I switched to using a pyproject.toml file because this will be getting published sometime, and I will probably also use poetry. For the sake of compatibility with the other established TOTP apps, as well as to use the full extent of the TOTP URIs (they contain the issuer and account name already), I decided to divide the keys into issuers and accounts under those issuers. I will work on redesigning the add command to do this. Progress!
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