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org-habit keeps track of my habits, e.g. taking a piece of melatonin pill every day before bed. Sometimes I go to sleep after midnight. I don't want the habit to count as failed in this case. I want orgmode and org-habit let me check the habit before or after midnight. How do I do that?

Right now I have it scheduled like this: SCHEDULED: <2017-10-04 Wed .+1d>

The other problem is that if I check it at 2 am, then it list it in the agenda on that day even if I want to go to sleep before midnight.

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You can set:

(setq org-extend-today-until 4)

And then use either org-agenda-todo to mark a habit as done after midnight or org-agenda-todo-yesterday to mark it done before midnight, as you prefer.

Alternatively, see the related link that Juancho pointed to for how to make org-agenda-todo (and org-todo) always use the previous "clock day" when marking items as done in the small hours of the morning.

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