v0.3.0

Parity pass against the MATLAB GECKO Toolbox: geckopy's core functions now reproduce every value GECKO's own unit-test suite pins down.

Added

• tests/test_gecko_matlab_parity.py — a 1:1 port of GECKO's test/unit_tests/geckoCoreFunctionTests.m (47 tests, MATLAB test cases tc0001–tc0013), run against the same ecTestGEM fixture MATLAB uses. Every expected value is copied verbatim from the MATLAB sources rather than re-derived from geckopy's output, so the file is the executable definition of "geckopy builds the same ecModel as GECKO". It needs no MATLAB to run and covers makeEcModel (full and light), applyComplexData, setProtPoolSize, getECfromGEM, getECfromDatabase, save/load round-trip, fuzzyKcatMatching, writeDLKcatInput, mergeDLKcatAndFuzzyKcats, selectKcatValue, applyKcatConstraints, getKcatAcrossIsozymes, applyCustomKcats, findMetSmiles and the proteomics-integration chain.

Fixed

• make_ec_model sorts identifiers for full models, as MATLAB makeEcModel does (sortIdentifiers, line 203, full models only, before the protein pseudoreactions are appended). geckopy kept the input GEM's reaction order, so a full ecModel came out with the same reactions in a different order from MATLAB's — visible in the saved YAML and in every downstream table that follows ec.rxns order.
• write_dlkcat_input emits rows in reaction order, matching MATLAB's column-major find(clearedRedS < 0). numpy's where is row-major, so geckopy grouped the DLKcat input by substrate instead of by reaction.
• EcModel.copy() clones the ec substructure. cobra.Model.copy rebuilds the network but carries every other attribute over by reference, so model.copy().ec was the same EcData object as model.ec: writing a kcat, eccode, source, conc or coupling coefficient on the copy silently changed the model it was copied from. The copy's enzymes view was likewise still bound to the original model, so reads and writes through model.enzymes went to the wrong model. copy() now clones ec and rebinds enzymes, giving the value semantics MATLAB GECKO has throughout. adapter stays a shared reference (project configuration, not model state). copy.deepcopy(model) was already correct and is unchanged.
• Reverse (_REV) reactions keep their EC code, via a fix in raven-toolbox's convert_to_irreversible (it now copies annotations, subsystem and notes onto the reverse reaction, as MATLAB's convertToIrrev copies eccodes / rxnMiriams / subSystems / rxnNotes). Without it fill_eccodes_from_gem returned '' for every _REV reaction, fuzzy BRENDA matching found no kcat, and reverse directions were left unconstrained. Requires raven-toolbox at or after that fix.
• copy.deepcopy(ec_model) (and of any cobra.Model) no longer RecursionErrors on Python 3.14. The cause was in cobra, not geckopy: Reaction.__copy__/__deepcopy__ delegated to super() as a way to avoid infinitely recursing into themselves, but that trick relies on copy memoizing an object before recursing into its state, and Python 3.14's copy module no longer does so for that code path. Every reaction holds its metabolites and every metabolite holds the reactions it participates in, so the resulting cycle exists in any real model, full ecModels included — deep-copying one recursed until the interpreter's recursion limit gave out. Fixed upstream in cobra 0.31.0 by deleting the overrides; requires cobra at or after 0.31.1.
• examples/yeast-GEM's adapter config used a rejected pydantic field. model_adapter.toml set uniprot.tax_id, but ModelParameters's schema (additionalProperties=false) has no such field — it's called id, and already defaults to the taxonomy id — so ModelAdapter.from_folder raised a validation error on this folder unconditionally. A parametrized regression test now runs over every examples/ subfolder so schema drift like this is caught for any future adapter config too. (#34)

Documentation

• Docstrings across geckopy's source and tests reviewed for clarity and accuracy: MATLAB-COMPAT comparison paragraphs replaced with plain statements of current behavior, other historical/regression narration dropped, and several docstrings that no longer matched the code corrected. Comment/docstring-only; no functional changes. (#36)
• protein_pool.py's module docstring no longer claims prot_pool_exchange's direction diverges from MATLAB pending a "future I/O layer". GECKO MATLAB's makeEcModel.m already writes the same forward (lb=0, ub=1000) convention as geckopy; the reverse convention only applies to legacy pre-GECKO-4 files, which load_ec_model.py already normalizes on load. (#38)
• mw.py's stale MATLAB-COMPAT comments removed now that calculate_mw matches GECKO MATLAB's current water-mass constant (18.01528) and mean X-residue mass (118.885), closed upstream as GECKO#459. No behavioral change — the code already computed the now-matching values. (#39)

Internal

• Removed the dead _run_preprocess stub from test_populate_ec: an empty helper (docstring and comments, no body) that was never called. The preprocessing stages it described are already exercised elsewhere. (#37)

Notes

• merge_kcats is n-ary and concatenates surviving rows list by list, so the equivalent of MATLAB's mergeDLKcatAndFuzzyKcats(dlkcat, fuzzy) — which always emits fuzzy rows first regardless of argument order — is merge_kcats(fuzzy, dlkcat, ...). The deprecated merge_dlkcat_and_fuzzy_kcats alias is merge_kcats, so it follows the geckopy convention, not MATLAB's signature. Row order has no numerical effect: apply_kcat_list aggregates per reaction.

Full changelog: https://github.com/SysBioChalmers/geckopy/blob/main/CHANGELOG.md
Compare: v0.2.1...v0.3.0