Amici

Features:
- Allow specifying sigma-parameters from Python interface

Major bugfixes:
- Fix dsigma_y/dp and downstream sensitivity errors

- Major revision of documentation
- Improved Python interface
- More comprehensive Python interface example
- Fixed sensitivity computation in Python-generated models
- Various other bug fixes

WARNING:
- For models with sigma-parameters and dsigma_y/dp != 0, dsigma_y/dp was computed incorrectly. This propagates to all dependent sensitivities. This applies also to some older releases and has been fixed in v0.7.1.

Implement experimental support for python via swig.
Python interface is now usable, but API will still receive some updates in the future.

WARNING:
- There is a bug in sensitivity computation for Python-generated models
- Matlab C++ compilation will fail due to undefined M_PI
-> Please use v0.7.0

Main new features are:

- Reimplemented support for DAE equations
- Added newton solver for steady state calculation and preequilibration
- Better caching for recompilation of models
- Blas support to allow compilation of large models with many observables
- Improved SBML support
- Added c++ interface
- Added support for second order adjoint computation

- Rewrote large parts of the code as proper c++11 code to allow easier code maintanance
- Substantially extended testing in continuous integration to assure code quality

* First citable version of AMICI (via zenodo integration).
* Better support for standalone compilation
* Improved SBML import scripts
* General Code Cleanup

This update comes with many improvements, bug fixes and several new features. Most notably:

1) AMICI should now run on older versions of MATLAB (back to R2014a)
2) AMICI now compiles using older versions of Visual Studio
3) AMICI now also supports second order adjoint sensitivities (full (via the o2flag = 1 and as a vector product via o2flag = 2)
4) AMICI now supports more SBML, SBML v2 and rate rules