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I've multiple header files (header-name.php), they are mainly being used by different custom post types. Is there any way to enqueue script to only a specific header?

At this moment I'm targeting it with conditional tag like if ( 'MYPOSTTYPE' == get_post_type() ) but I'm looking for a better alternative.

do we have something like is_header('name')?

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You load the header file probably with get_header(). There is a hook you can use: 'get_header'. You get the called header name as parameter.

add_action( 'get_header', 'wpse_54865_conditional_enqueue' );

function wpse_54865_conditional_enqueue( $name )
    if ( 'my_custom_header_name' === $name )
        // register your script loading function
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The wp_enqueue_scripts action is part of the wp_head hook, so the enqueue process isn't really tied to header.php. It's also the appropriate way to enqueue scripts and styles. You could possibly switch to the is_singlular ( 'MYPOSTTYPE' ) conditional tag, but I'm not sure that's really better.

You could set a global variable before the wp_head() function in your header.php's and then test for that variable to decide which scripts to enqueue.

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