alembic_with_data_manip.py

from alembic import op
import sqlalchemy as sa

def upgrade():
    t_files = sa.table('files', sa.column('id', sa.String(32)), sa.column('content', sa.Blob()))
    # we have to use get_bind() because op.execute() doesn't have a return value
    # but by using get_bind() we can no longer generate SQL scripts for the migration; we have to run it live
    connection = op.get_bind()
    my_id = '14c3e928ed9d4ecaa57226bc5b628132'
    data = connection.execute(sa.select([t_files.c.content]).where(t_files.c.id == my_id)).scalar()
    new_data = transform_data(data)
    connection.execute(t_files.update().where(t_files.c.id == my_id).values(content=new_data))

def downgrade():
    pass

I need to update my Alchemy then, yes.

And after the instant commit, will there be a new transaction or instant commits from thereon?

I’ve finally updated the SO answer here.