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what tool can I use to manage SQLite database, I do not have any website apps or tools or environments setup, pure python

The sqlite command line is sqlite3, usually followed by the path to the database you want to manage, eg:

sqlite3 /home/yomasa/myproject/db.sqlite

If you want to use sqlite from Python, you can use the low-level sqlite db-api: https://docs.python.org/3/library/sqlite3.html or you could use something like SQLAlchemy if you need an ORM...