Missing Files During PyTom Installation

[ChenchenXu0401]

Dear developers, we would like to setup PyTom on our lab workstations for cryo-ET processing, but I encountered some issues during the installation process. Specifically, I received the following warnings indicating that certain files were not found:

warning: no files found matching 'pytom/lib/*.so'
warning: no files found matching 'pytom/bin/pytom'
warning: no files found matching 'pytom/bin/ipytom'
warning: no files found matching 'pytom/bin/pytomGUI'
These missing files seem to be essential components of the PyTom installation. I have followed the installation instructions provided, but it appears that these files were not included in the package.

Therefore, I would be immensely grateful if you could kindly assist me in resolving this issue. Could you please provide me with the missing files or advise me on an alternative method to obtain them? Your guidance and support in this matter would be invaluable.

Thank you very much for your attention to this matter. I look forward to your prompt response.

[sroet]

Hey @ChenchenXu0401,

Those files are compiled/created during the installation process.
If they are missing, it means that some step errored out ion the installation (probably during the SWIG compilation).
Do you mind rerunning the install from scratch (the conda env create/conda activate and python setup.py commands) and providing me with all the output? (you can attach files to a github comment)

You might have to run certain commands with >> install.log 2>&1 added to them as they will generate so much output that you can't copy/paste everything from most terminals.
Y will need to remove the conda environment environment with conda env remove --name pytom_env so you can recreate the conda environment

[alncat]

That means your installation didn't compile. You can check if the openmpi library is loaded. Actually, you can go to pytom/pytomc and execute compile.py by yourself. Then you can learn which library is not loaded. I figured out this by executing python compile.py --miniCondaEnvDir /work/home/alncat/.conda/envs/pytom_env/ --pythonVersion 3.8