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<?php

//... lots of PHP code


add_shortcode('project','projects_shortcode');



function inc_js_shortcode() {
?>
    <script type="text/javascript">
        jQuery(document).ready(function(){
            var mycontainer = jQuery('#projects');
            mycontainer.isotope({
                filter: '*',
                animationOptions: {
                    duration: 750,
                    easing: 'liniar',
                    queue: false,
                }
            });

            jQuery('#projects-filter a').click(function(){
                var selector = jQuery(this).attr('data-filter');
                mycontainer.isotope({
                    filter: selector,
                    animationOptions: {
                        duration: 750,
                        easing: 'liniar',
                        queue: false,
                    }
                });
                return false;
            });
        });
    </script>

<?php
}

add_action('wp_footer','inc_js_shortcode');
// Lots of other PHP code below
// ...


?>