Amici

**NOTE: For Python-imported SBML-models this release may compute incorrect sensitivities w.r.t. sigma. Bug introduced in 0.10.14, fixed in 0.10.15.**

Python:

* Don't require use of ModelPtr.get to call ExpData(Model)
* Fix import in generated model Python package
* Setup AMICI standalone scripts as setuptools entrypoints
* Simplify symbolic sensitivity expressions during Python SBML import
Fixes Infs in the Jacobian when using Hill-functions with states of 0.0.
* Extended Newton solver 848
The changes that allow performing Newton tests from the paper:
G. T. Lines, Ł. Paszkowski, L. Schmiester, D. Weindl, P. Stapor, and J. Hasenauer. Efficient computation of steady states in large-scale ODE models of biochemical reaction networks. accepted for Proceedings of the 8th IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE), Valencia, Spain, October 2019.
* Use SWIG>=4.0 on travis to include PyDoc in sdist / pypi package (841)
* **Fix choice of likelihood formula; failed if observable names were not equal to observable IDs**
* Fix(sbml-import) Compartment IDs in right-hand side of Rules are not replaced and lead to undefined identifiers in c++ files
* Fix invalid logging level
* Speed up sympy simplification (871)

C++:

* Performance: Avoid unnecessary repeated function calls for SUNMatrixWrapper dimensions
* Add AmiciApplication class as context for handling so far global settings.
This allows for example setting custom logging functions for concurrent AMICI
runs, e.g. in multi-thread applications (Closes 576).

Misc:

* Setup performance test on github actions (853)
* Update documentation and FAQ for CBLAS requirement and others
* Update reference list

* BREAKING CHANGE: Renaming {get|set}tNewtonPreequilibration to {get|set}Preequilibration (Closes 720)
* Make wurlitzer non-optional requirement for AMICI python package (Fixes missing AMICI errors when running from jupyter notebooks)
* Compute initial state for Model::getInitialStates if not already set (Fixes 818)
* Make swig generate pydoc comments from doxygen comments 830 (Closes 745) to provide Python docstrings for C++ wrapper functions
* feature(cmake) Add option to disable compiler optimizations for wrapfunctions.cpp (Fixes 828) (829)
* Change SBML test suite to pytest to allow for parallel test execution… (824)
* Fix(cmake): -E option is not available in all sed versions. Neither is the equivalent -r. Use --regexp-extended instead (Closes 826)
* Refactor(python) Move PEtab import code from command line script… (825)
* Fix(core) Fix regular expressions for intel compiler (Closes 754) (822)
* Update workflow figure to include PySB (Closes 799)
* Fix compiler warnings

* Fix handling of species specified in PEtab condition table (813)
* Fix some Visual C++ issues, update cppcheck handling, cleanup (VisualC++ still not fully supported)
* Minor fixups (801)
* Create SBML test suite result files for upload to http://sbml.org/Facilities/Database/ (#798)

* Fixed setting initial conditions for preequilibration (784)
* Fixed species->parameter conversion during PEtab import (782)
* Set correct Matlab include directories in CMake (793)
* Extended and updated documentation (785, 787)
* Fix various SBML import issues
* Run SBML test suite using github actions instead of travisCI (789)

* Simplify/fix AMICI installation
* If available use environment modules to detect dependencies

* Add SWIG installation script

* Update list of publication
* Update documentation
* Update doc for SWIG build and custom SWIG location.
* Add AMICI interface overview / workflow figure and show in README
* Document environment variables for model/core compilation (Closes 737)

* Added handling of abs function, since there seem to be problems with case sensitivity (713) Closes 770

Detaills:
* cmake: Use package_ROOT environment variables
* fix(cmake) Fix finding version.txt
* cmake: Auto-detect loaded MKL environment module
* cmake: Use new FindPython3 modules where possible
* fix(python) Restore python3.6 compatibility
* Inside venv, use pip instead of pip3 which should point to the correct version
* fix(python) Workaround for missing ensurepip during venv creation [ci skip]
* feature(python) Use MKL from environment modules to provide cblas
* fix(python) Fix define_macros not being passed to setuptools for Extension
* fix(python) Fix define_macros not being passed to setuptools for clibs
* Do not always add 'cblas' library since users may want to override that by a cblas-compatible library with a different name (closes 736)
* Update HDF5 path hints; use shared library if static is not available.
* Check for HDF5_BASE from environment module
* Fix system-dependent sundials library directory (Fixes 749) (750)
* Handle OSTYPE==linux in scripts/buildBNGL.sh (Fixes 751)
* Add SWIG download and build script
* Improve finding swig executable and allow user override via SWIG environment variable
* Provide installation hints if no SWIG found (Closes 724)
* Allow overriding cmake executable with environment variables in build scripts (Closes 738)

Fixup for missing version bump in v0.10.8 release. No code changes compared to v0.10.8.