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fix: read notes maps in readYAMLmodel - #12
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cobrapy and raven-toolbox write other tools' notes on metabolites and reactions as a map under notes. readYAMLmodel stopped with 'Unknown entry' on them; it now reads each entry into metNotes or rxnNotes.
A key in a notes map named like an entry field (id, name, annotation) was read as that field, and list values in the map lost their items.
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Function test results433 tests 426 ✅ 1m 14s ⏱️ Results for commit 0d81bf1. |
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Main improvements in this PR:
readYAMLmodel: a metabolite or reaction whosenotesis a map, as cobrapy and raven-toolbox write the notes of other tools (for example geckopy'senzyme_usageandgeckopy_warning), stopped the read with "Unknown entry in yaml file", so GECKO could not load an ecModel saved by geckopy. The map is now read intometNotesorrxnNotesas text: anoteentry as its value, other entries askey: value, list values as comma-separated items, entries separated by;. Its lines are recognised by their indentation, so a key named like an entry field (id,name,annotation) stays in the note.Instructions on merging this PR:
developas target branch, and will be resolved with a squash-merge.mainas target branch, and will be resolved as described here.