[edkerk]

Documents all parameters of the public functions, aligns eleven functions with RAVEN, replaces comments that contradicted the corrected docstrings (#188) and removes the hard-coded big_m=100 from the sweep script.

Documentation

• Every function exported through __all__ has a Parameters entry for each argument (117 functions, 565 parameters), with Returns and Raises sections where the code returns a structure or raises. Defaults equal the signature defaults.
• Comments state the current behaviour: the prove_abs_gap measurements of ftinit, the case handling of template ids, the "RAVEN MILP" wording of get_min_nr_fluxes, the reason in _NON_DNF_REASON.
• set_exchange_bounds is annotated list[str | Metabolite], and compare_models accepts os.PathLike for tasks.
• scripts/analyze_init_params.py takes --big-m (default: the ftinit default of 1000) and keys its sweep cache on big_m.

Behaviour

Function	Behaviour
init.fill_tasks (resolve_ties=True, Gurobi)	Restores MIPGap and MIPGapAbs of reference_model after each gap-fill.
tasks.find_task_essential_reactions	Writes cache_path as JSON. A file that is not a JSON cache of the current version, such as a pickle, is ignored with a warning. checkpoint_every below 1 raises ValueError.
init.hpa_gene_scores	An empty level_scores mapping uses the default level scores.
init.rna_gene_scores	tissue is compared case-insensitively; the highest TPM over tissue names that differ in case is used, as in scoreModel.
localization.predict_localization (apply=True)	Returns a copy of the model when no gene has a score.
localization.assign_compartments	The default growth floor is 10 % of the maximum flux of biomass_reaction.
reconstruction.kegg.organisms_in_domain	An empty domain raises ValueError.
conditions.load_condition	An empty file returns {}, which apply_condition applies as a condition without steps, as RAVEN's parseYAML and applyCondition do.
analysis.reporter_metabolites	A scored gene without an entry in gene_fold_changes is in neither the "up" nor the "down" subset.
manipulation.constrain_reversible_reactions	Skips the Gurobi tolerance setting only when the solver has no Params attribute.
gapfilling.connect_blocked_reactions	The RuntimeError for a non-optimal MILP names the MILP.

The parity generator scripts/parity/generate_oracles.m records reporterMetabolites with fold changes and an empty condition file. The recorded oracles are in tests/data/parity/oracles/, with the RAVEN commit in PROVENANCE.md.

CHANGELOG.md has an entry for each change.