RAVEN 2.6.0 #393
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RAVEN 2.6.0 #393
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Co-authored-by: Mihail Anton <[email protected]>
fix: exportModel correct prefix compartment IDs
- only required for input files, as output files use system-provided tmp path
- prevents issues with problematic paths when running external software
feat: speed up getKEGGModelForOrganism
# Conflicts: # doc/external/kegg/getKEGGModelForOrganism.html
fix: if FASTA file in dir containing spaces
doc: remove reference to mosek and output MATLAB release
fix: correct formatting in getKEGGModelForOrganism
to correspond the testing order with testBlast(true) and checkInstallation
refactor: convertToIrrev speedup
fix: getKEGGModelForOrganism now checks organismID validity
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chore: update KEGG to version 100
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This PR has been automatically tested with GH Actions. Here is the output of the tests:
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haowang-bioinfo
approved these changes
Feb 8, 2022
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Main improvements in this PR:
exportModelcorrect handling if a compartment ID is i (solves unintended prefix for compartment i #366)getBlast) will copy this FASTA file to a temporary directory to avoid potential issues with the original path when running external software (e.g. BLAST) (PR fix: if FASTA file in dir containing spaces #368)compareModelstocompareRxnsGenesMetsComps(PR fix: rename compareModels into compareRxnsGenesMetsComps #388)convertToIrrev(PR refactor: convertToIrrev speedup #391)getKEGGModelForOrganismnow checks organismID validity (PR fix: getKEGGModelForOrganism now checks organismID validity #392)checkInstallationhasdevelMode, when set to true it also tests CD-HIT and MAFFT binaries, otherwise these are skipped by defaultsortIdentifierssorts metabolites, reactions, genes and compartments alphabetically by their identifier, and can be set as option (sortIds, default = false) when exporting models (PR feat: sort model alphabetically by identifiers #364)getKEGGModelForOrganismto take a preloaded model fromgetModelFromKEGG, to speed up generating many models for different species (PR feat: speed up getKEGGModelForOrganism #369)checkModelStructincludes check for objective function (PR feat: confirm single obj func by checkModelStruct #379)checkInstallation: remove reference to mosek, and output MATLAB release (PR doc: remove reference to mosek and output MATLAB release #373)updateDocumentationremoveskeggModel.mat(PR fix+feat: updateDocumentation now removes keggModel.mat file #389)main(PR chore: rename master to main #383)I hereby confirm that I have:
mainas a target branch