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Fabian Fröhlich; Daniel Weindl; Paul Stapor; Yannik Schälte; LeonardSchmiester; AMICI-developer; Łukasz Paszkowski; Jan Hasenauer; MerktSimon

  • 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


* 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/ (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)
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