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.

Fixes

• 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.

Documentation

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

Internal

• 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.