fix: yaml eccode annotation handling#613
Merged
Merged
Conversation
edkerk
force-pushed
the
fix/yaml-eccode-annotation
branch
from
d092fa1 to
0fc2fd0
Compare
EC numbers are a standard MIRIAM cross-reference, so cobrapy and geckopy read them from annotation['ec-code'] (a list). RAVEN wrote them as a top-level reaction `eccodes` key, which plain cobra.io ignores -- so EC codes never reached the annotation['ec-code'] location geckopy reads from, and raven-python had to special-case the top-level key. writeYAMLmodel now emits EC numbers inside the per-reaction `annotation` block as `ec-code`, fused with rxnMiriams the same way metabolite SMILES already is (writeAnnotation generalised to 'met' and 'rxn'); always a list, even for a single code, to match cobrapy/raven-python/geckopy. readYAMLmodel gains a `case 'ec-code'` that captures the annotation form into model.eccodes; the legacy top-level `eccodes` key is still read for older files. Verified end-to-end on yeast-GEM (MATLAB R2024b): read old top-level eccodes -> write annotation ec-code -> read back keeps all 2411/4102 reactions' EC codes unchanged. A permanent EC-code case in importExportTests.m would lock this in. Pairs with raven-python io.yaml (same change there).
edkerk
force-pushed
the
fix/yaml-eccode-annotation
branch
from
0fc2fd0 to
c997cc1
Compare
edkerk
changed the title
This was referenced Jun 7, 2026
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Main improvements in this PR:
Instructions on merging this PR:
develop3as target branch, and will be resolved with a squash-merge.mainas target branch, and will be resolved as descriped here.