Assuming you are running on ComputeCanada, I think it’s likely this was induced by anaconda somehow. They don’t support running conda on their systems (https://docs.computecanada.ca/wiki/Anaconda/en). I see you have 72 cores, so I assume you’re on an HPC system even if it’s not ComputeCanada.
I think this is a bug on our end, caused by only testing against conda which doesn’t fairly represent the diversity of systems, especially HPC systems like yours. We have a longstanding task (https://github.com/neuropoly/spinalcordtoolbox/issues/1526) to make this better.
I am curious about exactly what is failing. I would also like to see
$LD_LIBRARY_PATH, and to see what our tests say. If you have a moment, can you launch this and upload the output here?
pip install pytest
I’ll make some time this week to log onto ComputeCanada and try to investigate your issue. Thanks for bringing it to our attention!