Cobra

This is a minor bugfix release.

It fixes bugs in edge cases with savemat, cglpk, and cplex.

This is a minor bugfix release.

In addition to minor bugfixes, it brings support for OS 10.10 Yosemite, simplifies installation and adds reaction construction from strings.

This is a major release from 0.2.1, with many new features added. A brief summary is below:
- Revamped faster and simpler solver interface
- New "cglpk" solver to replace "pyglpk" as the default solver (compatible with the latest version of GLPK)
- Support for "exact" solving (126, 41d91e8b2bf9c7b6c58b5315a07768c3c460b2af)
- Rewritten documentation now available as IPython notebooks
- Major performance improvements to deletions and FVA
- More flux analysis tools (pFBA and phenotypic phase planes, loopless FBA)
- SBML fbc support
- Python 3 support
- Improvements to ArrayBasedModel
- Read-only attributes for gene/reaction/metabolite relationships

The following features were added:
- Improvements to solver interface
- Support for exact solving with esolver (Qsopt_ex) (126)
- Support for Mosek (f79248f89673025e37f1b9aa796bd8cb28ba157f)
- Support for "exact" solving with glpk (through cglpk) (41d91e8b2bf9c7b6c58b5315a07768c3c460b2af)
- cglpk is now the preferred binding to glpk (129)
- Implementation of loopless FBA (133)
- Update documentation to IPython notebooks (0e380963d3428d0fbd40135032efd24810048ce4)

- faster solver interface
- faster fva and single/double deletions with new interface
- cython-based glpk solver
- more flux analysis tools (pFBA and phenotypic phase planes)
- sbml fbc support
- improvements to ArrayBasedModel
- access read-only attributes for gene/reaction/metabolite relationships
- simplified installation
- python3 support