[edkerk]

Where geckopy and GECKO gave different results for the same input, both now behave alike. Invalid input raises, data that cannot apply to an item is skipped with a warning, and an explicitly empty list selects nothing. Each change has a test, and the CHANGELOG lists them.

Function	Behaviour
read_kcat_source	a row of empty quoted fields is skipped; a field that opens a quote and never closes it raises ValueError
read_dlkcat_output, write_dlkcat_input	non-finite kcats are dropped; rows are written in ec.rxns order
ECTree, kcats_from_ec_tree	k = NaN raises; an empty ec_rxns gives an empty list; a repeated reaction counts once
assign_standard_kcat	an exchange reaction is one without substrate or without product
review_assignment, EcStats, ec_stats_from_brenda	exported from geckopy.gather_kcats and geckopy; the sources custom and standard compare in any case
find_met_smiles	an empty metabolite name is skipped with a warning
screen_kcat_leverage, compute_excarbon	equal-rank rows keep the order of their tie groups; a model without metabolite formulas warns
best_parsimonious, cmaes_kcat_tuning	a NaN RMSE is skipped; the search does not stop on cma's flat-fitness criteria
geckopy.kcat_tuning.evotune	exports best_parsimonious, n_changed, parsimony_frontier and isozyme_tie_map
ec_fseof	targets are ranked by slope times correlation rounded to 9 significant digits, so scores equal up to solver noise keep model order
fill_enz_concs, constrain_enz_concs	a negative abundance or concentration raises; a prior lower bound above the new upper bound is reset to 0
load_flux_data, report_enzyme_usage, enzyme_usage	a missing file, a file without exchange columns and a ragged row raise; a negative top_abs_usage raises; an enzyme without a usage reaction is left out with a warning
apply_kcat_constraints	on a light model the update list takes cobra ids and ec ids
pfba_enzymes	a given fraction_of_optimum is multiplied by 0.999999, as the default is
save_ec_model	an ec reaction without enzymes is written without an enzymes entry (the readers still accept the older forms); an existing metaData description is kept

Depends on CompMetEng/raven-toolbox for the writer of the ec-rxns section and for the reader that turns GECKO 3 protein reactions forward. Parity: CompMetEng/raven-gecko-parity ledger and scenarios.