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I’m using in many places, Doctrine magic methods like below
Doctrine::getTable('User')->findByUserid(id);
Is it recommended to get data like this or should this be replaced with queries?
Also, are there any recommended settings in general when using Doctrine + CodeIgniter?
Yes, if you check the Doctrine source code you will see that it’s just a method forwarder. If you prefer you can just replace the magic methods with static ones- but I guess the performance advantage would be negligible.