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0.8.0
by The COBRApy Team
Fixes
- Tests no longer generates warnings about using deprecated functions.
- Gapfilling integrality thresholds now supported for all optlang solvers.
New features
Model.slim_optimize()
can be used perform optimization without creating a solution. Can lead to significant speedup compared toModel.optimize
when repeatedly doing optimizations and only making use of the objective value as avoiding the need to fetch all values from the solver object.- solution, model, metabolite and reaction now have html representation so they give more informative prints in jupyter notebooks.
- New convenience functions
cobra.flux_analysis.find_essential_genes
andcobra.flux_analysis.find_essential_reactions
. Model.optimize
has new parameterraise_error
to enable option to get trigger exception if no feasible solution could be found.str(reaction)
now gives the more useful reaction id and the reaction string.
Deprecated features
str(reaction)
no longer givesreaction.id
.