Read the model adapter from model_adapter.toml, shared with geckopy

[edkerk]

Copied from SysBioChalmers/GECKO#486, opened by edkerk on 2026-10-15.

A project's model adapter can now be model_adapter.toml, the file geckopy reads, so one file configures GECKO and geckopy. Adapter classes keep working. See CompMetEng/raven-gecko-parity#132.

Loading

• ModelAdapterManager.getAdapter and setDefault take the project folder, its model_adapter.toml, or an adapter class .m file as before.
• A TOML file gives a TomlAdapter.

New functions (src/model_adapter/)

Function	What it does
readAdapterToml, writeAdapterToml	Read and write the TOML subset adapters use: comments, strings, numbers, booleans, arrays (also over several lines), tables and arrays of tables. Anything else stops with an error that names the line.
loadAdapterParams	Maps the snake_case keys to GECKO's field names and fills geckopy's defaults, both from adapterParameters.tsv. Unknown keys are errors, as in geckopy. Paths are relative to the project folder. Evotune source groups become kcatSources and sigma0logSource.
TomlAdapter	Spontaneous reactions from [spontaneous] (name_contains, file). The anaerobic and protein-content functions used during tuning from [matlab]. Parameters only GECKO uses from [matlab.params]. A project that needs more code subclasses TomlAdapter.
convertAdapterToToml	Writes an existing adapter class to model_adapter.toml, keeping parameters without a geckopy name under [matlab.params]. Lists the methods it cannot carry over, with what to use instead.

Project creation: createGECKOproject writes model_adapter.toml from adapterTemplate.toml. 'adapterFormat','class' gives the class template.

Tutorials

• full_ecModel uses model_adapter.toml; YeastGEMAdapter.m is removed. The parameters are identical, and the same 6 reactions of yeast-GEM are spontaneous.
• light_ecModel's HumanGEMAdapter subclasses TomlAdapter and keeps getHumanGEMRootPath. The parameters are identical. All 14 reactions that data/spontaneousReactions.tsv marks are now spontaneous; the class found one.

Tests

• test/unit_tests/adapterTomlTests.m (tc0061–tc0068) covers:
  • the reader's features and errors;
  • write and read round trips;
  • defaults and unknown keys;
  • source groups;
  • converting TestGEMAdapter and a legacy-style class and loading the result back to the same parameters;
  • spontaneous reactions;
  • a new project.
• The new functions also read geckopy's tutorial and example adapters and ecModels' ecYeastGEM/model_adapter.toml.
• All 60 existing unit tests pass (MATLAB R2023a, RAVEN develop3, GLPK).

geckopy accepts the [spontaneous] and [matlab] sections in CompMetEng/geckopy#61.

[github-actions]

Unit test results

60 tests   60 ✅  8s ⏱️
 1 suites   0 💤
 1 files     0 ❌

Results for commit 34052a0.

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