Repository navigation
Share model_adapter.toml with GECKO - #61
Merged
Merged
Conversation
GECKO (MATLAB) now reads model_adapter.toml as well. Two sections make that possible without code in an adapter class: - [spontaneous]: name_contains and/or file set which reactions are spontaneous; the default get_spontaneous_reactions reads them. - [matlab]: settings that only GECKO reads (function names for anaerobic conditions and protein content, and [matlab.params]); geckopy accepts and ignores them. adapterParameters.tsv, the table GECKO uses to map keys to its MATLAB field names and defaults, is shipped here too, and a test checks it against the schema.
This was referenced Oct 15, 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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
GECKO (MATLAB) reads
model_adapter.tomlas well (SysBioChalmers/GECKO#486), so one file configures both tools. See CompMetEng/raven-gecko-parity#132.[spontaneous]:name_containsand/orfile(a TSV with a header row, reaction identifiers and optionally a 0/1 column, relative to the project folder) set which reactions are spontaneous. The defaultget_spontaneous_reactionsreads them. Without the section it returns an empty list, as before.[matlab]: settings only GECKO reads:make_model_anaerobic,change_protein_biomassand[matlab.params]. geckopy accepts and ignores them, so a file converted from a MATLAB adapter class loads.adapterParameters.tsv: the table GECKO uses to map each key to its MATLAB field name and default, shipped ingeckopy/adapter/. A test checks that it lists every schema key with geckopy's default.docs/migrating_from_gecko_matlab.mddescribes the shared file.Existing TOML files load unchanged. The full test suite passes (1,450 passed;
develophas 1,447 and this adds 3).