fix: read compartment annotations in readYAMLmodel - #676
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writeYAMLmodel emits an annotation block per compartment, but the reader's compartment section had no switch: every annotation line became a compartment of its own. Reproduced on tutorial/iAL1006 v1.00.xml, where a YAML round-trip turned 4 compartments into 12 (p, annotation, go, m, annotation, go, ...) with compNames of !!omap and GO:0005777, after which exportModel hard-errored on duplicate compartment IDs. The reader now recognises the annotation key and gathers the entries into compMiriams, mirroring the metabolite/reaction/gene sections. Annotation entries are indented deeper than the compartment they belong to, which is what separates them from the next compartment. Adds a round-trip test asserting comps, compNames and compMiriams; the existing YAML test only asserted a reaction count, which is why this survived.
Function test results241 tests 219 ✅ 1m 2s ⏱️ Results for commit cfc153d. |
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Main improvements in this PR:
readYAMLmodelread each compartment's annotation block as additional compartments, so a YAML round-trip of the tutorial model turned 4 compartments into 12 andexportModelthen failed on duplicate compartment IDs. Annotations are now read intocompMiriams.tIO.massertingcomps,compNamesandcompMiriams.Instructions on merging this PR:
develop3as target branch, and will be resolved with a squash-merge.