How do I remove a single HABTM associated item without deleting the item itself?

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I tend to use has_many :through, but have you tried

student.classes.delete(science)

I think needing to have the target object, not just the ID, is a limitation of HABTM (since the join table is abstracted away for your convenience). If you use has_many :through you can operate directly on the join table (since you get a Model) and that lets you optimize this sort of thing into fewer queries.

def leave_class(class_id)
  ClassMembership.delete(:all, :conditions => ["student_id = ? and class_id = ?", self.id, class_id)
end

If you want the simplicity of HABTM you need to use 

student.classes.delete(Class.find 2)

Also, calling a model “Class” is a really bad idea. Use a name that isn’t part of the core of Ruby!

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