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ModelSEED / ModelSEEDDatabase

This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno approach
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widespread update on correctly building transport equations #85

Closed samseaver closed 6 years ago

samseaver commented 6 years ago

This began as a simple exercise following up on travis messages that report whether "compound_ids" and "equation" are inconsistent. The compound_ids field has now been updated to correctly include compounds, and sorted in order.

But the work revealed that a lot of equations didn't have their text updated correctly for transport reactions (for which the compartmentalization was preserved in the stoichiometry field), so, now, the bug has been fixed in Reactions.py and all "code", "equation", and "definition" fields have been updated.

Finally, this work has led to protons being correctly removed from the "code" field.

JamesJeffryes commented 6 years ago

I'm mostly going to trust you on this one because the actual code delta is small