@hredestig hredestig released this Jul 21, 2017 · 145 commits to devel since this release

Assets 2

Release notes for cobrapy 0.8.0


  • 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
  • New convenience functions cobra.flux_analysis.find_essential_genes and
  • 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.