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Clean project structure for v3 - #2
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RAVEN moved its source folders under `src/` (CompMetEng/RAVEN#2). The API index looked for them at the top level, so every MATLAB category came out empty and the generator stopped on `curated_pairs.yml`. It now reads from `src/` when that folder exists, and the RAVEN submodule moves to a commit with the new layout. With it, 170 MATLAB functions are indexed and none are unmapped.
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Copied from SysBioChalmers/RAVEN#761, opened by ae-tafur on 2026-10-10.
Main improvements in this PR:
Justification: The repository root held about 25 top-level folders, with source code, tests, generated docs, third-party code and binaries all mixed together. This made it hard to navigate and put every folder on the MATLAB path. This PR moves to a conventional layout (
src/,tests/,docs/,tutorials/,img/). It changes no behaviour, and all paths that depended on the old layout are updated.analysis,annotation,biomass,comparison,conditions,conversion,core,curation,deprecated,gapfilling,INIT,installation,io,localization,manipulation,queries,reconstruction,solver,tasks,utils,visualization) undersrc/.GLPKmex,libSBML,m2html,mafft,scip,WoLFPSORT,blast+,diamond,hmmer) fromsoftware/tosrc/external/.testing/totests/andtutorial/totutorials/(data files now intutorials/data/).doc/todocs/html/andreadme/todocs/readme/.RAVEN.pngtoimg/.findRAVENrootlocated the installation throughRAVEN.pngin the root. It now usesversion.txt, so moving the image does not break root detection.checkRaven,optimizeProb,setRavenSolver,downloadRavenBinaries,getBlast,getDiamond,getKEGGModelForOrganism,ravenCobraWrapper,standardizeModelFieldOrder,runRAVENtestsand the KEGG functions.updateDocumentationnow scanssrc/and writes todocs/html/. It also no longer references the removedlegacy/softwarefolder.tSyntax,tBinaries,tInstallation,tIO,tTasks,tGenomeData,tReconstruction,tManipulation,RavenTestCase) to the new paths.tutorial1.m,CONTRIBUTING.md, tests README and_config.yml(logo andkeep_files) to the new paths.tests.yml,documentation.yml,release-bundle.yml,assemble_offline_software.pyand.gitignoreto the new paths.Instructions 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.