$index of ngRepeat inside angularjs directive

Instead of scope.$parent.$index you might consider passing $index as a directive attribute:

<li my-directive index="{{$index}}" ng-repeat="value in values">

Directive:

myApp.directive('myDirective', function() {
    return {
        replace: true,
        // transclude: true,
        scope: {
            index: '@'
        },
        template: '<div>testing {{index}}</div>',
        link: function(scope, element, attrs) {
            // ...
        }
    }
});

Fiddle.