"all except" function for assignments
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It seems that there is no feature that allows teachers to assign a standard version of an assignment to "all students except" those student who will get a modified version of the assignment. I believe that it would help student who receive modified versions if they weren't assigned both assignments.
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There has often been a request to assign something to "all except" some students. That functionality does not currently exist.
One way to accomplish something close to this is as follows.
Assuming there are a few students with the modified assignments, then assign the main assignment to everyone. Then go into the gradebook and excuse the main assignment for those who you do not want to take it. Then for the modified version, only assign it to those who you do want to take it.
For Excused assignments, students can see that there is an assignment, but they won't be able to submit it (that sort-of depends on the type of assignment as they can still post to discussions). It shows Excused! as a grade.
If a student is not assigned an assignment (the special one for most of the class), they don't see it at all.
The best way to do this is to communicate to the students with the modified assignment that they will see the regular one, but the Excused means they shouldn't complete it and to complete the other one instead.
In the gradebook, you can enter EX for excused or you can click on the right arrow in the grade cell to open the flyout and choose Excused.