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As spotted by @dinosk in this troubleshooting, the call to db.drop_all() will NOT delete the alembic table alembic_version.
This can lead to several unpredictable issues.
The drop_all() method should drop ALL tables, and not left something behind.
A workaround has been provided with the method invenio_db.utils.drop_alembic_version_table().
Proposed solution
Override the SQLAlchemy db.drop_all() method to (pseudo-code):
WARNING: this modification can potentially break other modules' tests. Moreover, whenever the function drop_alembic_version_table() is used after a drop_all(), it should be cleaned up.