0.11.0

Please see https://github.com/opencobra/cobrapy/tree/0.11.0/release-notes/0.11.0.md for the full release notes.

0.10.1

Please see https://github.com/opencobra/cobrapy/tree/0.10.1/release-notes/0.10.1.md for the full release notes.

0.10.0

Please see https://github.com/opencobra/cobrapy/tree/0.10.0/release-notes/0.10.0.md for the full release notes.

0.9.1

Please see https://github.com/opencobra/cobrapy/tree/0.9.1/release-notes/0.9.1.md for the full release notes.

0.9.0

Release notes for cobrapy 0.9.0

Fixes

• Model.compartment is now a dynamic property fetching the
  compartments from all metabolites therefore always
  up-to-date. Assigning a dictionary to the same property updates the
  internal dictionary of compartment descriptions. This change removes
  the need for the check for missing compartments from
  validation.check_metabolite_compartment_formula.
• Excessively long output of html representations in jupyter notebooks are now abbreviated #577.
• Reaction forward and reverse variables are no longer cached with those object. No visible effect but simplifies the code.
• Fix bug in summary methods when used with exchange reaction sas objective. #595.

New features

• Model.objective_direction is a new revertible property to set maximization / minimization using the context manager.
• Change output of production_envelope to wide data frame format #587. Also allow multiple carbon source reactions and better handling of zero-division exceptions.
• Enable summing lists of reactions, see #596

Deprecated features

• Model.get_metabolite_compartments is deprecated (use
  Model.compartments instead).
• Reaction.get_compartments is deprecated (use
  Reaction.compartments instead).

Backwards incompatible changes

• The format of the dataframe production_envelope changed listing max and min on different columns instead of the same.

0.8.2

Release notes for cobrapy 0.8.2

Fixes

• Guarantee that sampler._reproject always returns a feasible point
  and will not attempt to reproject already feasible
  points. #564
• Model.summary no longer fails when calling after the model has
  changed. Fixed by letting the summary function re-compute a solution
  (default) or letting user supply a prior computed solution
  object. #566
• Metabolites must now have valid identifiers before being added to a
  model or ValueError is raised.
• Fix use of underscores in key/value pairs in legacy sbml
  notes. #547

Backwards incompatible changes

• the Solution class no longer contains links progenitor model's
  reactions and metabolites. Removed since it those can change after
  the solution has been computed making them erroneous. This of course
  implies that Solution constructor changes to:

      def __init__(self, objective_value, status, fluxes, reduced_costs=None,
                 shadow_prices=None, **kwargs):
  

0.8.1

Release notes for cobrapy 0.8.1

Fixes

• Fix bug related to inhomogeneous sampling
  #558. During
  flux sampling, store the nullspace rather than the entire projection
  (N * N.T) which reduces the memory footprint since it uses memory in
  the order of 2 * n_reaction * n_metabolites instead of 4 * n_reactions^2 (no change in
  speed). PR #556

0.8.0

Release notes for cobrapy 0.8.0

Fixes

• Tests no longer generates warnings about using deprecated functions.
• Gapfilling integrality thresholds now supported for all optlang solvers.

New features

• Model.slim_optimize() can be used perform optimization without
  creating a solution. Can lead to significant speedup compared to
  Model.optimize when repeatedly doing optimizations and only making
  use of the objective value as avoiding the need to fetch all values
  from the solver object.
• solution, model, metabolite and reaction now have html
  representation so they give more informative prints in jupyter
  notebooks.
• New convenience functions cobra.flux_analysis.find_essential_genes and
  cobra.flux_analysis.find_essential_reactions.
• Model.optimize has new parameter raise_error to enable option to
  get trigger exception if no feasible solution could be found.
• str(reaction) now gives the more useful reaction id and the
  reaction string.

Deprecated features

• str(reaction) no longer gives reaction.id.

0.7.0

Release notes for cobrapy 0.7.0

Fixes

• cobra.flux_analysis.reaction.assess
  was broken
  following the release of 0.6.0 and has now been fixed (and now with
  unit tests).
• production_envelope failed when model C-source was formulated as
  -> x instead of x <-. Fixed added option to guess the C-source by
  taking the medium reaction with the highest input C flux.
• model_to_pymatbridge needs scipy and that's correctly handled now.

New features

• flux_variability_analysis now has the pfba_factor parameter
  which enables the inclusion of a constraint on the max sum of
  absolute fluxes when doing FVA.

Deprecated features

• cobra.flux_analysis.reaction.assess_{precursors,products} were
  essentially copies of each other and have been merged to
  cobra.flux_analysis.reaction.assess_component

0.6.2

Release notes for cobrapy 0.6.2

Fixes

• Fix in the ordering and rounding of FVA summary
  #525
• Shared memory, improve speed during sampling
  #521
• Debug model.remove_reactions to properly work with context manager.
  This lead to the deprecation of reaction.delete as this was not compatible
  with the concept of being able to later revert the change.
  #506,
  #508.
• Adding two models (modela + modelb) again results in a model with
  the objective set to the sum of the two models objectives
  #505.
• When adding reactions to a model, the reactions with identifiers
  identical to those in the model are
  ignored. #511

New features

• model.merge can be used to merge two models, more flexibly than
  the overloaded + and += operators.

Deprecated features

• reaction.delete has been deprecated in favor of reaction.remove_from_model
• overloaded + and += for cobra.Model are deprecated in favor of
  model.merge