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Duplicity by default asks for passwords to GnuPG keys on start up and caches them in memory throughout process lifetime. Is there a way to have it use /usr/bin/pinentry instead so I know I'm not passing the passphrase through Duplicity?

I'm using GnuPG hardware smart cards, so generally when a sign or decrypt operation is requested, I usually get a pinentry dialogue that pops up. I can configure gpg-agent to cache my passphrases for a set amount of time.

Is there a way to have Duplicity not know my GnuPG keys and use the GnuPG agent and pinentry to bypass inputting my passphrase into Duplicity?

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Duplicity does not cache gpg pass phrases by default (you can give them as env vars though). All prompts you see are from the gpg binary run underneath. Hence, when you configure your gpg into the desired state, duplicity will use it as configured and you are set.

For using gpg-agent read what the parameter --use-agent does on the manpage: http://duplicity.nongnu.org/duplicity.1.html

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