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* fix: predictLocalization with CELLO output * fix: setParam bug * WIP: mergeModels copyToComps * fix: copyToComps keeps ...From fields * chore: fitTasks correct flags to fillGaps * fix: mergeModels and copyToComps ...From fields * fix: addRxns make subSystems nested cell arrays * refactor: exportModel speedup subSystem parsing * feat: runRAVENtests for quick local tests
* chore: update MAFFT to 7.526 * chore: update HMMER to 3.4.0 * chore: update DIAMOND to 2.1.17 * chore: update BLAST+ to 2.17.0 * fix: use HMMER via WSL2 * chore: update kegg*.mat files with KEGG 116 * feat: getKEGGModelForOrganism refer to new HMMs * feat: getKEGGModelForOrganism HMM zip URL * fix: exportModel concatenate subSystems for groups
* fix: store ravenPath as MATLAB preference * fix: subSystems either nested or not * fix: regenerate keggRxns, bug in subSystems * fix: fully support subSystems as nested or not * fix: YAML file allowed to have no genes * chore: updateDocumentation * fix: subSystems * fix: ravenCobraWrapper subSystems, init-params * fix: mergeModels giving useless output * fix: ravenCobraWrapper
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Tests pass locally |
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Main improvements in this PR:
predictLocalizationandparseScoresto correctly handle output from CELLOsetParamreport reactions not found in modelmergeModelswill only make newmetFrom,rxnFormandgeneFromfields if none of the initial models have these fieldssubSystemsin various functions, RAVEN supports both cell arrays and nested cell arraysrunINITretainsparamsas flag foroptimizeProbinputcopyToCompsdoes not add or modifymetFrom,rxnFormorgeneFromfieldsaddRxnsmakes sure that subSystems are nested cell arraysfitTasksparses correct arguments tofillGapsexportModelspeed-up subSystems handlingrunRAVENtestsruns RAVEN unit testsparseTaskListclarifies that it can handle boht *.txt and *.xlsx as inputInstructions on merging this PR:
developas target branch, and will be resolved with a squash-merge.mainas target branch, and will be resolved as descriped here.