Do you prefer to function or come in one php file?
Use them as you need them. I use include for chunks of large processing code and functions for utility functions. The somethines I use include a function too ... it really depends on how much you like your code.
Consider many of them include more fopen () from the PHP module and they can slow down the entire script. So don't try to add too many inclusions.
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I usually use functions / classes for logic and include for display. I am getting something like this in the controller ...
case 'widgetlist':
$widgets = $DAO->getWidgets(); //get some query
include('view/showWidgets.php'); //assume a global $widgets variable
break;
I found it easier to give the HTML / CSS designer an include rather than a function call that is displayed. The downside is that I rely on globals to pass variables to include rather than arguments, which is much safer.
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I am making the classes in separate files with the correct namespace prefixes (until they are included at least). I also put functions as static methods in "static classes" for the namespace effect.
I use autoload to include files, so I don't have to write hundreds of includes. Save My_Example_Class as {lib} /My/Example/Class.php
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The thing I'm working on includes one file at the top of each page containing all the global functions and database settings. It works as it is, but now I'm moving the functions to separate files because with everything in a big chunk it is completely impractical to do any validation.