I worked around this issue:

# update-alternatives --config pinentry
and select either the curses or gtk2 options (avoid the gnome3 one).

Also I had to reimport my gpg1 secret keyring into gpg2

Also I had to remove the [gcrypt] section in the repo: git config -e

At this point I think this was a problem of old configurations being
somehow improperly carried on and could be closed.

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https://bugs.launchpad.net/bugs/1714222

Title:
  Cannot pull from gcrypt git remote since 17.04: No secret key

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