Releases

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.