Hello everyone, After the IRC investigation, it turned out the use of abspath in Lib/site.py was in fact the culprit. Replacing all its uses with realpath and doing `./pre-inst-env guix pack -RR python python-numpy -S /bin=bin -S /etc=etc` did in fact resolve the issue!
I've raised the issue upstream at [1]. The fix itself is pretty simple, but it's theoretically a breaking change, so we'll see how Python maintainers want to move forward with it. We could backport this fix for the next core-updates cycle, whether or not it gets accepted upstream, and we will also need to modify sitecustomize.py as well to call os.path.realpath on python_site. Best, -- Josselin Poiret
