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Is it possible to set certain settings from the theme functions file for example the setting Enable threaded (nested) comments ca I set it to allow 2 as the answer without having the user go into the admin panel and setting it for there wordpress comment settings?

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up vote 3 down vote accepted

Well, you can do something like this which will always reset the option to 2:

add_action('init', 'update_comment_depth');
function update_comment_depth() {
  update_option('thread_comments_depth', 2);
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