Problems with sbmlsim/amici on MacOS

[stemllb]

Checklist

• [x] I searched the documentation.
• [x] I looked through similar issues on GitHub.

Question

None of the used modules of sbmlsim can be found. After reinstalling using pip install -e . upgrade, I received the error message:

error: command '/var/folders/sy/f16zz6x50xz3113nwtb9bvq00000gp/T/abs_croot-8rcp3rdc/python-split_1649141342860/_build_env/bin/llvm-ar' failed: No such file or directory
ERROR: Failed building wheel for amici
Failed to build amici
ERROR: Could not build wheels for amici which use PEP 517 and cannot be installed directly

How can I fix this problem? (with macOS)

[matthiaskoenig]

Did you install the dependencies for AMICI, i.e.

sudo apt-get install libatlas-base-dev swig libhdf5-serial-dev

as documented here (https://amici.readthedocs.io/en/latest/python_installation.html#amici-python-installation)?

[matthiaskoenig]

For OSX the dependencies are

brew install swig

# optionally for HDF5 support:
brew install hdf5

# optionally for parallel simulations:
brew install libomp

[matthiaskoenig]

As a workaround you can comment the following line:

    amici>=0.11.28

in the setup.cfg in your sbmlsim folder. I.e.

   # amici>=0.11.28

[matthiaskoenig]

Made this an optional dependency for the next release. This should solve most issues for now. We have to solve the MacOS installation for AMICI.