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0.9.0
by The COBRApy Team
Release notes for cobrapy 0.9.0
Fixes
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 fromvalidation.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 (useModel.compartments
instead).Reaction.get_compartments
is deprecated (useReaction.compartments
instead).
Backwards incompatible changes
- The format of the dataframe
production_envelope
changed listing max and min on different columns instead of the same.