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Porthmeus / MeMoMe

Metabolic Model Merging - a semiautomated way to merge genome scale metabolic models
Apache License 2.0
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Addition of gapsec annotation and changes in VMH annotation. #144

Open DafniGi opened 1 month ago

Porthmeus commented 1 month ago

Hej Dafni - could you check and solve the error which is thrown by the test?

DafniGi commented 1 month ago

I changed the annotate(whatever database)_entry to give as output inchi, annotations, and names to avoid writing the same code twice in the other 2 annotate functions for the inchi strings. Do we want to keep this output strictly as annotations, names?

Porthmeus commented 1 month ago

I changed the annotate(whatever database)_entry to give as output inchi, annotations, and names to avoid writing the same code twice in the other 2 annotate functions for the inchi strings. Do we want to keep this output strictly as annotations, names?

That sounds reasonable - looking through your commit, it looks like you did this now for VMH but not the other databases. We should maybe make the functions consistent across databases - so that all annotate_entry functions will return the inchi string or None in the place, if no Inchi can be found. In that way, we know what to expect from these functions.

Porthmeus commented 1 month ago

BTW: tell us if you need help with the tests.