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My only concern is can we have it running like celery. Here if the app fails I also lose my apscheduler process. At the same time I also want to leverage the API and the sqlalchemy job store present. So it is more about daemonizing it and make it fault tolerant.
You can have only one instance running at the same time otherwise you will see duplicated tasks running. If your requirement includes fault tolerant I'd recommend you to use Celery/Beat.
Is it possible to start the apscheduler as a daemon running outside the flask app ? This is more of a question than an issue.
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