Documentation index, known-issues catalogue and MATLAB back-port doc#10
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read_yaml_model now opens+parses the file then delegates the post-parse work (capturing per-entry side-fields onto notes, restoring legacy metaData id/name, stashing unknown top-level sections onto model.notes['_yaml_sections']) to a new model_from_yaml_data(raw: dict) helper. This lets downstream packages that need to pre-normalise their YAML before cobra reads it (e.g. geckopy, which lifts legacy MATLAB ec-model quirks like top-level per-metabolite `smiles` into `annotation` and merges bare-`-` sequence-of-single-key-maps back to a mapping) hand the cleaned dict directly to the post-parse pipeline, without round-tripping through a temp file. Both functions are exported from raven_python.io.yaml. Pure refactor on the read side; no behaviour change for existing read_yaml_model callers.
cobra's model_to_dict serialises model.notes verbatim into the output doc as the 'notes' section. write_yaml_model already pops these three management keys from a local copy of model.notes to use them as top-level YAML fields, but the originals remained on model.notes and therefore also leaked into doc['notes'], producing duplicate sections in the file (the legitimate top-level emit AND a nested copy inside notes). Strip them from doc['notes'] post-model_to_dict and drop the notes section entirely when nothing else is left. Discovered while round-tripping a geckopy ecModel (it stashes ec-rxns / ec-enzymes / gecko_light on model.notes['_yaml_sections']); was visible as duplicated GECKO sections in the written YAML.
…d-matlab-docs # Conflicts: # src/raven_python/io/yaml.py
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The reader-facing documentation: the docs index, the function-by-function RAVEN→raven-python migration map, the CHANGELOG, the closed known-issues catalogue (sections A–F with regression-test pointers), and a consolidated list of fixes and improvements proposed for back-port into MATLAB RAVEN.
Base: feature/localization.