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by The COBRApy Team

Release notes for cobrapy 0.9.0


  • Model.compartment is now a dynamic property fetching the compartments from all metabolites therefore always up-to-date. Assigning a dictionary to the same property updates the internal dictionary of compartment descriptions. This change removes the need for the check for missing compartments from validation.check_metabolite_compartment_formula.
  • Excessively long output of html representations in jupyter notebooks are now abbreviated #577.
  • Reaction forward and reverse variables are no longer cached with those object. No visible effect but simplifies the code.
  • Fix bug in summary methods when used with exchange reaction sas objective. #595.

New features

  • Model.objective_direction is a new revertible property to set maximization / minimization using the context manager.
  • Change output of production_envelope to wide data frame format #587. Also allow multiple carbon source reactions and better handling of zero-division exceptions.
  • Enable summing lists of reactions, see #596

Deprecated features

  • Model.get_metabolite_compartments is deprecated (use Model.compartments instead).
  • Reaction.get_compartments is deprecated (use Reaction.compartments instead).

Backwards incompatible changes

  • The format of the dataframe production_envelope changed listing max and min on different columns instead of the same.