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@simas232 simas232 released this 04 Jun 12:55
v2.4.0
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Main improvements in this release:

  • Features:
    • removed MOSEK compatibility (PR #258)
    • added Zenodo badge, re-arranged badges and updated citation information in README.md (PR #275)
    • compareMultipleModels: allowed execution permission for Unix systems (PR #276)
    • parseTaskList can now also read tab-separated ".txt" files (PR #284)
    • constructPathwayFromCelldesigner is now classified as the legacy function due to its malfunction in MATLAB 2014b and later. An error is thrown if this function is used in any incompatible MATLAB version. (PR #287)
    • checkInstallation: RAVEN is now added to MATLAB path automatically, since this is imperative for RAVEN functionality (PR #289)
    • added .gitattributes file, which allows to prevent issues with different end-of-line (EOL) characters that are used by Windows and Unix/macOS (PR #291)
  • Fixes:
    • optimizeProb: fixed LP and MILP inconsistencies (PR #258)
    • checkTasks/fitTasks: fixed "IN" and "OUT" metabolites parsing (PR #277)
    • getMetaCycModelOrganism: fixed a bug resulting in the output with mismatched genes and grRules fields. This was done by updating genes according to the newly generated rxnGeneMat. (PR #278)
    • exportModel: fixed an issue for the models without subSystems field. Previously, models without subSystems resulted in invalid SBML files, as they specified that the 'groups' package was used but no groups were specified. Now if a model has no subSystems field, the SBML package 'groups' is not considered when exporting to SBML. (PR #279)
    • checkInstallation: renamed empty to emptyModel thereby preventing the issues with the MATLAB built-in function empty() (PR #289)
    • ravenCobraWrapper: add exceptions for metabolite KEGG and PubChem IDs (PR #290)
    • ravenCobraWrapper: grRules are no longer saved during RAVEN -> COBRA conversion to prevent potential discrepancies between grRules and rules fields (PR #295)
  • External software, database updates:
    • Updated MetaCyc to version 23.5 (PR #224)
    • Updated KEGG to Release 94.0 (PR #293)
    • Updated HMMER to 3.3 and MAFFT to 7.467 (PR #293). Updated BLAST+ to 2.10.0 and DIAMOND to 0.9.32. (PR #294)
  • Code refactoring:
    • refactored LP and MILP parsing (PR #258)
    • refactored ravenCobraWrapper (PR #286)
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