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0.19.0

by The COBRApy Team


Release notes for cobrapy 0.19.0

We now have an official code of conduct and a committee of three people to handle reports! You can contact them at conduct@opencobra.org. You can also contact them individually at:

Many thanks to them for taking on this responsibility.

New features

  • Deletion result DataFrames as returned by functions from cobra.deletions now have a new knockout accessor. See the docs on usage examples.
  • All summaries are now persistent objects. The same summary can be displayed in multiple ways. The underlying data for the summary can also be accessed.
  • The model summary now displays elementary (by default carbon) uptake and secretion.
  • The JSON schema is now available as a stand-alone JSON file.

Fixes

  • Remove the frozenset indexing in deletion DataFrames that is now unsupported in pandas.
  • Summaries for models, metabolites, and reactions are now calculated instantaneously and thus also work with model contexts.
  • JSON models can now contain infinity and NaN values as bounds.
  • The Matlab bridge for reading Matlab models should be restored. Any testing or problem reports are greatly appreciated.

Deprecated features

  • We are progressively updating our codebase. That means that more and more parts will require Python 3.6+.

Backwards incompatible changes

  • Deletion result DataFrames have no frozenset index anymore but now carry the deleted elements in the ids column.