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  Can we add bonuses/penalty?

Yes, it is possible to add a bonus or a penalty to the average of a service. To do this, the option Take into consideration the bonus/penalty must be ticked when configuring the services. 
In the tab Grading > Entry of the grades >  Grades, a column Bonus/Penalty is added: you can enter points to add/deduct (in this case, precede the value with a minus sign).
The display of the bonus on the report card depends on what you tick in the report card template (tab Body): Add the bonus/penalty in the average or Display the bonus/penalty of the average separately.
It is also possible to add a bonus/penalty to the overall average by correcting it manually or to calculate a penalty according to the absences.