures that binaries (blastp etc.) and MEX files (TranslateSBML etc.) are executable on Mac, as this is not the case if RAVEN is installed as MATLAB Add-On
  • checkInstallation runtests on MATLAB < 2018b
  • getModelFromHomology no longer includes "OLD_" genes from the template model(s) if this gene is only involved in "OR" gene associations (= isoenzyme), but only if involved in "AND" gene associations (= subunit).
  • constructS trim spaces around metabolites for matching

• feat:

  • writeYAMLmodel and readYAMLmodel functionality
  • support in various functions for a model.metSmiles field, which contains SMILES for each metabolite
  • solveLP (via optimizeProb) reports shadow prices and reduced costs
  • new runRobustnessAnalysis, runDynamicFBA, runPhenotypePhasePlane, runProductionEnvelope and runSimpleOptKnock functions
  • printFluxes can print multiple flux vectors
  • convertToIrrev gives output specifying match between reversible and novel irreversible reactions

• refactor:

  • randomSampling speed-up with hot-start LPs
  • expandModel speed improvement