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Read a metabolite SMILES annotation whatever shape it is in - #56
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cobra returns an annotation value as the object it was assigned, and as a list for a model read back from a file. A metabolite annotated in memory by find_met_smiles carries "CCO"; the same metabolite after save_ec_model + load_ec_model carries ["CCO"]. extract_enzyme_substrate_pairs -- which both write_dlkcat_input and the OpenKineticsPredictor input builder go through -- assumed the string. On a reloaded model the ignore-list membership test hashed a list and the whole step died with TypeError, and had it not, the list would have been written into the DLKcat input in place of the SMILES. The tutorial does not hit this because it annotates and writes in one session, but it documents reloading from the saved stage-1 model between those steps, which is enough to reach it. databases.met_smiles reads either shape and is the one place that knows the difference.
`parse_okp_output`: indexing metabolites by `annotation['smiles']` used the annotation value as a dict key, which raises `TypeError: cannot use 'list' as a dict key` on a saved-and-reloaded model, the same shape mismatch `met_smiles` already handles for the DLKcat input writer.
…ion-round-trip # Conflicts: # CHANGELOG.md
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cobra returns an annotation value as the object it was assigned, and as a list for a model read back from a file. A metabolite annotated in memory by
find_met_smilescarries"CCO"; the same metabolite aftersave_ec_model+load_ec_modelcarries["CCO"].extract_enzyme_substrate_pairs— which bothwrite_dlkcat_inputand the OpenKineticsPredictor input builder go through — assumed the string:On a reloaded model that raises
TypeError: cannot use 'list' as a set element (unhashable type: 'list'), and had it not, the list would have been written into the DLKcat input in place of the SMILES.Reproduced on the full_ecModel tutorial: save the stage-1 model after
find_met_smiles, reload it, callwrite_dlkcat_input— TypeError. The tutorial itself does not hit it because it annotates and writes in one session, but it documents reloading from the saved model between those steps.databases.met_smilesnow reads either shape and is the one place that knows the difference. Two regression tests cover the list-valued annotation: that the SMILES still reaches the output, and that the ignore-list check still matches.Found while benchmarking something unrelated, where it silently degraded structure-based substrate matching to name-only matching rather than raising.