docs: update RAVEN cross-references for the post-reorg folder layout#20
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RAVEN moved its functions out of the core/ catch-all into purpose-based top-level folders (SysBioChalmers/RAVEN#614). Repoint every RAVEN file path in the cross-reference docs (IMPROVEMENTS.md, docs/reference/matlab_raven_backports.md): - FSEOF / randomSampling / reporterMetabolites -> analysis/ - parseTaskList / checkTasks -> tasks/ - fillGaps -> gapfilling/ - addRxns / changeRxns / standardizeGrRules -> manipulation/ - getIndexes / checkModelStruct / getElementalBalance -> queries/ - getModelFromHomology -> reconstruction/homology/ - getKEGGModelForOrganism -> reconstruction/kegg/ - runINIT / ftINIT -> INIT/ Also corrects references that were stale even before the reorg (getKEGGModelForOrganism was in external/kegg/) and points the proposed GPR-lint back-port findPotentialErrors at manipulation/, alongside standardizeGrRules. Doc-only: raven-python's module layout already matches RAVEN's new structure (it was the template the reorg mirrored), so no code changes are needed.
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What
RAVEN reorganised its MATLAB functions out of the
core/catch-all into purpose-based top-level folders (SysBioChalmers/RAVEN#614, ondevelop3). This repoints the RAVEN file paths in raven-python's cross-reference docs to their current locations.IMPROVEMENTS.mdanddocs/reference/matlab_raven_backports.md— everycore/<fn>.mreference updated:analysis/tasks/gapfilling/manipulation/queries/reconstruction/homology/reconstruction/kegg/INIT/Doc-only; no code changes. raven-python's module layout already matches RAVEN's new structure (it was the template the reorg mirrored), so the only thing that drifted was these textual cross-references. (Two were stale even before the reorg —
getKEGGModelForOrganismlived inexternal/kegg/— and the proposed GPR-lint back-portfindPotentialErrorsnow points atmanipulation/.)Assessed but intentionally not done (follow-ups)
plotting/→visualization/— RAVEN unifiedpathway/+plotting/intovisualization/. raven-python'splotting/is an unused stub, and renaming it would also churn the user-facing[plotting]pip extra — better done when that subpackage is actually implemented.reconstruction/metacyc/— RAVEN has MetaCyc reconstruction; porting it is feature work, out of scope for a folder-alignment change.