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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 newknockout
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.