How do I report bi-weekly hours for a partial pay period with non-duty days?

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Non-duty days are not paid time and should not be reported.  In this case, report your actual hours worked.

Example: If your normal bi-weekly hours are 80, but the pay period only had seven duty days in it, you should report 56 hours. This is different if the days not worked were duty days in which you used sick/vacation hours.