Investigating this a bit further, changing the shebang in /usr/bin/ipython3 from "#!/usr/bin/python3" to "#!/usr/bin/env python" solves the issue. But I guess this is in conflict with Debian's policy on interpreter location, that says "/usr/bin/env name" should not be used: https://www.debian.org/doc/packaging-manuals/python-policy/ch-python.html#s-interpreter_loc

Replacing /usr/bin/ipython3 with Fedora's ipython3 initialization script:

#!/usr/bin/python3
# This script was automatically generated by setup.py
if __name__ == '__main__':
    from IPython import start_ipython
    start_ipython()

Fixes the issue, although I'm not certain what other consequences this has.

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