AMICI v0.10.10

• 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)

AMICI v0.10.9

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

AMICI v0.10.8

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

AMICI v0.10.7

Python

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

AMICI v0.10.6

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

AMICI v0.10.5

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

AMICI v0.10.4

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

AMICI v0.10.3

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

AMICI v0.10.2

Features / improvements:

• extended ExpData interface to allow for condition specific parameters, parameter scales, parameter lists, initial conditions and initial condition sensitivities.

Bugfixes:

• fixed output values of ReturnData::x_ss and ReturnData::sx_ss

AMICI v0.10.1

• travis-ci.com migration
• fix problem with has{variable} functions
• allow to import sbml model from string, not only file