@g_paternicola I realize you submitted this quite a while ago, but I had the same issue in my lab. I resolved this issue by:
copying the following lines out of the /etc/apps/python_upgrade_readiness_app/default/inputs.conf and pasting them into /etc/apps/python_upgrade_readiness_app/local/inputs.conf (which you'll have to create first).
[script://$SPLUNK_HOME/etc/apps/python_upgrade_readiness_app/bin/pura_get_all_apps.py]
passAuth = admin
[script://$SPLUNK_HOME/etc/apps/python_upgrade_readiness_app/bin/pura_scan_apps.py]
passAuth = admin
[script://$SPLUNK_HOME/etc/apps/python_upgrade_readiness_app/bin/pura_send_email.py]
passAuth = admin
Replace "admin" with your admin account name.