Chore: update COBRA+RAVEN toolboxes #253
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xml changes due to opencobra/cobratoolbox#1631
* change in yml: use of quotes for fields (SysBioChalmers/RAVEN#309) * adpated saveYeastModel to be compliant with new exporting structure introduced in SysBioChalmers/RAVEN#303 (temporal)
after COBRA (opencobra/cobratoolbox#1604) and RAVEN (SysBioChalmers/RAVEN#313) added functionality for them
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Main improvements in this PR:
Updated COBRA and RAVEN to their latest versions, with the following effects:
.xmlfile, after feat: SBO terms for reaction bounds opencobra/cobratoolbox#1631.ymlfile, after feat: preserveQuotes flag in writeYaml RAVEN#309. This will take care of fix: cobrapy parsing errors of yaml #238.model.subSystemstomodel.rxnKEGGpathways, now that both COBRA (feat: new annotation fields opencobra/cobratoolbox#1604) and RAVEN (chore: update COBRA structure fields RAVEN#313) have functionality for them. This will allow fix: subSystems field #11 to proceed ;)NB: In order to be compliant with the new exporting structure introduced in SysBioChalmers/RAVEN#303,
saveYeastModelwas temporally adapted, until we switch to thestandard-GEMformat (more discussion at #232).I hereby confirm that I have:
develas a target branch (top left drop-down menu)