Amici

Changes in this release:

All:
- Updated / extended documentation
- Fix reuse of `Solver` instances (541)

C++:
- Check for correct AMICI version for model in CMake
- Add reporting of computation times (699)

Python:
- Fix manifest file (698)
- Fix initial amounts/concentrations in SBML import

... and various other minor fixes/improvements

Python
* fix unset noise distribution when automatically generating observables in case None are passed (691)

C++
- Add SuperLUMT support (681)
- Sparsified dJydy (686)
- Enabled support of impulse-free events for DAE models (687) - thanks to Sebastien Sten for providing a testcase for this

Python
- Enabled support for piecewise functions in SBML import (662)
- Fix numeric type when constructing ExpData from Dataframes (690)
- Fix dynamic override in PETab

Bugfix release

Doc
- Update documentation of Windows installation

C++
- Fix missing source files in CMakeLists.txt (658)
- Set CMake policies to prevent warnings (Closes 676) (677)
- Start using gsl::span instead of raw pointers (393) (678)

Python
- PySB parsing fix (669)
- Fix failure to propagate BLAS_LIBS contents (665)
- Require setuptools at setup (673)
- Updated PEtab import to allow for different noise models

Features / improvements:

* Implement ReturnData and ExpData wrappers as more efficient views (657)
* Add list of references using AMICI (659)
* Custom llh (normal/laplace, lin/log/log10) (656)

Bugfixes:

+ Speedup and fix travis build

Features / improvements:

- adds the option for early termination on integration failures for runAmiciSimulations
- improve runtime of `SUNMatrixWrapper::mutliply`
- expose finite difference routines in public API
- enable parallel compilation of clib source files

Bugfixes:

- fixed symbolic processing for unreleased pysb features