Release notes for cobrapy 0.22.1

Fixes

• Fix an old bug with double gene deletion that was not knocking-out combinations (#1103).
• Lots of syntax, annotation, and docstring fixes (#1081, #1083, #1084, #1085, #1086, #1088, #1090, #1091, #1092, #1093, #1094, #1095, #1096).

Deprecated features

• find_gene_knockout_reactions is deprecated.

Release notes for cobrapy 0.22.0

New features

• Add support for the OSQP and COIN-OR CBC solvers (#946)

Fixes

• Fix the Reaction.compartments attribute not updating after metabolite changes (#1055)
• Lots of syntax, annotation, and docstring fixes (#1058, #1059, #1060, #1063, #1065, #1066, #1076, #1077, #1080)
• Multiprocessing on windows now sends data to processes via a pickle file which should speed up any multiprocessing initialization (#1070)
• Upgrade optlang and fix some tolerance issues (#1011)
• Enable Python 3.9 (#1082)

Documentation

• Document boundary reactions (#1038)
• Documentation is now built again on each release (#1047)
• Clarify pfba in the documentation (#1049)

Other

• COBRApy source code releases are now deposited on Zenodo which provides a citeable DOI (#1061)
• COBRApy creates automatic releases to BioSimulators (#1064)
• Fix deployment of releases to the website (#1068)
• Improve the pyproject.toml config (#1067)

Backwards incompatible changes

• Remove some particular cobra.Reaction.lower_bound and .upper_bound behaviour that has been deprecated for a long time.

Release notes for cobrapy 0.21.0

Other

• Update libSBML dependency to python-libsbml==5.19.0.
• Docstring and style changes.

Release notes for cobrapy 0.20.0

New features

• There is a new function inspired by cameo that can load models directly from BiGG or BioModels and by default will cache them locally (#995), for example,

  from cobra.io import load_model
  
  ecoli = load_model("iML1515")
  ylipo = load_model("MODEL1604280017")
  

Fixes

• Over a series of pull requests, @synchon has been modernizing parts of the codebase for Python 3.6+ (#993, #999, #1000, #1003)
• Upgrade the dependency python-libsbml-experimental to 5.18.3

Release notes for cobrapy 0.18.1

Fixes

• Use the correct SBO term for unbounded (infinite bounds) reactions.

Other

• Pin dependency on python-libsbml-experimental 5.18.1.

Release notes for cobrapy 0.18.0

New features

• Support writing SBML notes on model objects

Fixes

• Test alternative solver
• Handle repeated infeasible optimizations in minimal_medium
• Allow newline characters in SBML notes

Backwards incompatible changes

• Change the container type of groups from set to DictList
• Expect annotation attributes to be of type dict

Internal

• Update Travis CI configuration
• Add Python 3.8 to PyPI classifiers

Contributors

• @BenjaSanchez
• @cdiener
• @ecederstrand
• @Hemant27031999

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 [email protected]. You can also contact them individually at:

• Maureen Carey
• Svetlana Kutuzova
• Greg Medlock

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.