0.8.0

Release notes for cobrapy 0.8.0

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 to
  Model.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 and
  cobra.flux_analysis.find_essential_reactions.
• Model.optimize has new parameter raise_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 gives reaction.id.