This the easiest way to again use PHP in Atahualpa 3.6.7 and later versions.
We will have to edit functions.php file.

Add this below code functions.php file. (Code has been take from Atahualpa 3.5.3)

PHP Code:

function bfa_html_inserts($custom_code) {
    global $bfa_ata; 
    if($custom_code != '') {
        if ( strpos($custom_code,'<?php ') !== FALSE ) {
            ob_start(); 
                eval('?>'.$custom_code); 
                $custom_code = ob_get_contents(); 
            ob_end_clean();
        }
    } 
    return $custom_code; 
}

Edit function bfa_parse_widget_areas($content)

PHP Code:

function bfa_parse_widget_areas($content) {
                
    if ( strpos($content,'<?php bfa_widget_area') !== FALSE ) {
        $content = preg_replace_callback("|<\?php bfa_widget_area(.*)\((.*)'(.*?)'(.*)\)(.*)\?>|","bfa_parse_widget_areas_callback",$content);
    }
       $content=bfa_html_inserts($content); /******** ADD THIS LINE *************/
    return $content; 
}

Logic behind the changes
The extra added function evaluates PHP using the eval function.
I have added a call to that function from function bfa_parse_widget_areas because bfa_parse_widget_areas is used to create custom widget areas. So if you can create a custom widget area at a particular place then you will also be able to use PHP in that section.
Still you wont be able to use php in CSS Insert. But now you know how it is done so you can easily figure out how to even use PHP in CSS Insert. You are just require to call bfa_html_inserts function before returning the result

Remember, the eval() was taken out because of WordPress requirements. However as the user of the theme, you can make what ever modifications you want.

That said, you will have to continue to put this mod in each time the theme is upgraded and if you do this for a customer and they do an upgrade, it will be lost and you will have one unhappy customer.

So if you want to do it for your self, I say go ahead. If , however, you are doing this for another, I would recommend against making this mode and find a different work around.

You are right JD. Even i don't recommend to use this mod. And for those who can't live without the PHP then I recommend they they should still stick to version 3.6.4 till some alternatives is found by Flynn.

It seems that all the "fixes" are ugly hacks. I hate to think of editing functions.php, only to have it overwritten at the next upgrade. Speaking of ugly hacks, I suppose you COULD put your own custom functions somewhere else, and have Apache append that file (using the ReadmeName directive) to the bottom of functions.php whenever it's served up. That would solve the problem of upgrades overwriting your custom functions. Yes, that's so ugly, even I'm ashamed.

Jack

Would it be possible for Atahualpa to look for 'user PHP functions' in a separate file? e.g. user_function.php. This would, by default, be empty.

Users could add all their bespoke functions in this one file and then use a 'placeholder' in the theme options to call them?

i.e. %user_function(function name, parameter1, parameter2,...)%

Just a thought...

While not exactly what you are looking for you might want to check out this plugin.