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@edkerk edkerk released this 01 Jul 11:38
· 58 commits to main since this release
v2.8.3
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Learn about vigilant mode.

  • 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.
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