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by The COBRApy Team

Release notes for cobrapy 0.14.0

New features

  • Adding boundary reactions is now much more flexible and accepts user-defined identifiers.
  • It is now possible to run FVA and loopless FVA in parallel.
  • Some utilities and an example of how to perform static optimization dynamic FBA.
  • There now is a global configuration singleton cobra.Configuration() that can be used to set default bounds for newly created reactions and set a default solver for all newly created or parsed models.
  • Setting a time limit on solvers now still allows users to retrieve the flux distribution at the point of time out.


  • Infinity values are now properly handled and passed down to optlang.
  • Properly update the model objective on leaving a model context.
  • New metabolites are now included in the gapfilling process.

Deprecated features

  • We are deprecating a special case of lower and upper bound behavior. Please read more about it in #793 and let us know what you think.

Backwards incompatible changes

  • The old solver interfaces that were deprecated for a long time have been removed.


  • Better documentation for the minimal medium functionality.
  • Additions to the contribution guidelines.


  • Improve indexing for find_blocked_reactions.
  • Adjust the test suite for pytest 4.0 and update the configuration.
  • The module structure and corresponding tests are broken up and re-organized.