Releases

0.13.4

patch release

This is a bug fix release. It is considered stable but does not include any significant new features. All changes are backwards-compatible.

Release notes for cobrapy 0.13.4

Fixes

  • Internal re-organization of the test suite.
  • Upgrade the ruamel.yaml version making it compatible with Python 3.7.
  • Fix a bug with a regular expression in the Matlab interface.

0.13.3

patch release

This is a bug fix release. It is considered stable but does not include any significant new features. All changes are backwards-compatible.

Release notes for cobrapy 0.13.3

  • Make a clean release for PyPI, website, and GitHub.

0.13.0

minor release

This is a stable release. It may include new functionality or backwards-incompatible changes.

Release notes for cobrapy 0.13.0

New features

  • New properties for the cobra.Model that give access to specific boundary reactions.
  • New functions for handling media and computing minimal media. Please read the new documentation chapter on media.

Backwards incompatible changes

0.12.1

patch release

This is a bug fix release. It is considered stable but does not include any significant new features. All changes are backwards-compatible.

Release notes for cobrapy 0.12.1

New features

  • Fix/feature that allows summaries to work properly for models with multiple exchange reactions for the same metabolite.
  • Require a later optlang version so that Gurobi can now be used for quadratic problems.
  • cobrapy can now extract primal values from a wider range of solver states. This is particularly useful to investigate problems in non-optimal states.

0.12.0

minor release

This is a stable release. It may include new functionality or backwards-incompatible changes.

Release notes for cobrapy 0.12.0

New features

  • Add geometric FBA as a method.
  • Add (linear) ROOM as a flux simulation method.
  • Allow a reference solution to be used with deletion methods when using MOMA or ROOM.

Fixes

0.11.3

patch release

This is a bug fix release. It is considered stable but does not include any significant new features. All changes are backwards-compatible.

Release notes for cobrapy 0.11.3

Fixes

  • Improve convergence and stability of sampling.
  • Reverse inplace operations after leaving a context.

Docs

0.11.2

patch release

This is a bug fix release. It is considered stable but does not include any significant new features. All changes are backwards-compatible.

Release notes for cobrapy 0.11.2

Fixes

  • Correctly set the constraint for a previous minimization objective in FVA.

0.11.1

patch release

This is a bug fix release. It is considered stable but does not include any significant new features. All changes are backwards-compatible.

Release notes for cobrapy 0.11.1

Fixes

  • Catch all optlang errors and re-raise them as OptimizationError with corresponding message.

0.11.0

minor release

This is a stable release. It may include new functionality or backwards-incompatible changes.

Release notes for cobrapy 0.11.0

New features

  • Add an argument processes to the functions find_essential_genes and find_essential_reactions.
  • Automatic documentation generation should hopefully mean that it’s never out-of-date.

Backwards incompatible changes

0.10.0

minor release

This is a stable release. It may include new functionality or backwards-incompatible changes.

Release notes for cobrapy 0.10.0

Fixes

  • The solvers packaged with cobrapy have been removed.
  • cobra is now a pure Python package and no longer has compiled extensions.
  • Massively simplified continuous testing and deployment.
  • The solver argument and configuration keyword arguments have been removed. Please set the solver on the model and configure it before calling optimization functions.

0.10.1

patch release

This is a bug fix release. It is considered stable but does not include any significant new features. All changes are backwards-compatible.

Release notes for cobrapy 0.10.1

Fixes

  • pandas has dropped support for Python 3.4 and we are doing the same for our automated tests. If you are running Python 3.4 and have a working installation of numpy and pandas, adding cobrapy on top of that is no problem.
  • Updated some URLs in the links.

0.9.1

patch release

This is a bug fix release. It is considered stable but does not include any significant new features. All changes are backwards-compatible.

Release notes for cobrapy 0.9.1

Fixes

  • All around improvements to cobrapy’s continuous integration.
  • Pin the scipy version to 0.19.1 until we can upgrade our sparse matrix code to scipy 1.0.

New features

0.9.0

minor release

This is a stable release. It may include new functionality or backwards-incompatible changes.

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.

0.8.2

patch release

This is a bug fix release. It is considered stable but does not include any significant new features. All changes are backwards-compatible.

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

0.8.1

patch release

This is a bug fix release. It is considered stable but does not include any significant new features. All changes are backwards-compatible.

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

minor release

This is a stable release. It may include new functionality or backwards-incompatible changes.

Fixes

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

0.7.0

minor release

This is a stable release. It may include new functionality or backwards-incompatible changes.

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).

0.6.2

patch release

This is a bug fix release. It is considered stable but does not include any significant new features. All changes are backwards-compatible.

Fixes

  • Fix in the ordering and rounding of FVA summary #525
  • Shared memory, improve speed during sampling #521

0.6.1

patch release

This is a bug fix release. It is considered stable but does not include any significant new features. All changes are backwards-compatible.

Fixes

  • Debug metabolite.add_metabolites with combine=False (#503)
  • Fix broken printing of metabolites (#502), by removing unnecessary Frozendict

0.6.0

minor release

This is a stable release. It may include new functionality or backwards-incompatible changes.

In this release we have made major changes to pretty much all corners of cobrapy and we hope that you will enjoy the new features as much as we do, and that any negative impacts on existing workflows will be limited. The major change is the ongoing move away from cobrapy’s internal solver interfaces to those provided by optlang which provides a single unified interface to glpk, cplex and gurobi enhanced by the ability to deal with symbolic expressions.

0.5.11

minor release

This is a stable release. It may include new functionality or backwards-incompatible changes.

This was the last release of the 0.5 series which was based on cobrapy’s own solver interfaces.

For a list of features please see the documentation.