make test error

[ask-more-questions]

Hi, i have a problem on the make test step in the Installation. And i have tried some methods mentioned online and failed , and i wonder why this package was not install correctly. i appreciate it that you made a guidebook for your package but i may need some extra help.

Best wishes

[mattjones315]

Hello,

Thanks for the posted issue here and apologies for the delay. It appears that you did not install Cassiopeia correctly. If you have cloned the repository, can you please ensure that everything installs correctly if you run make install?

Thanks,
Matt

[ask-more-questions]

Hi Matt,
Thanks for your response .
Yes，I have installed from the respsitory, and run make install. And all the errors seems to be related to the module cassiopeia.preprocess.collapse_cython. This snip below is the returned result. I wonder what could be the problem

[ask-more-questions]

Hi Matt, i have solved the problem here. So close this question here

[pavelToman]

Hello, I am facing the same error after installation. Could you tell me how you solved this problem with cassiopeia.preprocess.collapse_cython please?

[mattjones315]

Hi @pavelToman,

Can you let me know how you are attempting to install Cassiopeia? Are you sure you have Cython installed and a gcc compiler?

Thanks,
Matt

[pavelToman]

Hello @mattjones315,
I am working for UGent HPC and we are using Easybuild for installing the scientific software.
I have GCC 12.3.0 and Cython 0.29.35.
For an installation I am not using your "make install" but our "PythonBundle" easyconfig - it can handle dependencies better for HPC, but still using pip install and setup.py build.
python -c "import cassiopeia" check passed OK.

[mattjones315]

Hi @pavelToman,

I'm not familiar with UGent or Easybuild, but I suspect that the cython files are not getting compiled correctly. Are you able to use make install as opposed to Easybuild for the purposes of testing if this is the issue?

I would suggest installing into a clean conda environment with 3.9<=python<=3.7.

Thanks,
Matt

[pavelToman]

Thank you for your response Matt,
I am able to use your "make install" but I have to use python 3.11.3 and I can not use conda. Best way is to install from source.
I have a log from the installing process, if it helps.
cassiopeia_log.txt